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numerous bugfixs (tree panel synchs) and DatastoreRegistry clas.
author
jprocter
<Jim Procter>
Fri, 12 Jun 2009 15:54:09 +0000
(15:54 +0000)
committer
jprocter
<Jim Procter>
Fri, 12 Jun 2009 15:54:09 +0000
(15:54 +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
886f515
..
e21a9ed
100644
(file)
--- a/
src/jalview/io/VamsasAppDatastore.java
+++ b/
src/jalview/io/VamsasAppDatastore.java
@@
-33,6
+33,7
@@
import jalview.gui.Desktop;
import jalview.gui.TreePanel;
import jalview.io.vamsas.Datasetsequence;
import jalview.io.vamsas.DatastoreItem;
import jalview.gui.TreePanel;
import jalview.io.vamsas.Datasetsequence;
import jalview.io.vamsas.DatastoreItem;
+import jalview.io.vamsas.DatastoreRegistry;
import jalview.io.vamsas.Rangetype;
import jalview.util.UrlLink;
import jalview.io.vamsas.Rangetype;
import jalview.util.UrlLink;
@@
-334,7
+335,6
@@
public class VamsasAppDatastore
}
// update dataset
Sequence sequence;
}
// update dataset
Sequence sequence;
- DbRef dbref;
// set new dataset and alignment sequences based on alignment Nucleotide
// flag.
// this *will* break when alignment contains both nucleotide and amino
// set new dataset and alignment sequences based on alignment Nucleotide
// flag.
// this *will* break when alignment contains both nucleotide and amino
@@
-367,7
+367,7
@@
public class VamsasAppDatastore
}
// dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));
// ////////////////////////////////////////////
}
// dataset.setProvenance(getVamsasProvenance(jal.getDataset().getProvenance()));
// ////////////////////////////////////////////
- if (!av.getAlignment().isAligned())
+ if (alignmentWillBeSkipped(av))
{
// TODO: trees could be written - but for the moment we just
addToSkipList(av);
{
// TODO: trees could be written - but for the moment we just
addToSkipList(av);
@@
-687,7
+687,7
@@
public class VamsasAppDatastore
{
TreePanel tp = (TreePanel) frames[t];
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.getAlignment() == jal)
+ if (tp.getViewPort().getSequenceSetId().equals(av.getSequenceSetId()))
{
DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
jal, alignment);
{
DatastoreItem vtree = new jalview.io.vamsas.Tree(this, tp,
jal, alignment);
@@
-707,6
+707,17
@@
public class VamsasAppDatastore
return true;
}
return true;
}
+ /**
+ * very quick test to see if the viewport would be stored in the vamsas document.
+ * Reasons for not storing include the unaligned flag being false.
+ * @param av
+ * @return true if alignment associated with this view will be stored in document.
+ */
+ public boolean alignmentWillBeSkipped(AlignViewport av)
+ {
+ return (!av.getAlignment().isAligned());
+ }
+
private void addToSkipList(AlignViewport av)
{
if (skipList == null)
private void addToSkipList(AlignViewport av)
{
if (skipList == null)
@@
-1520,8
+1531,9
@@
public class VamsasAppDatastore
}
/**
* synchronize Jalview from the vamsas document
}
/**
* synchronize Jalview from the vamsas document
+ * @return number of new views from document
*/
*/
- public void updateToJalview()
+ public int updateToJalview()
{
VAMSAS _roots[] = cdoc.getVamsasRoots();
{
VAMSAS _roots[] = cdoc.getVamsasRoots();
@@
-1652,9
+1664,8
@@
public class VamsasAppDatastore
jal = (av.hasHiddenRows()) ? av.getAlignment()
.getHiddenSequences().getFullAlignment() : av
.getAlignment();
jal = (av.hasHiddenRows()) ? av.getAlignment()
.getHiddenSequences().getFullAlignment() : av
.getAlignment();
- }
+ }
iSize = alignment.getAlignmentSequenceCount();
iSize = alignment.getAlignmentSequenceCount();
- boolean newal = (jal == null) ? true : false;
boolean refreshal = false;
Vector newasAnnots = new Vector();
char gapChar = ' '; // default for new alignments read in from the
boolean refreshal = false;
Vector newasAnnots = new Vector();
char gapChar = ' '; // default for new alignments read in from the
@@
-1908,6
+1919,7
@@
public class VamsasAppDatastore
}
}
}
}
}
}
+ return newAlignmentViews.size();
}
public AlignViewport findViewport(Alignment alignment)
}
public AlignViewport findViewport(Alignment alignment)
@@
-2715,4
+2727,16
@@
public class VamsasAppDatastore
{
this.skipList = skipList;
}
{
this.skipList = skipList;
}
+ /**
+ * registry for datastoreItems
+ */
+ DatastoreRegistry dsReg = new DatastoreRegistry();
+ public DatastoreRegistry getDatastoreRegisty()
+ {
+ if (dsReg==null)
+ {
+ dsReg = new DatastoreRegistry();
+ }
+ return dsReg;
+ }
}
}