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JAL-1177 JAL-905 cannot recover sequences from dataset if dataset is currently being...
[jalview.git]
/
src
/
jalview
/
gui
/
Jalview2XML.java
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
dfacd54
..
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";
@@
-1419,7
+1419,16
@@
public class Jalview2XML
calcIdSet.add(aa[i].getCalcId());
an.setCalcId(aa[i].getCalcId());
}
calcIdSet.add(aa[i].getCalcId());
an.setCalcId(aa[i].getCalcId());
}
-
+ if (aa[i].hasProperties())
+ {
+ for (String pr : aa[i].getProperties())
+ {
+ Property prop = new Property();
+ prop.setName(pr);
+ prop.setValue(aa[i].getProperty(pr));
+ an.addProperty(prop);
+ }
+ }
AnnotationElement ae;
if (aa[i].annotations != null)
{
AnnotationElement ae;
if (aa[i].annotations != null)
{
@@
-1447,8
+1456,7
@@
public class Jalview2XML
}
ae.setPosition(a);
}
ae.setPosition(a);
- if (aa[i].annotations[a].secondaryStructure != ' '
- && aa[i].annotations[a].secondaryStructure != '\0')
+ if (aa[i].annotations[a].secondaryStructure > ' ')
{
ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ "");
{
ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ "");
@@
-2305,7
+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);
}
// ///////////////////////////////
}
// ///////////////////////////////
@@
-2631,6
+2642,14
@@
public class Jalview2XML
jaa.belowAlignment = an[i].isBelowAlignment();
}
jaa.setCalcId(an[i].getCalcId());
jaa.belowAlignment = an[i].isBelowAlignment();
}
jaa.setCalcId(an[i].getCalcId());
+ if (an[i].getPropertyCount() > 0)
+ {
+ for (jalview.schemabinding.version2.Property prop : an[i]
+ .getProperty())
+ {
+ jaa.setProperty(prop.getName(), prop.getValue());
+ }
+ }
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
@@
-3969,7
+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;
@@
-3981,7
+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)
@@
-4010,7
+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
@@
-4021,7
+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)
{