[MOBY-guts] biomoby commit

Yan Wong yanwong at pub.open-bio.org
Tue Feb 1 14:11:12 UTC 2005


yanwong
Tue Feb  1 09:20:44 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv14364/bioMoby/ontology

Modified Files:
	AlleleAssociation.py Allele_freq.py AminoAcidSequence.py 
	B64_Encoded_PNG.py B64_Encoded_Postscript.py 
	B64_encoded_PDB.py B64_encoded_gif.py B64_encoded_jpeg.py 
	BLASTText.py BasicGFFSequenceFeature.py 
	ClustalAlnFormattedText.py ClustalMsfFormattedText.py 
	CommentedAASequence.py CommentedDNASequence.py 
	CommentedRNASequence.py DNASequence.py 
	DNASequenceWithGFFFeatures.py DateTime.py Decypher_Text.py 
	Edge.py EmblFlatfile.py FASTA.py FASTA_AA.py FASTA_NA.py 
	FASTA_Text.py GFF.py GFF1.py GFF2.py GFF2_5.py GFF3.py 
	GO_Term.py GenbankFlatfile.py GenericSequence.py 
	GeneticElement.py Genotype.py Germplasm_Details.py 
	Germplasm_List.py Global_Keyword.py HBond_Pair.py 
	HFormatText.py Haplotyping_Study_obj.py ICIS_Query.py 
	ICIS_Query2.py ICIS_Query3.py IntAct_XML.py Interaction.py 
	InteractionMethod.py Interaction_partner.py Interactor.py 
	MEME_Text.py MGIS_ACCESSION.py MMP_Locus.py MO_Term_Test.py 
	MmCIFText.py Multi_key_value_pair.py 
	MyTestingDataType_11024145298313.py MyTree.py 
	NCBI_BLAST_Text.py NCBI_Blast_XML.py NCBI_Blast_XML_Gif.py 
	NCBI_Blast_XML_Gif_Map.py NCBI_MEME_Text.py 
	NucleotideSequence.py PDBFormattedText.py PDBText.py PDGJOB.py 
	PHDText.py PMUTText.py PSeaTextFormatted.py 
	PhenotypeDescription.py PubMedMEDLINE.py RNASequence.py 
	SINGER_ACCESSION.py Sample.py SchematikonMotifID.py 
	SchematikonMotifSupport.py SchematikonSegmentAttributes.py 
	SchematikonSegmentID.py SchematikonStructureAnnotation.py 
	SchematikonVorocodeName.py Scored_acronym_string.py 
	SimpleAnnotatedGIFImage.py SimpleAnnotatedJPEGImage.py 
	Simple_key_value_pair.py Snp_allele.py Snp_genotype.py 
	Study.py TEST.py TargetP_result.py Testout.py TextBase64.py 
	TextFormatted.py TextHtml.py TextPlain.py TextUuencoded.py 
	TextXml.py Text_plain.py Trait_Details.py Tree.py 
	TropGENE_ACCESSION.py TropGENE_Diversity_Matrix.py 
	TropGENE_LOCUS.py VirtualSequence.py WU_BLAST_Text.py 
	Wildcard_Query.py 
Log Message:


moby-live/Python/bioMoby/ontology AlleleAssociation.py,1.4,1.5 Allele_freq.py,1.4,1.5 AminoAcidSequence.py,1.4,1.5 B64_Encoded_PNG.py,1.4,1.5 B64_Encoded_Postscript.py,1.4,1.5 B64_encoded_PDB.py,1.4,1.5 B64_encoded_gif.py,1.4,1.5 B64_encoded_jpeg.py,1.4,1.5 BLASTText.py,1.4,1.5 BasicGFFSequenceFeature.py,1.4,1.5 ClustalAlnFormattedText.py,1.4,1.5 ClustalMsfFormattedText.py,1.4,1.5 CommentedAASequence.py,1.4,1.5 CommentedDNASequence.py,1.4,1.5 CommentedRNASequence.py,1.4,1.5 DNASequence.py,1.4,1.5 DNASequenceWithGFFFeatures.py,1.4,1.5 DateTime.py,1.4,1.5 Decypher_Text.py,1.4,1.5 Edge.py,1.4,1.5 EmblFlatfile.py,1.4,1.5 FASTA.py,1.4,1.5 FASTA_AA.py,1.4,1.5 FASTA_NA.py,1.4,1.5 FASTA_Text.py,1.4,1.5 GFF.py,1.4,1.5 GFF1.py,1.4,1.5 GFF2.py,1.4,1.5 GFF2_5.py,1.4,1.5 GFF3.py,1.4,1.5 GO_Term.py,1.4,1.5 GenbankFlatfile.py,1.4,1.5 GenericSequence.py,1.4,1.5 GeneticElement.py,1.4,1.5 Genotype.py,1.4,1.5 Germplasm_Details.py,1.4,1.5 Germplasm_List.py,1.4,1.5 Global_Keyword.py,1.4,1.5 HBon!
