[MOBY-guts] biomoby commit

Yan Wong yanwong at pub.open-bio.org
Thu Jan 27 08:34:09 UTC 2005


yanwong
Thu Jan 27 03:44:05 EST 2005
Update of /home/repository/moby/moby-live/Python/bioMoby/ontology
In directory pub.open-bio.org:/tmp/cvs-serv14606/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,1.2,1.3 Allele_freq.py,1.2,1.3 AminoAcidSequence.py,1.2,1.3 B64_Encoded_PNG.py,1.2,1.3 B64_Encoded_Postscript.py,1.2,1.3 B64_encoded_PDB.py,1.2,1.3 B64_encoded_gif.py,1.2,1.3 B64_encoded_jpeg.py,1.2,1.3 BLASTText.py,1.2,1.3 BasicGFFSequenceFeature.py,1.2,1.3 ClustalAlnFormattedText.py,1.2,1.3 ClustalMsfFormattedText.py,1.2,1.3 CommentedAASequence.py,1.2,1.3 CommentedDNASequence.py,1.2,1.3 CommentedRNASequence.py,1.2,1.3 DNASequence.py,1.2,1.3 DNASequenceWithGFFFeatures.py,1.2,1.3 DateTime.py,1.2,1.3 Decypher_Text.py,1.2,1.3 Edge.py,1.2,1.3 EmblFlatfile.py,1.2,1.3 FASTA.py,1.2,1.3 FASTA_AA.py,1.2,1.3 FASTA_NA.py,1.2,1.3 FASTA_Text.py,1.2,1.3 GFF.py,1.2,1.3 GFF1.py,1.2,1.3 GFF2.py,1.2,1.3 GFF2_5.py,1.2,1.3 GFF3.py,1.2,1.3 GO_Term.py,1.2,1.3 GenbankFlatfile.py,1.2,1.3 GenericSequence.py,1.2,1.3 GeneticElement.py,1.2,1.3 Genotype.py,1.2,1.3 Germplasm_Details.py,1.2,1.3 Germplasm_List.py,1.2,1.3 Global_Keyword.py,1.2,1.3 HBon!
d_Pair.py,1.2,1.3 HFormatText.py,1.2,1.3 Haplotyping_Study_obj.py,1.2,1.3 ICIS_Query.py,1.2,1.3 ICIS_Query2.py,1.2,1.3 ICIS_Query3.py,1.2,1.3 IntAct_XML.py,1.2,1.3 Interaction.py,1.2,1.3 InteractionMethod.py,1.2,1.3 Interaction_partner.py,1.2,1.3 Interactor.py,1.2,1.3 MEME_Text.py,1.2,1.3 MGIS_ACCESSION.py,1.2,1.3 MMP_Locus.py,1.2,1.3 MO_Term_Test.py,1.2,1.3 MmCIFText.py,1.2,1.3 Multi_key_value_pair.py,1.2,1.3 MyTestingDataType_11024145298313.py,1.2,1.3 MyTree.py,1.2,1.3 NCBI_BLAST_Text.py,1.2,1.3 NCBI_Blast_XML.py,1.2,1.3 NCBI_Blast_XML_Gif.py,1.2,1.3 NCBI_Blast_XML_Gif_Map.py,1.2,1.3 NCBI_MEME_Text.py,1.2,1.3 NucleotideSequence.py,1.2,1.3 PDBFormattedText.py,1.2,1.3 PDBText.py,1.2,1.3 PDGJOB.py,1.2,1.3 PHDText.py,1.2,1.3 PMUTText.py,1.2,1.3 PSeaTextFormatted.py,1.2,1.3 PhenotypeDescription.py,1.2,1.3 PubMedMEDLINE.py,1.2,1.3 RNASequence.py,1.2,1.3 SINGER_ACCESSION.py,1.2,1.3 Sample.py,1.2,1.3 SchematikonMotifID.py,1.2,1.3 SchematikonMotifSupport.py,1.2,1.3 SchematikonSegme!
ntAttributes.py,1.2,1.3 SchematikonSegmentID.py,1.2,1.3 Schem!
atikonStructureAnnotation.py,1.2,1.3 SchematikonVorocodeName.py,1.2,1.3 Scored_acronym_string.py,1.2,1.3 SimpleAnnotatedGIFImage.py,1.2,1.3 SimpleAnnotatedJPEGImage.py,1.2,1.3 Simple_key_value_pair.py,1.2,1.3 Snp_allele.py,1.2,1.3 Snp_genotype.py,1.2,1.3 Study.py,1.2,1.3 TEST.py,1.2,1.3 TargetP_result.py,1.2,1.3 Testout.py,1.2,1.3 TextBase64.py,1.2,1.3 TextFormatted.py,1.2,1.3 TextHtml.py,1.2,1.3 TextPlain.py,1.2,1.3 TextUuencoded.py,1.2,1.3 TextXml.py,1.2,1.3 Text_plain.py,1.2,1.3 Trait_Details.py,1.2,1.3 Tree.py,1.2,1.3 TropGENE_ACCESSION.py,1.2,1.3 TropGENE_Diversity_Matrix.py,1.2,1.3 TropGENE_LOCUS.py,1.2,1.3 VirtualSequence.py,1.2,1.3 WU_BLAST_Text.py,1.2,1.3 Wildcard_Query.py,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AlleleAssociation.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Allele_freq.py	2005/01/27 08:44:05	1.3
@@ -44,7 +44,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/AminoAcidSequence.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_PNG.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_Encoded_Postscript.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_PDB.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_gif.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/B64_encoded_jpeg.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BLASTText.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/BasicGFFSequenceFeature.py	2005/01/27 08:44:05	1.3
@@ -60,7 +60,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalAlnFormattedText.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ClustalMsfFormattedText.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedAASequence.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedDNASequence.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/CommentedRNASequence.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequence.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DNASequenceWithGFFFeatures.py	2005/01/27 08:44:05	1.3
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/DateTime.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Decypher_Text.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Edge.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/EmblFlatfile.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_AA.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_NA.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/FASTA_Text.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF1.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF2_5.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GFF3.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GO_Term.py	2005/01/27 08:44:05	1.3
@@ -48,7 +48,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenbankFlatfile.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GenericSequence.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/GeneticElement.py	2005/01/27 08:44:05	1.3
@@ -47,7 +47,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Genotype.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_Details.py	2005/01/27 08:44:05	1.3
@@ -55,7 +55,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Germplasm_List.py	2005/01/27 08:44:05	1.3
@@ -55,7 +55,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Global_Keyword.py	2005/01/27 08:44:05	1.3
@@ -45,4 +45,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HBond_Pair.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/HFormatText.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Haplotyping_Study_obj.py	2005/01/27 08:44:05	1.3
