[MOBY-guts] biomoby commit
senger@ebi.ac.uk
senger at pub.open-bio.org
Fri May 9 15:51:11 UTC 2003
senger
Fri May 9 11:51:11 EDT 2003
Update of /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared
In directory pub.open-bio.org:/tmp/cvs-serv9113/docs/API/org/biomoby/shared
Modified Files:
Central.html MobyDataType.html MobyException.html
MobyNamespace.html MobyService.html MobyServiceType.html
NoSuccessException.html Utils.html package-frame.html
package-summary.html package-tree.html
Log Message:
changes reflecting the main API change in BioMoby
moby-live/Java/docs/API/org/biomoby/shared Central.html,1.1,1.2 MobyDataType.html,1.1,1.2 MobyException.html,1.1,1.2 MobyNamespace.html,1.1,1.2 MobyService.html,1.1,1.2 MobyServiceType.html,1.1,1.2 NoSuccessException.html,1.1,1.2 Utils.html,1.1,1.2 package-frame.html,1.1,1.2 package-summary.html,1.1,1.2 package-tree.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/Central.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/Central.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/Central.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:09 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:08 BST 2003 -->
<TITLE>
Central (MOBY Registry in Java)
</TITLE>
@@ -35,7 +35,7 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
@@ -75,9 +75,6 @@
org.biomoby.shared</FONT>
<BR>
Interface Central</H2>
-<DL>
-<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../../org/biomoby/client/CentralImpl.html">CentralImpl</A></DD>
-</DL>
<HR>
<DL>
<DT>public interface <B>Central</B></DL>
@@ -101,8 +98,8 @@
<p>
For details describing and explaining the methods see the original documentation at
- <a href="http://biomoby.org/Documentation/MOBY_Central.html" target="_top">
- http://biomoby.org/Documentation/MOBY_Central.html</a>.
+ <a href="http://biomoby.org/" target="_top">
+ http://biomoby.org</a>.
<p>
<P>
@@ -149,31 +146,33 @@
<TD><CODE><B><A HREF="../../../org/biomoby/shared/Central.html#findService(org.biomoby.shared.MobyService)">findService</A></B>(<A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A> pattern)</CODE>
<BR>
- Find services by their input and/or output data types.</TD>
+ Find services matching whatever is non-empty in the given 'pattern'.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> <A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A>[]</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/Central.html#findService(java.lang.String)">findService</A></B>(java.lang.String serviceType)</CODE>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/Central.html#findService(org.biomoby.shared.MobyService, java.lang.String[])">findService</A></B>(<A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A> pattern,
+ java.lang.String[] keywords)</CODE>
<BR>
- Find services of the given type and its sub-types.</TD>
+ Find service matching both all non-empty fields in the 'pattern' and
+ the 'keywords'.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> <A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A>[]</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/Central.html#findService(java.lang.String[])">findService</A></B>(java.lang.String[] keywords)</CODE>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/Central.html#findService(java.lang.String)">findService</A></B>(java.lang.String serviceType)</CODE>
<BR>
- Find services by given keywords.</TD>
+ Find services of the given type and its sub-types.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE> java.lang.String</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/Central.html#getDataType(java.lang.String)">getDataType</A></B>(java.lang.String dataTypeName)</CODE>
+<CODE> <A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/Central.html#findService(java.lang.String[])">findService</A></B>(java.lang.String[] keywords)</CODE>
<BR>
- Get XML Schema definition of the given data type.</TD>
+ Find services by given keywords.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
@@ -268,6 +267,15 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/Central.html#setDebug(boolean)">setDebug</A></B>(boolean debug)</CODE>
+
+<BR>
+ Ask the implementation to create more verbose logs or messages about
+ what is going on.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/Central.html#unregisterDataType(org.biomoby.shared.MobyDataType)">unregisterDataType</A></B>(<A HREF="../../../org/biomoby/shared/MobyDataType.html">MobyDataType</A> dataType)</CODE>
<BR>
@@ -411,25 +419,6 @@
</DL>
<HR>
-<A NAME="getDataType(java.lang.String)"><!-- --></A><H3>
-getDataType</H3>
-<PRE>
-public java.lang.String <B>getDataType</B>(java.lang.String dataTypeName)
- throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A>,
- <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></PRE>
-<DL>
-<DD>Get XML Schema definition of the given data type.
