From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Tue, 12 Sep 2006 10:04:04 +0000 (+0000)
Subject: added id for RangeAnnotation types.
X-Git-Tag: Release_0.2~282
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=81f025aa7331bcfa4fe29a62f7436a028a89d416;p=vamsas.git

added id for RangeAnnotation types.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@238 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/schemas/document.xml b/schemas/document.xml
index 7113ae1..b2c3ed1 100644
--- a/schemas/document.xml
+++ b/schemas/document.xml
@@ -53,6 +53,21 @@
                 <name>Q87N22</name>
             </Sequence>
             <Alignment gapChar="-">
+                <AlignmentAnnotation type="recombinationbreakpoint" graph="false">
+                    <seg start="1" end="163" inclusive="false"/>
+                    <annotationElement position="50" after="true">
+                        <description>Topali Breakpoint</description>
+                        <glyph dict="utf8">?</glyph>
+                    </annotationElement>
+                    <Provenance>
+                        <entry>
+                            <User>Jim</User>
+                            <App>topali</App>
+                            <Action>added-by hand</Action>
+                            <Date>2006-09-11</Date>
+                        </entry>
+                    </Provenance>
+                </AlignmentAnnotation>
                 <alignmentSequence start="1" end="167" refid="a1127235554296">
                     <sequence>KTAIITGGSRGIGKSIAIKLGKLGASIVLNYRNNTDALKNTIRELEDLN--INVIAVQGDISNYKECEKIIKAALDKFNG--IDILVNNAGITADNLILRMKEEEFDKVIETNLKGTFNCVKHCIPMIKRRYGKIINISSVVGVAGNVGQCNYAAAKAGVIGFTKSLAKEL</sequence>
                     <name>Q899P0</name>
diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index 996c187..f83f12c 100644
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -797,6 +797,16 @@
 																	<xs:element
 																		ref="vamsas:Provenance" minOccurs="1" maxOccurs="1" />
 																</xs:sequence>
+																<xs:attribute name="id"
+																	type="xs:ID" use="optional">
+																	<xs:annotation>
+																		<xs:documentation>
+																			Primary Key for
+																			vamsas object
+																			referencing
+																		</xs:documentation>
+																	</xs:annotation>
+																</xs:attribute>
 																<xs:attribute
 																	name="graph" type="xs:boolean" use="required">
 																	<xs:annotation>
diff --git a/src/org/vamsas/objects/core/AlignmentSequenceAnnotationDescriptor.java b/src/org/vamsas/objects/core/AlignmentSequenceAnnotationDescriptor.java
index a4aa126..9b8fbdc 100644
--- a/src/org/vamsas/objects/core/AlignmentSequenceAnnotationDescriptor.java
+++ b/src/org/vamsas/objects/core/AlignmentSequenceAnnotationDescriptor.java
@@ -67,6 +67,12 @@ public class AlignmentSequenceAnnotationDescriptor extends org.vamsas.objects.co
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;
         //-- initialize attribute descriptors
         
+        desc = (org.exolab.castor.xml.util.XMLFieldDescriptorImpl) getFieldDescriptor("id", nsURI, org.exolab.castor.xml.NodeType.Attribute);
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
         //-- _graph
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);
         handler = new org.exolab.castor.xml.XMLFieldHandler() {