d_Pair.py,1.4,1.5 HFormatText.py,1.4,1.5 Haplotyping_Study_obj.py,1.4,1.5 ICIS_Query.py,1.4,1.5 ICIS_Query2.py,1.4,1.5 ICIS_Query3.py,1.4,1.5 IntAct_XML.py,1.4,1.5 Interaction.py,1.4,1.5 InteractionMethod.py,1.4,1.5 Interaction_partner.py,1.4,1.5 Interactor.py,1.4,1.5 MEME_Text.py,1.4,1.5 MGIS_ACCESSION.py,1.4,1.5 MMP_Locus.py,1.4,1.5 MO_Term_Test.py,1.4,1.5 MmCIFText.py,1.4,1.5 Multi_key_value_pair.py,1.4,1.5 MyTestingDataType_11024145298313.py,1.4,1.5 MyTree.py,1.4,1.5 NCBI_BLAST_Text.py,1.4,1.5 NCBI_Blast_XML.py,1.4,1.5 NCBI_Blast_XML_Gif.py,1.4,1.5 NCBI_Blast_XML_Gif_Map.py,1.4,1.5 NCBI_MEME_Text.py,1.4,1.5 NucleotideSequence.py,1.4,1.5 PDBFormattedText.py,1.4,1.5 PDBText.py,1.4,1.5 PDGJOB.py,1.4,1.5 PHDText.py,1.4,1.5 PMUTText.py,1.4,1.5 PSeaTextFormatted.py,1.4,1.5 PhenotypeDescription.py,1.4,1.5 PubMedMEDLINE.py,1.4,1.5 RNASequence.py,1.4,1.5 SINGER_ACCESSION.py,1.4,1.5 Sample.py,1.4,1.5 SchematikonMotifID.py,1.4,1.5 SchematikonMotifSupport.py,1.4,1.5 SchematikonSegme!
ntAttributes.py,1.4,1.5 SchematikonSegmentID.py,1.4,1.5 Schem!