-<p>
-<P>
-<DD><DL>
-
-<DT><B>Throws:</B>
-<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE> - if communication with the Moby Registry fails
-<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if 'dataTypeName' was not found</DL>
-</DD>
-</DL>
-<HR>
-
<A NAME="getServiceWSDL(java.lang.String, java.lang.String)"><!-- --></A><H3>
getServiceWSDL</H3>
<PRE>
@@ -476,7 +465,8 @@
<PRE>
public void <B>registerDataType</B>(<A HREF="../../../org/biomoby/shared/MobyDataType.html">MobyDataType</A> dataType)
throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A>,
- <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></PRE>
+ <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A>,
+ <A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></PRE>
<DL>
<DD>Register new data type. It also updates 'dataType' with an ID given
by the registration process - this ID will be the only way how to
@@ -489,7 +479,8 @@
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE> - if communication with the Moby Registry fails
-<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if registration failed</DL>
+<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if registration failed
+<DD><CODE><A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></CODE></DL>
</DD>
</DL>
<HR>
@@ -499,7 +490,8 @@
<PRE>
public void <B>unregisterDataType</B>(<A HREF="../../../org/biomoby/shared/MobyDataType.html">MobyDataType</A> dataType)
throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A>,
- <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></PRE>
+ <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A>,
+ <A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></PRE>
<DL>
<DD>Unregister given Moby data type. Note that it may not work if the
given object does not contain registration ID. But this may change
@@ -510,7 +502,8 @@
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE> - if communication with the Moby Registry fails
-<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if unregistration failed</DL>
+<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if unregistration failed
+<DD><CODE><A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></CODE></DL>
</DD>
</DL>
<HR>
@@ -520,7 +513,8 @@
<PRE>
public void <B>registerServiceType</B>(<A HREF="../../../org/biomoby/shared/MobyServiceType.html">MobyServiceType</A> serviceType)
throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A>,
- <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></PRE>
+ <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A>,
+ <A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></PRE>
<DL>
<DD>Register new service type. It also updates 'serviceType' with an ID
given by the registration process - this ID will be the only way how to
@@ -534,7 +528,8 @@
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE> - if communication with the Moby Registry fails
-<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if registration failed</DL>
+<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if registration failed
+<DD><CODE><A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></CODE></DL>
</DD>
</DL>
<HR>
@@ -544,7 +539,8 @@
<PRE>
public void <B>unregisterServiceType</B>(<A HREF="../../../org/biomoby/shared/MobyServiceType.html">MobyServiceType</A> serviceType)
throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A>,
- <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></PRE>
+ <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A>,
+ <A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></PRE>
<DL>
<DD>Unregister given Moby service type. Note that it may not work if the
given object does not contain registration ID. But this may change
@@ -555,7 +551,8 @@
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE> - if communication with the Moby Registry fails
-<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if unregistration failed</DL>
+<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if unregistration failed
+<DD><CODE><A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></CODE></DL>
</DD>
</DL>
<HR>
@@ -565,7 +562,8 @@
<PRE>
public void <B>registerNamespace</B>(<A HREF="../../../org/biomoby/shared/MobyNamespace.html">MobyNamespace</A> namespace)
throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A>,
- <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></PRE>
+ <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A>,
+ <A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></PRE>
<DL>
<DD>Register new namespace. It also updates 'namespace' with an ID
given by the registration process - this ID will be the only way how to
@@ -578,7 +576,8 @@
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE> - if communication with the Moby Registry fails
-<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if registration failed</DL>
+<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if registration failed
+<DD><CODE><A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></CODE></DL>
</DD>
</DL>
<HR>
@@ -588,7 +587,8 @@
<PRE>
public void <B>unregisterNamespace</B>(<A HREF="../../../org/biomoby/shared/MobyNamespace.html">MobyNamespace</A> namespace)
throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A>,
- <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></PRE>
+ <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A>,
+ <A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></PRE>
<DL>
<DD>Unregister given Moby namespace. Note that it may not work if the
given object does not contain registration ID. But this may change
@@ -599,7 +599,8 @@
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE> - if communication with the Moby Registry fails
-<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if unregistration failed</DL>
+<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if unregistration failed
+<DD><CODE><A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></CODE></DL>
</DD>
</DL>
<HR>
@@ -609,7 +610,8 @@
<PRE>
public void <B>registerService</B>(<A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A> service)
throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A>,
- <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></PRE>
+ <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A>,
+ <A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></PRE>
<DL>
<DD>Register a new service. It also updates 'service' with an ID
given by the registration process - this ID will be the only way how to
@@ -623,7 +625,8 @@
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE> - if communication with the Moby Registry fails
-<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if registration failed</DL>
+<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if registration failed
+<DD><CODE><A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></CODE></DL>
</DD>
</DL>
<HR>
@@ -633,7 +636,8 @@
<PRE>
public void <B>unregisterService</B>(<A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A> service)
throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A>,
- <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></PRE>
+ <A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A>,
+ <A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></PRE>
<DL>
<DD>Unregister given Moby service. Note that it may not work if the
given object does not contain registration ID. But this may change
@@ -644,7 +648,8 @@
<DT><B>Throws:</B>
<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE> - if communication with the Moby Registry fails
-<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if unregistration failed</DL>
+<DD><CODE><A HREF="../../../org/biomoby/shared/NoSuccessException.html">NoSuccessException</A></CODE> - if unregistration failed
+<DD><CODE><A HREF="../../../org/biomoby/shared/PendingCurationException.html">PendingCurationException</A></CODE></DL>
</DD>
</DL>
<HR>
@@ -694,14 +699,8 @@
public <A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A>[] <B>findService</B>(<A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A> pattern)
throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></PRE>
<DL>
-<DD>Find services by their input and/or output data types. If the 'pattern'
- has a non-empty array of input data types, it looks for services with
- such inputs. If the 'pattern' has a non-empty array of output data
- types, it looks for services with such outputs. If both input and
- output data types are present, the returned set is a intersection.
-<p>
- Note that some other fields of the 'pattern' must be filled as well
- (at the moment of writting this these fields are: type and authority).
+<DD>Find services matching whatever is non-empty in the given 'pattern'.
+ If more fields are given the logical AND is applied on them.
<p>
<P>
<DD><DL>
@@ -712,6 +711,23 @@
</DL>
<HR>
+<A NAME="findService(org.biomoby.shared.MobyService, java.lang.String[])"><!-- --></A><H3>
+findService</H3>
+<PRE>
+public <A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A>[] <B>findService</B>(<A HREF="../../../org/biomoby/shared/MobyService.html">MobyService</A> pattern,
+ java.lang.String[] keywords)
+ throws <A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></PRE>
+<DL>
+<DD>Find service matching both all non-empty fields in the 'pattern' and
+ the 'keywords'.