@@ -45,4 +45,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query2.py	2005/01/27 08:44:05	1.3
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/ICIS_Query3.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/IntAct_XML.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction.py	2005/01/27 08:44:05	1.3
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/InteractionMethod.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interaction_partner.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Interactor.py	2005/01/27 08:44:05	1.3
@@ -47,7 +47,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MEME_Text.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MGIS_ACCESSION.py	2005/01/27 08:44:05	1.3
@@ -66,7 +66,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MMP_Locus.py	2005/01/27 08:44:05	1.3
@@ -45,4 +45,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MO_Term_Test.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MmCIFText.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Multi_key_value_pair.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTestingDataType_11024145298313.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/MyTree.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_BLAST_Text.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif.py	2005/01/27 08:44:05	1.3
@@ -48,7 +48,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_Blast_XML_Gif_Map.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NCBI_MEME_Text.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/NucleotideSequence.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBFormattedText.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDBText.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PDGJOB.py	2005/01/27 08:44:05	1.3
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PHDText.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PMUTText.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PSeaTextFormatted.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PhenotypeDescription.py	2005/01/27 08:44:05	1.3
@@ -47,7 +47,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/PubMedMEDLINE.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/RNASequence.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SINGER_ACCESSION.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Sample.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifID.py	2005/01/27 08:44:05	1.3
@@ -47,7 +47,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonMotifSupport.py	2005/01/27 08:44:05	1.3
@@ -48,7 +48,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentAttributes.py	2005/01/27 08:44:05	1.3
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonSegmentID.py	2005/01/27 08:44:05	1.3
@@ -47,7 +47,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonStructureAnnotation.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SchematikonVorocodeName.py	2005/01/27 08:44:05	1.3
@@ -47,7 +47,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Scored_acronym_string.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedGIFImage.py	2005/01/27 08:44:05	1.3
@@ -48,7 +48,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/SimpleAnnotatedJPEGImage.py	2005/01/27 08:44:05	1.3
@@ -49,7 +49,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Simple_key_value_pair.py	2005/01/27 08:44:05	1.3
@@ -48,7 +48,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_allele.py	2005/01/27 08:44:05	1.3
@@ -37,7 +37,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Snp_genotype.py	2005/01/27 08:44:05	1.3
@@ -38,7 +38,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Study.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TEST.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TargetP_result.py	2005/01/27 08:44:05	1.3
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Testout.py	2005/01/27 08:44:05	1.3
@@ -51,7 +51,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextBase64.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextFormatted.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextHtml.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextPlain.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextUuencoded.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TextXml.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Text_plain.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Trait_Details.py	2005/01/27 08:44:05	1.3
@@ -52,7 +52,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Tree.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_ACCESSION.py	2005/01/27 08:44:05	1.3
@@ -66,7 +66,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_Diversity_Matrix.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/TropGENE_LOCUS.py	2005/01/27 08:44:05	1.3
@@ -45,4 +45,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/VirtualSequence.py	2005/01/27 08:44:05	1.3
@@ -47,7 +47,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/WU_BLAST_Text.py	2005/01/27 08:44:05	1.3
@@ -46,4 +46,5 @@
             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
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
\ No newline at end of file

===================================================================
RCS file: /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/01/18 13:46:22	1.2
+++ /home/repository/moby/moby-live/Python/bioMoby/ontology/Wildcard_Query.py	2005/01/27 08:44:05	1.3
@@ -50,7 +50,8 @@
             if elt.nodeName=="CrossReference" or elt.nodeName=="moby:CrossReference":
                 self.__cross__=[]
                 for ref in elt.childNodes:
-                    self.__cross__.append(ref.toxml())
+                    if ref.nodeType==ref.ELEMENT_NODE:
+                        self.__cross__.append(um.loads(ref.toxml()))
             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())




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