atikonStructureAnnotation.py,1.4,1.5 SchematikonVorocodeName.py,1.4,1.5 Scored_acronym_string.py,1.4,1.5 SimpleAnnotatedGIFImage.py,1.4,1.5 SimpleAnnotatedJPEGImage.py,1.4,1.5 Simple_key_value_pair.py,1.4,1.5 Snp_allele.py,1.4,1.5 Snp_genotype.py,1.4,1.5 Study.py,1.4,1.5 TEST.py,1.4,1.5 TargetP_result.py,1.4,1.5 Testout.py,1.4,1.5 TextBase64.py,1.4,1.5 TextFormatted.py,1.4,1.5 TextHtml.py,1.4,1.5 TextPlain.py,1.4,1.5 TextUuencoded.py,1.4,1.5 TextXml.py,1.4,1.5 Text_plain.py,1.4,1.5 Trait_Details.py,1.4,1.5 Tree.py,1.4,1.5 TropGENE_ACCESSION.py,1.4,1.5 TropGENE_Diversity_Matrix.py,1.4,1.5 TropGENE_LOCUS.py,1.4,1.5 VirtualSequence.py,1.4,1.5 WU_BLAST_Text.py,1.4,1.5 Wildcard_Query.py,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Snp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="pValue" or elt.getAttribute("moby:articleName")=="pValue"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PValue=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="validity" or elt.getAttribute("moby:articleName")=="validity"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Validity=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -44,17 +46,17 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="panel_lsid" or elt.getAttribute("moby:articleName")=="panel_lsid"):
                 self.Panel_lsid=MobyObject()
-                self.Panel_lsid.fromMoby(elt.toxml())
+                self.Panel_lsid.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="snp_lsid" or elt.getAttribute("moby:articleName")=="snp_lsid"):
                 self.Snp_lsid=MobyObject()
-                self.Snp_lsid.fromMoby(elt.toxml())
+                self.Snp_lsid.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele_freq" or elt.getAttribute("moby:articleName")=="allele_freq"):
                 self.Allele_freq=MobySnp_allele()
-                self.Allele_freq.fromMoby(elt.toxml())
+                self.Allele_freq.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="frequency" or elt.getAttribute("moby:articleName")=="frequency"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Frequency.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/02/01 14:20:44	1.5
@@ -39,7 +39,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -60,43 +62,43 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="reference" or elt.getAttribute("moby:articleName")=="reference"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Reference=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="source" or elt.getAttribute("moby:articleName")=="source"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Source=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start" or elt.getAttribute("moby:articleName")=="start"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="stop" or elt.getAttribute("moby:articleName")=="stop"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Stop=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="strand" or elt.getAttribute("moby:articleName")=="strand"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Strand=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="frame" or elt.getAttribute("moby:articleName")=="frame"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Frame=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="phase" or elt.getAttribute("moby:articleName")=="phase"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Phase=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="multi_key_value_pair" or elt.nodeName=="moby:multi_key_value_pair") and (elt.getAttribute("articleName")=="column9_tag_value" or elt.getAttribute("moby:articleName")=="column9_tag_value"):
                 self.Column9_tag_value=MobyMulti_key_value_pair()
-                self.Column9_tag_value.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Column9_tag_value.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/02/01 14:20:44	1.5
@@ -31,7 +31,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,15 +54,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="BasicGFFSequenceFeature" or elt.nodeName=="moby:BasicGFFSequenceFeature") and (elt.getAttribute("articleName")=="DNASequenceWithGFFFeatures" or elt.getAttribute("moby:articleName")=="DNASequenceWithGFFFeatures"):
                 self.DNASequenceWithGFFFeatures=MobyBasicGFFSequenceFeature()
-                self.DNASequenceWithGFFFeatures.fromMoby(elt.toxml())
\ No newline at end of file
+                self.DNASequenceWithGFFFeatures.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Partner=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Direction=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Term" or elt.getAttribute("moby:articleName")=="Term"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Term=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Definition" or elt.getAttribute("moby:articleName")=="Definition"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Definition=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GeneticElement" or elt.getAttribute("moby:articleName")=="GeneticElement"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.GeneticElement=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="snp" or elt.getAttribute("moby:articleName")=="snp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Snp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="sample" or elt.getAttribute("moby:articleName")=="sample"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Sample=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Result=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 08:52:15	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/02/01 14:20:44	1.5
@@ -35,7 +35,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -55,36 +57,36 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="date" or elt.getAttribute("moby:articleName")=="date"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Date=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="country" or elt.getAttribute("moby:articleName")=="country"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Country=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="prefered_name" or elt.getAttribute("moby:articleName")=="prefered_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Prefered_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="alternative_names" or elt.getAttribute("moby:articleName")=="alternative_names"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Alternative_names=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="name_type" or elt.getAttribute("moby:articleName")=="name_type"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Name_type=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="location" or elt.getAttribute("moby:articleName")=="location"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Location=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_id=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/02/01 14:20:44	1.5