+<P>
+<DD><DL>
+
+<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE></DL>
+</DD>
+</DL>
+<HR>
+
<A NAME="call(java.lang.String, java.lang.String)"><!-- --></A><H3>
call</H3>
<PRE>
@@ -730,6 +746,20 @@
<DD><CODE><A HREF="../../../org/biomoby/shared/MobyException.html">MobyException</A></CODE></DL>
</DD>
</DL>
+<HR>
+
+<A NAME="setDebug(boolean)"><!-- --></A><H3>
+setDebug</H3>
+<PRE>
+public void <B>setDebug</B>(boolean debug)</PRE>
+<DL>
+<DD>Ask the implementation to create more verbose logs or messages about
+ what is going on. The behaviour is completely implementation dependent.
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
<!-- ========= END OF CLASS DATA ========= -->
<HR>
@@ -751,7 +781,7 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
@@ -785,6 +815,6 @@
<!-- =========== END OF NAVBAR =========== -->
<HR>
-<font size="-1"><a href="mailto:mwilkinson at gene.pbi.nrc.ca,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Sun Mar 2 18:52:04 GMT 2003</font>
+<font size="-1"><a href="mailto:markw at illuminae.com,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Fri May 9 16:41:04 BST 2003</font>
</BODY>
</HTML>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyDataType.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyDataType.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyDataType.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:09 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:08 BST 2003 -->
<TITLE>
MobyDataType (MOBY Registry in Java)
</TITLE>
@@ -35,13 +35,13 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- PREV CLASS
+ <A HREF="../../../org/biomoby/shared/MobyData.html"><B>PREV CLASS</B></A>
<A HREF="../../../org/biomoby/shared/MobyNamespace.html"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
@@ -139,6 +139,16 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#addChild(java.lang.String, java.lang.String)">addChild</A></B>(java.lang.String name,
+ java.lang.String typeName)</CODE>
+
+<BR>
+ 'name' is a name given to this child (attribute)
+ 'typeName' is a name of a type represented byte this child</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#addParentName(java.lang.String)">addParentName</A></B>(java.lang.String value)</CODE>
<BR>
@@ -147,6 +157,14 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#format(int)">format</A></B>(int indent)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#getAuthority()">getAuthority</A></B>()</CODE>
<BR>
@@ -154,6 +172,15 @@
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.util.Hashtable</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#getChildren()">getChildren</A></B>()</CODE>
+
+<BR>
+ Describes what children this data type has (expressing ontology
+ term HAS-A).</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#getDescription()">getDescription</A></B>()</CODE>
@@ -163,6 +190,14 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#getEmailContact()">getEmailContact</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#getId()">getId</A></B>()</CODE>
<BR>
@@ -186,8 +221,8 @@
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE> java.lang.String</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#getXSD()">getXSD</A></B>()</CODE>
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#setAuthority(java.lang.String)">setAuthority</A></B>(java.lang.String value)</CODE>
<BR>
</TD>
@@ -195,7 +230,7 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#setAuthority(java.lang.String)">setAuthority</A></B>(java.lang.String value)</CODE>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#setChildren(java.util.Hashtable)">setChildren</A></B>(java.util.Hashtable value)</CODE>
<BR>
</TD>
@@ -211,7 +246,7 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#setId(java.lang.String)">setId</A></B>(java.lang.String value)</CODE>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#setEmailContact(java.lang.String)">setEmailContact</A></B>(java.lang.String value)</CODE>
<BR>
</TD>
@@ -219,7 +254,7 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#setParentNames(java.lang.String[])">setParentNames</A></B>(java.lang.String[] value)</CODE>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#setId(java.lang.String)">setId</A></B>(java.lang.String value)</CODE>
<BR>
</TD>
@@ -227,7 +262,7 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#setXSD(java.lang.String)">setXSD</A></B>(java.lang.String value)</CODE>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyDataType.html#setParentNames(java.lang.String[])">setParentNames</A></B>(java.lang.String[] value)</CODE>
<BR>
</TD>
@@ -341,10 +376,10 @@
</DL>
<HR>
-<A NAME="getDescription()"><!-- --></A><H3>
-getDescription</H3>
+<A NAME="getEmailContact()"><!-- --></A><H3>
+getEmailContact</H3>
<PRE>
-public java.lang.String <B>getDescription</B>()</PRE>
+public java.lang.String <B>getEmailContact</B>()</PRE>
<DL>
<DD><DL>
</DL>
@@ -352,10 +387,10 @@
</DL>
<HR>
-<A NAME="setDescription(java.lang.String)"><!-- --></A><H3>
-setDescription</H3>
+<A NAME="setEmailContact(java.lang.String)"><!-- --></A><H3>
+setEmailContact</H3>
<PRE>
-public void <B>setDescription</B>(java.lang.String value)</PRE>
+public void <B>setEmailContact</B>(java.lang.String value)</PRE>
<DL>
<DD><DL>
</DL>
@@ -363,10 +398,10 @@
</DL>
<HR>
-<A NAME="getXSD()"><!-- --></A><H3>
-getXSD</H3>
+<A NAME="getDescription()"><!-- --></A><H3>
+getDescription</H3>
<PRE>
-public java.lang.String <B>getXSD</B>()</PRE>
+public java.lang.String <B>getDescription</B>()</PRE>
<DL>
<DD><DL>
</DL>
@@ -374,10 +409,10 @@
</DL>
<HR>
-<A NAME="setXSD(java.lang.String)"><!-- --></A><H3>
-setXSD</H3>
+<A NAME="setDescription(java.lang.String)"><!-- --></A><H3>
+setDescription</H3>
<PRE>
-public void <B>setXSD</B>(java.lang.String value)</PRE>
+public void <B>setDescription</B>(java.lang.String value)</PRE>
<DL>
<DD><DL>
</DL>
@@ -418,6 +453,50 @@
</DL>
<HR>
+<A NAME="getChildren()"><!-- --></A><H3>
+getChildren</H3>
+<PRE>
+public java.util.Hashtable <B>getChildren</B>()</PRE>
+<DL>
+<DD>Describes what children this data type has (expressing ontology
+ term HAS-A). The returned value is a hashtable with:
+ key is a name of a data type (an existing or a basic type)
+ value is a name of this child; note that this value may be
+ int some cases be equal to the 'key' (this happens
+ especially for the basic data types - but we do not care)
