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JAL-1177 JAL-905 cannot recover sequences from dataset if dataset is currently being...
author
Jim Procter
<jprocter@dundee.ac.uk>
Thu, 27 Nov 2014 15:58:51 +0000
(15:58 +0000)
committer
Jim Procter
<jprocter@dundee.ac.uk>
Thu, 27 Nov 2014 15:58:51 +0000
(15:58 +0000)
src/jalview/gui/Jalview2XML.java
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diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
d56a0dd
..
d003cb0
100644
(file)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-498,7
+498,7
@@
public class Jalview2XML
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
for (String dssids : dsses.keySet())
{
AlignFrame _af = dsses.get(dssids);
- String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()});
+ String jfileName = fileName + " Dataset for " + _af.getTitle();
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
if (!jfileName.endsWith(".xml"))
{
jfileName = jfileName + ".xml";
@@
-2313,7
+2313,10
@@
public class Jalview2XML
}
else
{
}
else
{
- recoverDatasetFor(vamsasSet, al);
+ // recover dataset - passing on flag indicating if this a 'viewless'
+ // sequence set (a.k.a. a stored dataset for the project)
+ recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
+ .getViewportCount() == 0);
}
// ///////////////////////////////
}
// ///////////////////////////////
@@
-3985,7
+3988,8
@@
public class Jalview2XML
}
}
}
}
- private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
+ private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
+ boolean ignoreUnrefed)
{
jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
Vector dseqs = null;
{
jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
Vector dseqs = null;
@@
-3997,7
+4001,7
@@
public class Jalview2XML
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
- ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
}
// create a new dataset
if (ds == null)
}
// create a new dataset
if (ds == null)
@@
-4026,7
+4030,7
@@
public class Jalview2XML
* vector to add new dataset sequence to
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
* vector to add new dataset sequence to
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
- AlignmentI ds, Vector dseqs)
+ AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
@@
-4037,7
+4041,10
@@
public class Jalview2XML
{
dsq = sq.getDatasetSequence();
}
{
dsq = sq.getDatasetSequence();
}
-
+ if (sq == null && ignoreUnrefed)
+ {
+ return;
+ }
String sqid = vamsasSeq.getDsseqid();
if (dsq == null)
{
String sqid = vamsasSeq.getDsseqid();
if (dsq == null)
{