@@ -35,7 +35,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -55,36 +57,36 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="germplasm_id" or elt.getAttribute("moby:articleName")=="germplasm_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="germplasm_name" or elt.getAttribute("moby:articleName")=="germplasm_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_value" or elt.getAttribute("moby:articleName")=="trait_value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_value=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="trait_id" or elt.getAttribute("moby:articleName")=="trait_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="scale" or elt.getAttribute("moby:articleName")=="scale"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scale=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="scale_desc" or elt.getAttribute("moby:articleName")=="scale_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scale_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="method" or elt.getAttribute("moby:articleName")=="method"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Method=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_id" or elt.getAttribute("moby:articleName")=="study_id"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_id=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="A" or elt.getAttribute("moby:articleName")=="A"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.A=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="H" or elt.getAttribute("moby:articleName")=="H"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.H=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="D" or elt.getAttribute("moby:articleName")=="D"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.D=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text" or elt.getAttribute("moby:articleName")=="search_text"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text1=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text2" or elt.getAttribute("moby:articleName")=="search_text2"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text2=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="search_text3" or elt.getAttribute("moby:articleName")=="search_text3"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text3=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text1" or elt.getAttribute("moby:articleName")=="search_text1"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text1=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="search_text2" or elt.getAttribute("moby:articleName")=="search_text2"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Search_text2=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -51,15 +53,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="result" or elt.getAttribute("moby:articleName")=="result"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Result=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="resultUnits" or elt.getAttribute("moby:articleName")=="resultUnits"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ResultUnits=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Interactor" or elt.nodeName=="moby:Interactor") and (elt.getAttribute("articleName")=="participant" or elt.getAttribute("moby:articleName")=="participant"):
                 self.Participant=MobyInteractor()
-                self.Participant.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Participant.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,16 +51,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="shortlabel" or elt.getAttribute("moby:articleName")=="shortlabel"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Shortlabel=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="term" or elt.getAttribute("moby:articleName")=="term"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Term=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="definition" or elt.getAttribute("moby:articleName")=="definition"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Definition=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="direction" or elt.getAttribute("moby:articleName")=="direction"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Direction=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="partner" or elt.getAttribute("moby:articleName")=="partner"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Partner=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="role" or elt.getAttribute("moby:articleName")=="role"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Role=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -46,7 +46,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -66,84 +68,84 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Yellowsig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Yellowsig"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Yellowsig=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:ORIGCTY" or elt.getAttribute("moby:articleName")=="mcpd:ORIGCTY"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdORIGCTY=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mgis:SECTION" or elt.getAttribute("moby:articleName")=="mgis:SECTION"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.MgisSECTION=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:SPECIES" or elt.getAttribute("moby:articleName")=="mcpd:SPECIES"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdSPECIES=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="mcpd:COLLCODE" or elt.getAttribute("moby:articleName")=="mcpd:COLLCODE"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.McpdCOLLCODE=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Blacksig" or elt.getAttribute("moby:articleName")=="Biotic_stress_Blacksig"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Blacksig=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Fusarium" or elt.getAttribute("moby:articleName")=="Biotic_stress_Fusarium"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Fusarium=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_pseudomonas" or elt.getAttribute("moby:articleName")=="Biotic_stress_pseudomonas"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_pseudomonas=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Radopholus" or elt.getAttribute("moby:articleName")=="Biotic_stress_Radopholus"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Radopholus=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Pratylenchuscof" or