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setChildren(java.util.Hashtable)"><!-- --></A><H3>
+setChildren</H3>
+<PRE>
+public void <B>setChildren</B>(java.util.Hashtable value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="addChild(java.lang.String, java.lang.String)"><!-- --></A><H3>
+addChild</H3>
+<PRE>
+public void <B>addChild</B>(java.lang.String name,
+ java.lang.String typeName)</PRE>
+<DL>
+<DD>'name' is a name given to this child (attribute)
+ 'typeName' is a name of a type represented byte this child
+<P>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
<A NAME="toString()"><!-- --></A><H3>
toString</H3>
<PRE>
@@ -430,6 +509,17 @@
</DL>
</DD>
</DL>
+<HR>
+
+<A NAME="format(int)"><!-- --></A><H3>
+format</H3>
+<PRE>
+public java.lang.String <B>format</B>(int indent)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
<!-- ========= END OF CLASS DATA ========= -->
<HR>
@@ -451,13 +541,13 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- PREV CLASS
+ <A HREF="../../../org/biomoby/shared/MobyData.html"><B>PREV CLASS</B></A>
<A HREF="../../../org/biomoby/shared/MobyNamespace.html"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
@@ -485,6 +575,6 @@
<!-- =========== END OF NAVBAR =========== -->
<HR>
-<font size="-1"><a href="mailto:mwilkinson at gene.pbi.nrc.ca,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Sun Mar 2 18:52:04 GMT 2003</font>
+<font size="-1"><a href="mailto:markw at illuminae.com,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Fri May 9 16:41:04 BST 2003</font>
</BODY>
</HTML>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyException.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyException.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyException.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:10 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:09 BST 2003 -->
<TITLE>
MobyException (MOBY Registry in Java)
</TITLE>
@@ -35,7 +35,7 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
@@ -269,7 +269,7 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
@@ -303,6 +303,6 @@
<!-- =========== END OF NAVBAR =========== -->
<HR>
-<font size="-1"><a href="mailto:mwilkinson at gene.pbi.nrc.ca,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Sun Mar 2 18:52:04 GMT 2003</font>
+<font size="-1"><a href="mailto:markw at illuminae.com,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Fri May 9 16:41:04 BST 2003</font>
</BODY>
</HTML>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyNamespace.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyNamespace.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyNamespace.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:09 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:08 BST 2003 -->
<TITLE>
MobyNamespace (MOBY Registry in Java)
</TITLE>
@@ -35,14 +35,14 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../org/biomoby/shared/MobyDataType.html"><B>PREV CLASS</B></A>
- <A HREF="../../../org/biomoby/shared/MobyService.html"><B>NEXT CLASS</B></A></FONT></TD>
+ <A HREF="../../../org/biomoby/shared/MobyPrimaryDataSet.html"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
<A HREF="MobyNamespace.html" TARGET="_top"><B>NO FRAMES</B></A>
@@ -136,6 +136,14 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyNamespace.html#format(int)">format</A></B>(int indent)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyNamespace.html#getAuthority()">getAuthority</A></B>()</CODE>
<BR>
@@ -152,6 +160,14 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyNamespace.html#getEmailContact()">getEmailContact</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyNamespace.html#getId()">getId</A></B>()</CODE>
<BR>
@@ -184,6 +200,14 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyNamespace.html#setEmailContact(java.lang.String)">setEmailContact</A></B>(java.lang.String value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyNamespace.html#setId(java.lang.String)">setId</A></B>(java.lang.String value)</CODE>
<BR>
@@ -298,6 +322,28 @@
</DL>
<HR>
+<A NAME="getEmailContact()"><!-- --></A><H3>
+getEmailContact</H3>
+<PRE>
+public java.lang.String <B>getEmailContact</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setEmailContact(java.lang.String)"><!-- --></A><H3>
+setEmailContact</H3>
+<PRE>
+public void <B>setEmailContact</B>(java.lang.String value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
<A NAME="getDescription()"><!-- --></A><H3>
getDescription</H3>
<PRE>
@@ -332,6 +378,17 @@
</DL>
</DD>
</DL>
+<HR>
+
+<A NAME="format(int)"><!-- --></A><H3>
+format</H3>
+<PRE>
+public java.lang.String <B>format</B>(int indent)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
<!-- ========= END OF CLASS DATA ========= -->
<HR>
@@ -353,14 +410,14 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../org/biomoby/shared/MobyDataType.html"><B>PREV CLASS</B></A>
- <A HREF="../../../org/biomoby/shared/MobyService.html"><B>NEXT CLASS</B></A></FONT></TD>
+ <A HREF="../../../org/biomoby/shared/MobyPrimaryDataSet.html"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
<A HREF="MobyNamespace.html" TARGET="_top"><B>NO FRAMES</B></A>
@@ -387,6 +444,6 @@
<!-- =========== END OF NAVBAR =========== -->
<HR>
-<font size="-1"><a href="mailto:mwilkinson at gene.pbi.nrc.ca,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Sun Mar 2 18:52:04 GMT 2003</font>
+<font size="-1"><a href="mailto:markw at illuminae.com,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Fri May 9 16:41:04 BST 2003</font>
</BODY>
</HTML>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyService.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyService.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyService.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:09 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:09 BST 2003 -->
<TITLE>
MobyService (MOBY Registry in Java)
</TITLE>
@@ -35,13 +35,13 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- <A HREF="../../../org/biomoby/shared/MobyNamespace.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../org/biomoby/shared/MobySecondaryData.html"><B>PREV CLASS</B></A>
<A HREF="../../../org/biomoby/shared/MobyServiceType.html"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
@@ -136,8 +136,7 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#addInput(java.lang.String, java.lang.String)">addInput</A></B>(java.lang.String inputType,
