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javadoc, and unimplemented warning for group associated annotation (not shared to...
author
jprocter
<Jim Procter>
Mon, 5 Apr 2010 15:38:53 +0000
(15:38 +0000)
committer
jprocter
<Jim Procter>
Mon, 5 Apr 2010 15:38:53 +0000
(15:38 +0000)
src/jalview/io/VamsasAppDatastore.java
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diff --git
a/src/jalview/io/VamsasAppDatastore.java
b/src/jalview/io/VamsasAppDatastore.java
index
a9219a6
..
e313470
100644
(file)
--- a/
src/jalview/io/VamsasAppDatastore.java
+++ b/
src/jalview/io/VamsasAppDatastore.java
@@
-58,7
+58,9
@@
import uk.ac.vamsas.objects.utils.Properties;
* "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
*
*/
* "org.exolab.castor.serializer", "org.apache.xml.serialize.XMLSerilazizer"); }
*
*/
-
+/*
+ * TODO: check/verify consistency for vamsas sync with group associated alignment annotation
+ */
public class VamsasAppDatastore
{
/**
public class VamsasAppDatastore
{
/**
@@
-516,6
+518,12
@@
public class VamsasAppDatastore
{
continue;
}
{
continue;
}
+ if (aa[i].groupRef!=null)
+ {
+ // TODO: store any group associated annotation references
+ Cache.log.warn("Group associated sequence annotation is not stored in VAMSAS document.");
+ continue;
+ }
if (aa[i].sequenceRef != null)
{
// Deal with sequence associated annotation
if (aa[i].sequenceRef != null)
{
// Deal with sequence associated annotation