elt.getAttribute("moby:articleName")=="Biotic_stress_Pratylenchuscof"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Pratylenchuscof=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_Pratylenchusgood" or elt.getAttribute("moby:articleName")=="Biotic_stress_Pratylenchusgood"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_Pratylenchusgood=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Biotic_stress_cosmopolites" or elt.getAttribute("moby:articleName")=="Biotic_stress_cosmopolites"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Biotic_stress_cosmopolites=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Lowtemp" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Lowtemp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Lowtemp=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Drought" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Drought"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Drought=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Flooding" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Flooding"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Flooding=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Mineraldef" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Mineraldef"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Mineraldef=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Winds" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Winds"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Winds=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Soilacidity" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Soilacidity"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Soilacidity=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Manganesetox" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Manganesetox"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Manganesetox=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Abiotic_stress_Hightemp" or elt.getAttribute("moby:articleName")=="Abiotic_stress_Hightemp"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Abiotic_stress_Hightemp=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_name" or elt.getAttribute("moby:articleName")=="class_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Class_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="individual_name" or elt.getAttribute("moby:articleName")=="individual_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Individual_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="individual_desc" or elt.getAttribute("moby:articleName")=="individual_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Individual_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="class_desc" or elt.getAttribute("moby:articleName")=="class_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Class_desc=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Key=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Value.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,7 +50,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
-                self.HitGraph.fromMoby(elt.toxml())
\ No newline at end of file
+                self.HitGraph.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,10 +52,10 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="b64_encoded_gif" or elt.nodeName=="moby:b64_encoded_gif") and (elt.getAttribute("articleName")=="hitGraph" or elt.getAttribute("moby:articleName")=="hitGraph"):
                 self.HitGraph=MobyB64_encoded_gif()
-                self.HitGraph.fromMoby(elt.toxml())
+                self.HitGraph.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="text-html" or elt.nodeName=="moby:text-html") and (elt.getAttribute("articleName")=="areaMap" or elt.getAttribute("moby:articleName")=="areaMap"):
                 self.AreaMap=MobyTextHtml()
-                self.AreaMap.fromMoby(elt.toxml())
\ No newline at end of file
+                self.AreaMap.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,23 +54,23 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="answerService" or elt.getAttribute("moby:articleName")=="answerService"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.AnswerService=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="authURI" or elt.getAttribute("moby:articleName")=="authURI"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.AuthURI=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DateTime" or elt.nodeName=="moby:DateTime") and (elt.getAttribute("articleName")=="timeout" or elt.getAttribute("moby:articleName")=="timeout"):
                 self.Timeout=MobyDateTime()
-                self.Timeout.fromMoby(elt.toxml())
+                self.Timeout.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="killcode" or elt.getAttribute("moby:articleName")=="killcode"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Killcode=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="killService" or elt.getAttribute("moby:articleName")=="killService"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.KillService=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Phenotype" or elt.getAttribute("moby:articleName")=="Phenotype"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Phenotype=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SequenceString" or elt.getAttribute("moby:articleName")=="SequenceString"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SequenceString=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ACCNO" or elt.getAttribute("moby:articleName")=="ACCNO"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ACCNO=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ORIGCTY" or elt.getAttribute("moby:articleName")=="ORIGCTY"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ORIGCTY=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="GENUS" or elt.getAttribute("moby:articleName")=="GENUS"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.GENUS=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="SPECIES" or elt.getAttribute("moby:articleName")=="SPECIES"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.SPECIES=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/02/01 14:20:44	1.5