- java.lang.String namespace)</CODE>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#addInput(org.biomoby.shared.MobyData)">addInput</A></B>(<A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A> value)</CODE>
<BR>
</TD>
@@ -145,7 +144,7 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#addOutputType(java.lang.String)">addOutputType</A></B>(java.lang.String value)</CODE>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#addOutput(org.biomoby.shared.MobyData)">addOutput</A></B>(<A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A> value)</CODE>
<BR>
</TD>
@@ -185,6 +184,14 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#getEmailContact()">getEmailContact</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#getId()">getId</A></B>()</CODE>
<BR>
@@ -192,32 +199,32 @@
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE> java.lang.String[]</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#getInputNamespaces()">getInputNamespaces</A></B>()</CODE>
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#getName()">getName</A></B>()</CODE>
<BR>
</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE> java.lang.String[]</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#getInputTypes()">getInputTypes</A></B>()</CODE>
+<CODE> <A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#getPrimaryInputs()">getPrimaryInputs</A></B>()</CODE>
<BR>
</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE> java.lang.String</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#getName()">getName</A></B>()</CODE>
+<CODE> <A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#getPrimaryOutputs()">getPrimaryOutputs</A></B>()</CODE>
<BR>
</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE> java.lang.String[]</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#getOutputTypes()">getOutputTypes</A></B>()</CODE>
+<CODE> <A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A>[]</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#getSecondaryInputs()">getSecondaryInputs</A></B>()</CODE>
<BR>
</TD>
@@ -240,6 +247,22 @@
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> boolean</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#isAuthoritative()">isAuthoritative</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#setAuthoritative(boolean)">setAuthoritative</A></B>(boolean value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#setAuthority(java.lang.String)">setAuthority</A></B>(java.lang.String value)</CODE>
@@ -265,6 +288,14 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#setEmailContact(java.lang.String)">setEmailContact</A></B>(java.lang.String value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#setId(java.lang.String)">setId</A></B>(java.lang.String value)</CODE>
<BR>
@@ -273,8 +304,7 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#setInputs(java.lang.String[], java.lang.String[])">setInputs</A></B>(java.lang.String[] types,
- java.lang.String[] names)</CODE>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#setInputs(org.biomoby.shared.MobyData[])">setInputs</A></B>(<A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A>[] value)</CODE>
<BR>
</TD>
@@ -282,7 +312,7 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#setOutputTypes(java.lang.String[])">setOutputTypes</A></B>(java.lang.String[] value)</CODE>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyService.html#setOutputs(org.biomoby.shared.MobyData[])">setOutputs</A></B>(<A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A>[] value)</CODE>
<BR>
</TD>
@@ -390,6 +420,28 @@
</DL>
<HR>
+<A NAME="isAuthoritative()"><!-- --></A><H3>
+isAuthoritative</H3>
+<PRE>
+public boolean <B>isAuthoritative</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setAuthoritative(boolean)"><!-- --></A><H3>
+setAuthoritative</H3>
+<PRE>
+public void <B>setAuthoritative</B>(boolean value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
<A NAME="getAuthority()"><!-- --></A><H3>
getAuthority</H3>
<PRE>
@@ -412,6 +464,28 @@
</DL>
<HR>
+<A NAME="getEmailContact()"><!-- --></A><H3>
+getEmailContact</H3>
+<PRE>
+public java.lang.String <B>getEmailContact</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setEmailContact(java.lang.String)"><!-- --></A><H3>
+setEmailContact</H3>
+<PRE>
+public void <B>setEmailContact</B>(java.lang.String value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
<A NAME="getCategory()"><!-- --></A><H3>
getCategory</H3>
<PRE>
@@ -500,10 +574,10 @@
</DL>
<HR>
-<A NAME="getInputTypes()"><!-- --></A><H3>
-getInputTypes</H3>
+<A NAME="setInputs(org.biomoby.shared.MobyData[])"><!-- --></A><H3>
+setInputs</H3>
<PRE>
-public java.lang.String[] <B>getInputTypes</B>()</PRE>
+public void <B>setInputs</B>(<A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A>[] value)</PRE>
<DL>
<DD><DL>
</DL>
@@ -511,10 +585,10 @@
</DL>
<HR>
-<A NAME="getInputNamespaces()"><!-- --></A><H3>
-getInputNamespaces</H3>
+<A NAME="addInput(org.biomoby.shared.MobyData)"><!-- --></A><H3>
+addInput</H3>
<PRE>
-public java.lang.String[] <B>getInputNamespaces</B>()</PRE>
+public void <B>addInput</B>(<A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A> value)</PRE>
<DL>
<DD><DL>
</DL>
@@ -522,11 +596,10 @@
</DL>
<HR>
-<A NAME="setInputs(java.lang.String[], java.lang.String[])"><!-- --></A><H3>
-setInputs</H3>
+<A NAME="setOutputs(org.biomoby.shared.MobyData[])"><!-- --></A><H3>
+setOutputs</H3>
<PRE>
-public void <B>setInputs</B>(java.lang.String[] types,
- java.lang.String[] names)</PRE>
+public void <B>setOutputs</B>(<A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A>[] value)</PRE>
<DL>
<DD><DL>
</DL>
@@ -534,11 +607,10 @@
</DL>
<HR>
-<A NAME="addInput(java.lang.String, java.lang.String)"><!-- --></A><H3>
-addInput</H3>
+<A NAME="addOutput(org.biomoby.shared.MobyData)"><!-- --></A><H3>
+addOutput</H3>
<PRE>
-public void <B>addInput</B>(java.lang.String inputType,
- java.lang.String namespace)</PRE>
+public void <B>addOutput</B>(<A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A> value)</PRE>
<DL>
<DD><DL>
</DL>
@@ -546,10 +618,10 @@
</DL>
<HR>
-<A NAME="getOutputTypes()"><!-- --></A><H3>
-getOutputTypes</H3>
+<A NAME="getPrimaryInputs()"><!-- --></A><H3>
+getPrimaryInputs</H3>
<PRE>
-public java.lang.String[] <B>getOutputTypes</B>()</PRE>
+public <A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A>[] <B>getPrimaryInputs</B>()</PRE>
<DL>
<DD><DL>
</DL>
@@ -557,10 +629,10 @@
</DL>
<HR>
-<A NAME="setOutputTypes(java.lang.String[])"><!-- --></A><H3>
-setOutputTypes</H3>
+<A NAME="getSecondaryInputs()"><!-- --></A><H3>
+getSecondaryInputs</H3>
<PRE>
-public void <B>setOutputTypes</B>(java.lang.String[] value)</PRE>
+public <A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A>[] <B>getSecondaryInputs</B>()</PRE>
<DL>
<DD><DL>
</DL>
@@ -568,10 +640,10 @@
</DL>
<HR>
-<A NAME="addOutputType(java.lang.String)"><!-- --></A><H3>
-addOutputType</H3>
+<A NAME="getPrimaryOutputs()"><!-- --></A><H3>
+getPrimaryOutputs</H3>
<PRE>
-public void <B>addOutputType</B>(java.lang.String value)</PRE>
+public <A HREF="../../../org/biomoby/shared/MobyData.html">MobyData</A>[] <B>getPrimaryOutputs</B>()</PRE>
<DL>
<DD><DL>
</DL>
@@ -623,13 +695,13 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- <A HREF="../../../org/biomoby/shared/MobyNamespace.html"><B>PREV CLASS</B></A>
+ <A HREF="../../../org/biomoby/shared/MobySecondaryData.html"><B>PREV CLASS</B></A>
<A HREF="../../../org/biomoby/shared/MobyServiceType.html"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
@@ -657,6 +729,6 @@
<!-- =========== END OF NAVBAR =========== -->
<HR>
-<font size="-1"><a href="mailto:mwilkinson at gene.pbi.nrc.ca,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Sun Mar 2 18:52:04 GMT 2003</font>
+<font size="-1"><a href="mailto:markw at illuminae.com,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Fri May 9 16:41:04 BST 2003</font>
</BODY>
</HTML>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyServiceType.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyServiceType.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/MobyServiceType.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:09 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:09 BST 2003 -->
<TITLE>
MobyServiceType (MOBY Registry in Java)
</TITLE>
@@ -35,7 +35,7 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
@@ -144,6 +144,22 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyServiceType.html#format(int)">format</A></B>(int indent)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyServiceType.html#getAuthority()">getAuthority</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyServiceType.html#getDescription()">getDescription</A></B>()</CODE>
<BR>
@@ -152,6 +168,14 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyServiceType.html#getEmailContact()">getEmailContact</A></B>()</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyServiceType.html#getId()">getId</A></B>()</CODE>
<BR>
@@ -176,6 +200,14 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyServiceType.html#setAuthority(java.lang.String)">setAuthority</A></B>(java.lang.String value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyServiceType.html#setDescription(java.lang.String)">setDescription</A></B>(java.lang.String value)</CODE>
<BR>
@@ -184,6 +216,14 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE> void</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyServiceType.html#setEmailContact(java.lang.String)">setEmailContact</A></B>(java.lang.String value)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE> void</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/MobyServiceType.html#setId(java.lang.String)">setId</A></B>(java.lang.String value)</CODE>
<BR>
@@ -339,6 +379,50 @@
</DL>
<HR>
+<A NAME="getEmailContact()"><!-- --></A><H3>
+getEmailContact</H3>
+<PRE>
+public java.lang.String <B>getEmailContact</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setEmailContact(java.lang.String)"><!-- --></A><H3>
+setEmailContact</H3>
+<PRE>
+public void <B>setEmailContact</B>(java.lang.String value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="getAuthority()"><!-- --></A><H3>
+getAuthority</H3>
+<PRE>
+public java.lang.String <B>getAuthority</B>()</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
+<A NAME="setAuthority(java.lang.String)"><!-- --></A><H3>
+setAuthority</H3>
+<PRE>
+public void <B>setAuthority</B>(java.lang.String value)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
<A NAME="toString()"><!-- --></A><H3>
toString</H3>
<PRE>
@@ -351,6 +435,17 @@
</DL>
</DD>
</DL>
+<HR>
+
+<A NAME="format(int)"><!-- --></A><H3>
+format</H3>
+<PRE>
+public java.lang.String <B>format</B>(int indent)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
<!-- ========= END OF CLASS DATA ========= -->
<HR>
@@ -372,7 +467,7 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
@@ -406,6 +501,6 @@
<!-- =========== END OF NAVBAR =========== -->
<HR>
-<font size="-1"><a href="mailto:mwilkinson at gene.pbi.nrc.ca,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Sun Mar 2 18:52:04 GMT 2003</font>
+<font size="-1"><a href="mailto:markw at illuminae.com,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Fri May 9 16:41:04 BST 2003</font>
</BODY>
</HTML>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/NoSuccessException.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/NoSuccessException.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/NoSuccessException.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:10 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:09 BST 2003 -->
<TITLE>
NoSuccessException (MOBY Registry in Java)
</TITLE>
@@ -35,14 +35,14 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../org/biomoby/shared/MobyException.html"><B>PREV CLASS</B></A>
- NEXT CLASS</FONT></TD>
+ <A HREF="../../../org/biomoby/shared/PendingCurationException.html"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
<A HREF="NoSuccessException.html" TARGET="_top"><B>NO FRAMES</B></A>
@@ -254,14 +254,14 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../org/biomoby/shared/MobyException.html"><B>PREV CLASS</B></A>
- NEXT CLASS</FONT></TD>
+ <A HREF="../../../org/biomoby/shared/PendingCurationException.html"><B>NEXT CLASS</B></A></FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
<A HREF="NoSuccessException.html" TARGET="_top"><B>NO FRAMES</B></A>
@@ -288,6 +288,6 @@
<!-- =========== END OF NAVBAR =========== -->
<HR>
-<font size="-1"><a href="mailto:mwilkinson at gene.pbi.nrc.ca,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Sun Mar 2 18:52:04 GMT 2003</font>
+<font size="-1"><a href="mailto:markw at illuminae.com,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Fri May 9 16:41:04 BST 2003</font>