@@ -29,7 +29,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,12 +51,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="code" or elt.getAttribute("moby:articleName")=="code"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Code=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="affectation" or elt.getAttribute("moby:articleName")=="affectation"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Affectation=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="UniqueSupport" or elt.getAttribute("moby:articleName")=="UniqueSupport"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.UniqueSupport=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Support" or elt.getAttribute("moby:articleName")=="Support"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Support=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Insert code" or elt.getAttribute("moby:articleName")=="Insert code"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.InsertCode=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Starting amino acid position" or elt.getAttribute("moby:articleName")=="Starting amino acid position"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.StartingAminoAcidPosition=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Chain ID" or elt.getAttribute("moby:articleName")=="Chain ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ChainID=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PDB ID" or elt.getAttribute("moby:articleName")=="PDB ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PDBID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="ID" or elt.getAttribute("moby:articleName")=="ID"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.ID=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,20 +52,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF gamma-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF gamma-turn"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PROMOTIFGammaTurn=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="PROMOTIF beta-turn" or elt.getAttribute("moby:articleName")=="PROMOTIF beta-turn"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.PROMOTIFBetaTurn=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="DSSP" or elt.getAttribute("moby:articleName")=="DSSP"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.DSSP=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="STRIDE" or elt.getAttribute("moby:articleName")=="STRIDE"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.STRIDE=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="VorocodeName" or elt.getAttribute("moby:articleName")=="VorocodeName"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.VorocodeName=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,15 +52,15 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="score" or elt.getAttribute("moby:articleName")=="score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Object" or elt.nodeName=="moby:Object") and (elt.getAttribute("articleName")=="string_component" or elt.getAttribute("moby:articleName")=="string_component"):
                 self.String_component=MobyObject()
-                self.String_component.fromMoby(elt.toxml())
+                self.String_component.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="acronym" or elt.getAttribute("moby:articleName")=="acronym"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Acronym=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,8 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -49,8 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="Description" or elt.getAttribute("moby:articleName")=="Description"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Description.append(t.content)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/02/01 14:20:44	1.5
@@ -28,7 +28,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -48,12 +50,12 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="value" or elt.getAttribute("moby:articleName")=="value"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Value=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="key" or elt.getAttribute("moby:articleName")=="key"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Key=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/02/01 14:20:44	1.5
@@ -23,7 +23,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -37,7 +39,7 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="DNASequence" or elt.nodeName=="moby:DNASequence") and (elt.getAttribute("articleName")=="snp_allele" or elt.getAttribute("moby:articleName")=="snp_allele"):
                 self.Snp_allele=MobyDNASequence()
-                self.Snp_allele.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Snp_allele.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/02/01 14:20:44	1.5
@@ -24,7 +24,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
 
@@ -38,10 +40,10 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele1" or elt.getAttribute("moby:articleName")=="allele1"):
                 self.Allele1=MobySnp_allele()
-                self.Allele1.fromMoby(elt.toxml())
+                self.Allele1.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="snp_allele" or elt.nodeName=="moby:snp_allele") and (elt.getAttribute("articleName")=="allele2" or elt.getAttribute("moby:articleName")=="allele2"):
                 self.Allele2=MobySnp_allele()
-                self.Allele2.fromMoby(elt.toxml())
\ No newline at end of file
+                self.Allele2.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_name" or elt.getAttribute("moby:articleName")=="study_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_name=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="study_id" or elt.getAttribute("moby:articleName")=="study_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="study_desc" or elt.getAttribute("moby:articleName")=="study_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Study_desc=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="o_score" or elt.getAttribute("moby:articleName")=="o_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.O_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="s_score" or elt.getAttribute("moby:articleName")=="s_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.S_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="m_score" or elt.getAttribute("moby:articleName")=="m_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.M_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Float" or elt.nodeName=="moby:Float") and (elt.getAttribute("articleName")=="c_score" or elt.getAttribute("moby:articleName")=="c_score"):
                 t=MobyFloat()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.C_score=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="compartment" or elt.getAttribute("moby:articleName")=="compartment"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Compartment=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/02/01 14:20:44	1.5