</BODY>
</HTML>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/Utils.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/Utils.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/Utils.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:10 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:09 BST 2003 -->
<TITLE>
Utils (MOBY Registry in Java)
</TITLE>
@@ -35,7 +35,7 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
@@ -157,6 +157,15 @@
<TR BGCOLOR="white" CLASS="TableRowColor">
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
<CODE>static java.lang.String</CODE></FONT></TD>
+<TD><CODE><B><A HREF="../../../org/biomoby/shared/Utils.html#format(java.lang.Object, int)">format</A></B>(java.lang.Object objectToBeFormatted,
+ int indent)</CODE>
+
+<BR>
+ </TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<CODE>static java.lang.String</CODE></FONT></TD>
<TD><CODE><B><A HREF="../../../org/biomoby/shared/Utils.html#formatFault(org.apache.axis.AxisFault)">formatFault</A></B>(org.apache.axis.AxisFault e)</CODE>
<BR>
@@ -299,6 +308,18 @@
</DL>
<HR>
+<A NAME="format(java.lang.Object, int)"><!-- --></A><H3>
+format</H3>
+<PRE>
+public static java.lang.String <B>format</B>(java.lang.Object objectToBeFormatted,
+ int indent)</PRE>
+<DL>
+<DD><DL>
+</DL>
+</DD>
+</DL>
+<HR>
+
<A NAME="getDOMParser(java.lang.String)"><!-- --></A><H3>
getDOMParser</H3>
<PRE>
@@ -381,7 +402,7 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
@@ -415,6 +436,6 @@
<!-- =========== END OF NAVBAR =========== -->
<HR>
-<font size="-1"><a href="mailto:mwilkinson at gene.pbi.nrc.ca,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Sun Mar 2 18:52:04 GMT 2003</font>
+<font size="-1"><a href="mailto:markw at illuminae.com,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Fri May 9 16:41:04 BST 2003</font>
</BODY>
</HTML>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/package-frame.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/package-frame.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/package-frame.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:09 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:08 BST 2003 -->
<TITLE>
org.biomoby.shared (MOBY Registry in Java)
</TITLE>
@@ -35,10 +35,18 @@
Classes</FONT>
<FONT CLASS="FrameItemFont">
<BR>
+<A HREF="MobyData.html" TARGET="classFrame">MobyData</A>
+<BR>
<A HREF="MobyDataType.html" TARGET="classFrame">MobyDataType</A>
<BR>
<A HREF="MobyNamespace.html" TARGET="classFrame">MobyNamespace</A>
<BR>
+<A HREF="MobyPrimaryDataSet.html" TARGET="classFrame">MobyPrimaryDataSet</A>
+<BR>
+<A HREF="MobyPrimaryDataSimple.html" TARGET="classFrame">MobyPrimaryDataSimple</A>
+<BR>
+<A HREF="MobySecondaryData.html" TARGET="classFrame">MobySecondaryData</A>
+<BR>
<A HREF="MobyService.html" TARGET="classFrame">MobyService</A>
<BR>
<A HREF="MobyServiceType.html" TARGET="classFrame">MobyServiceType</A>
@@ -56,7 +64,9 @@
<BR>
<A HREF="MobyException.html" TARGET="classFrame">MobyException</A>
<BR>
-<A HREF="NoSuccessException.html" TARGET="classFrame">NoSuccessException</A></FONT></TD>
+<A HREF="NoSuccessException.html" TARGET="classFrame">NoSuccessException</A>
+<BR>
+<A HREF="PendingCurationException.html" TARGET="classFrame">PendingCurationException</A></FONT></TD>
</TR>
</TABLE>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/package-summary.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/package-summary.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/package-summary.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:09 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:08 BST 2003 -->
<TITLE>
org.biomoby.shared (MOBY Registry in Java)
</TITLE>
@@ -35,13 +35,13 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- <A HREF="../../../org/biomoby/client/package-summary.html"><B>PREV PACKAGE</B></A>
+ PREV PACKAGE
NEXT PACKAGE</FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
@@ -94,6 +94,11 @@
<B>Class Summary</B></FONT></TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="MobyData.html">MobyData</A></B></TD>
+<TD>A container keeping input or output data types together with few
+ other attributes.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="MobyDataType.html">MobyDataType</A></B></TD>
<TD>A container representing a data type used in the Moby registry.</TD>
</TR>
@@ -102,6 +107,21 @@
<TD>A container representing a namespace used in the Moby registry.</TD>
</TR>
<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="MobyPrimaryDataSet.html">MobyPrimaryDataSet</A></B></TD>
+<TD>A container representing a way how a named collection of various
+ primary data types is used in a service.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="MobyPrimaryDataSimple.html">MobyPrimaryDataSimple</A></B></TD>
+<TD>A container representing a way how various primary data types
+ are used in a service.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="MobySecondaryData.html">MobySecondaryData</A></B></TD>
+<TD>A container representing a way how various secondary data types
+ are used in a service.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
<TD WIDTH="15%"><B><A HREF="MobyService.html">MobyService</A></B></TD>
<TD>A container representing a service.</TD>
</TR>
@@ -135,6 +155,12 @@
fulfilled because something was not correctly specified, or was not
found.</TD>
</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="PendingCurationException.html">PendingCurationException</A></B></TD>
+<TD>A specific exception indicating that a request should not be
+ fulfilled because registration or deregistration of an entity
+ was not yet successful - but may be later.</TD>
+</TR>
</TABLE>
@@ -151,14 +177,9 @@
The cornerstone piece is the interface <A HREF="../../../org/biomoby/shared/Central.html"><CODE>Central</CODE></A> that
defines how to access Moby registry without any knowledge of
the used transport protocol (SOAP, XML, etc.). This interface
-uses several "containers" representing pieces of the Moby mosaic
-(classes <A HREF="../../../org/biomoby/shared/MobyService.html"><CODE>MobyService</CODE></A>, <A HREF="../../../org/biomoby/shared/MobyDataType.html"><CODE>MobyDataType</CODE></A>,
-<A HREF="../../../org/biomoby/shared/MobyServiceType.html"><CODE>MobyServiceType</CODE></A>, and <A HREF="../../../org/biomoby/shared/MobyNamespace.html"><CODE>MobyNamespace</CODE></A>).