@@ -31,7 +31,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -51,20 +53,20 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="gid" or elt.getAttribute("moby:articleName")=="gid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Gid=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="dvalue" or elt.getAttribute("moby:articleName")=="dvalue"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Dvalue=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="scaleid" or elt.getAttribute("moby:articleName")=="scaleid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Scaleid=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="tmethid" or elt.getAttribute("moby:articleName")=="tmethid"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Tmethid=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/02/01 14:20:44	1.5
@@ -32,7 +32,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -52,24 +54,24 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_desc" or elt.getAttribute("moby:articleName")=="trait_desc"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_desc=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="num_studies" or elt.getAttribute("moby:articleName")=="num_studies"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Num_studies=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_abbr" or elt.getAttribute("moby:articleName")=="trait_abbr"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_abbr=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="trait_id" or elt.getAttribute("moby:articleName")=="trait_id"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_id=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="trait_name" or elt.getAttribute("moby:articleName")=="trait_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Trait_name=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/02/01 14:20:44	1.5
@@ -36,7 +36,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -66,34 +68,34 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RFLP" or elt.getAttribute("moby:articleName")=="RFLP"):
                 self.RFLP=MobyTropGENE_LOCUS()
-                self.RFLP.fromMoby(elt.toxml())
+                self.RFLP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="AFLP" or elt.getAttribute("moby:articleName")=="AFLP"):
                 self.AFLP=MobyTropGENE_LOCUS()
-                self.AFLP.fromMoby(elt.toxml())
+                self.AFLP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="RAPD" or elt.getAttribute("moby:articleName")=="RAPD"):
                 self.RAPD=MobyTropGENE_LOCUS()
-                self.RAPD.fromMoby(elt.toxml())
+                self.RAPD.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Isozyme" or elt.getAttribute("moby:articleName")=="Isozyme"):
                 self.Isozyme=MobyTropGENE_LOCUS()
-                self.Isozyme.fromMoby(elt.toxml())
+                self.Isozyme.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Polyphenol" or elt.getAttribute("moby:articleName")=="Polyphenol"):
                 self.Polyphenol=MobyTropGENE_LOCUS()
-                self.Polyphenol.fromMoby(elt.toxml())
+                self.Polyphenol.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Morphological" or elt.getAttribute("moby:articleName")=="Morphological"):
                 self.Morphological=MobyTropGENE_LOCUS()
-                self.Morphological.fromMoby(elt.toxml())
+                self.Morphological.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="Microsatellite" or elt.getAttribute("moby:articleName")=="Microsatellite"):
                 self.Microsatellite=MobyTropGENE_LOCUS()
-                self.Microsatellite.fromMoby(elt.toxml())
+                self.Microsatellite.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="SNP" or elt.getAttribute("moby:articleName")=="SNP"):
                 self.SNP=MobyTropGENE_LOCUS()
-                self.SNP.fromMoby(elt.toxml())
+                self.SNP.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="CAPS" or elt.getAttribute("moby:articleName")=="CAPS"):
                 self.CAPS=MobyTropGENE_LOCUS()
-                self.CAPS.fromMoby(elt.toxml())
+                self.CAPS.fromMoby(elt)
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="TropGENE_LOCUS" or elt.nodeName=="moby:TropGENE_LOCUS") and (elt.getAttribute("articleName")=="TAMPL" or elt.getAttribute("moby:articleName")=="TAMPL"):
                 self.TAMPL=MobyTropGENE_LOCUS()
-                self.TAMPL.fromMoby(elt.toxml())
\ No newline at end of file
+                self.TAMPL.fromMoby(elt)
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/02/01 14:20:44	1.5
@@ -25,7 +25,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -45,4 +47,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/02/01 14:20:44	1.5
@@ -27,7 +27,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -47,8 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="Length" or elt.getAttribute("moby:articleName")=="Length"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Length=t.content
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/02/01 14:20:44	1.5
@@ -26,7 +26,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -46,4 +48,4 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
\ No newline at end of file
+                    self.__cross__.append(um.loads(ref))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 08:52:16	1.4
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/02/01 14:20:44	1.5
@@ -30,7 +30,9 @@
         """ Load the attributes from an XML string
         """
         from bioMoby.mobyMarshal import MobyUnmarshaller
-        doc=parseString(value).firstChild
+        doc=value
+        if isinstance(value, str):
+            doc=parseString(value).firstChild
         um=MobyUnmarshaller()
         self.content=""
         self.namespace=doc.getAttribute("moby:namespace")
@@ -50,16 +52,16 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    self.__cross__.append(um.loads(ref))
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="end_row" or elt.getAttribute("moby:articleName")=="end_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.End_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="Integer" or elt.nodeName=="moby:Integer") and (elt.getAttribute("articleName")=="start_row" or elt.getAttribute("moby:articleName")=="start_row"):
                 t=MobyInteger()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Start_row=t.content
             if elt.nodeType==elt.ELEMENT_NODE and (elt.nodeName=="String" or elt.nodeName=="moby:String") and (elt.getAttribute("articleName")=="germplasm_name" or elt.getAttribute("moby:articleName")=="germplasm_name"):
                 t=MobyString()
-                t.fromMoby(elt.toxml())
+                t.fromMoby(elt)
                 self.Germplasm_name=t.content
\ No newline at end of file




More information about the MOBY-guts mailing list