+uses several "containers" representing pieces of the Moby mosaic -
+but most of them may not be necessary for the client.
<p>
-
-The idea is that a client developers does need only classes from package
-<A HREF="../../../org/biomoby/client/package-summary.html">org.biomoby.client</A> and from this package while the server developer
-may need only package <tt>org.biomoby.registry</tt> and again this package.
<P>
<P>
@@ -182,13 +203,13 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- <A HREF="../../../org/biomoby/client/package-summary.html"><B>PREV PACKAGE</B></A>
+ PREV PACKAGE
NEXT PACKAGE</FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
@@ -210,6 +231,6 @@
<!-- =========== END OF NAVBAR =========== -->
<HR>
-<font size="-1"><a href="mailto:mwilkinson at gene.pbi.nrc.ca,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Sun Mar 2 18:52:04 GMT 2003</font>
+<font size="-1"><a href="mailto:markw at illuminae.com,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Fri May 9 16:41:04 BST 2003</font>
</BODY>
</HTML>
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/package-tree.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/package-tree.html 2003/03/02 20:48:25 1.1
+++ /home/repository/moby/moby-live/Java/docs/API/org/biomoby/shared/package-tree.html 2003/05/09 15:51:11 1.2
@@ -2,7 +2,7 @@
<!--NewPage-->
<HTML>
<HEAD>
-<!-- Generated by javadoc on Sun Mar 02 18:52:09 GMT 2003 -->
+<!-- Generated by javadoc on Fri May 09 16:41:08 BST 2003 -->
<TITLE>
org.biomoby.shared Class Hierarchy (MOBY Registry in Java)
</TITLE>
@@ -34,13 +34,13 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- <A HREF="../../../org/biomoby/client/package-tree.html"><B>PREV</B></A>
+ PREV
NEXT</FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
@@ -75,10 +75,12 @@
</H2>
<UL>
<LI TYPE="circle">class java.lang.Object<UL>
+<LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/MobyData.html"><B>MobyData</B></A><UL>
+<LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/MobyPrimaryDataSet.html"><B>MobyPrimaryDataSet</B></A><LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/MobyPrimaryDataSimple.html"><B>MobyPrimaryDataSimple</B></A><LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/MobySecondaryData.html"><B>MobySecondaryData</B></A></UL>
<LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/MobyDataType.html"><B>MobyDataType</B></A><LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/MobyNamespace.html"><B>MobyNamespace</B></A><LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/MobyService.html"><B>MobyService</B></A><LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/MobyServiceType.html"><B>MobyServiceType</B></A><LI TYPE="circle">class java.lang.Throwable (implements java.io.Serializable)
<UL>
<LI TYPE="circle">class java.lang.Exception<UL>
-<LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/MobyException.html"><B>MobyException</B></A><LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/NoSuccessException.html"><B>NoSuccessException</B></A></UL>
+<LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/MobyException.html"><B>MobyException</B></A><LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/NoSuccessException.html"><B>NoSuccessException</B></A><LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/PendingCurationException.html"><B>PendingCurationException</B></A></UL>
</UL>
<LI TYPE="circle">class org.biomoby.shared.<A HREF="../../../org/biomoby/shared/Utils.html"><B>Utils</B></A></UL>
</UL>
@@ -107,13 +109,13 @@
</TABLE>
</TD>
<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>
-<font size="-1">Generated: Sun Mar 2 18:52:04 GMT 2003</font></EM>
+<font size="-1">Generated: Fri May 9 16:41:04 BST 2003</font></EM>
</TD>
</TR>
<TR>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
- <A HREF="../../../org/biomoby/client/package-tree.html"><B>PREV</B></A>
+ PREV
NEXT</FONT></TD>
<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
<A HREF="../../../index.html" TARGET="_top"><B>FRAMES</B></A>
@@ -135,6 +137,6 @@
<!-- =========== END OF NAVBAR =========== -->
<HR>
-<font size="-1"><a href="mailto:mwilkinson at gene.pbi.nrc.ca,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Sun Mar 2 18:52:04 GMT 2003</font>
+<font size="-1"><a href="mailto:markw at illuminae.com,senger at ebi.ac.uk">Submit a bug or feature</a><BR>Generated: Fri May 9 16:41:04 BST 2003</font>
</BODY>
</HTML>
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