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minor bug fixes and temporary alignment title setting to vamsas object id. this versi...
author
jprocter
<Jim Procter>
Sun, 17 Sep 2006 20:42:21 +0000
(20:42 +0000)
committer
jprocter
<Jim Procter>
Sun, 17 Sep 2006 20:42:21 +0000
(20:42 +0000)
src/jalview/io/VamsasDatastore.java
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diff --git
a/src/jalview/io/VamsasDatastore.java
b/src/jalview/io/VamsasDatastore.java
index
77189db
..
cb1a466
100755
(executable)
--- a/
src/jalview/io/VamsasDatastore.java
+++ b/
src/jalview/io/VamsasDatastore.java
@@
-636,6
+636,8
@@
public class VamsasDatastore {
vProperty.setName(name);
if (type!=null)
vProperty.setType(type);
vProperty.setName(name);
if (type!=null)
vProperty.setType(type);
+ else
+ vProperty.setType("String");
vProperty.setContent(content);
return vProperty;
}
vProperty.setContent(content);
return vProperty;
}
@@
-1064,8
+1066,16
@@
public class VamsasDatastore {
// construct alignment view
alignFrame = new AlignFrame(jal);
av=alignFrame.getViewport();
// construct alignment view
alignFrame = new AlignFrame(jal);
av=alignFrame.getViewport();
+ String title = alignment.getProvenance().getEntry(alignment.getProvenance().getEntryCount()-1).getAction();
+ if (alignment.getPropertyCount()>0) {
+ for (int p=0,pe=alignment.getPropertyCount(); p<pe; p++) {
+ if (alignment.getProperty(p).getName().equals("jalview:AlTitle")) {
+ title = alignment.getProperty(p).getContent();
+ }
+ }
+ }
// TODO: automatically create meaningful title for a vamsas alignment using its provenance.
// TODO: automatically create meaningful title for a vamsas alignment using its provenance.
- jalview.gui.Desktop.addInternalFrame(alignFrame, alignment.getProvenance().getEntry(alignment.getProvenance().getEntryCount()-1).getAction(),
+ jalview.gui.Desktop.addInternalFrame(alignFrame, title + "("+alignment.getVorbaId()+")",
AlignFrame.NEW_WINDOW_WIDTH,
AlignFrame.NEW_WINDOW_HEIGHT);
bindjvvobj(av, alignment);
AlignFrame.NEW_WINDOW_WIDTH,
AlignFrame.NEW_WINDOW_HEIGHT);
bindjvvobj(av, alignment);
@@
-1094,7
+1104,7
@@
public class VamsasDatastore {
inputData = (AlignmentView) idata[0];
tp = alignFrame.ShowNewickTree(
new jalview.io.NewickFile(tree.getNewick(0).getContent()),
inputData = (AlignmentView) idata[0];
tp = alignFrame.ShowNewickTree(
new jalview.io.NewickFile(tree.getNewick(0).getContent()),
- tree.getNewick(0).getTitle(),inputData,
+ tree.getNewick(0).getTitle()+" ("+tree.getVorbaId()+")",inputData,
600, 500,
t * 20 + 50, t * 20 + 50);
bindjvvobj(tp, tree);
600, 500,
t * 20 + 50, t * 20 + 50);
bindjvvobj(tp, tree);
@@
-1285,6
+1295,7
@@
public class VamsasDatastore {
jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow, min, max, type);
} else {
jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow);
jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow, min, max, type);
} else {
jan = new jalview.datamodel.AlignmentAnnotation(a_label, a_descr, arow);
+ jan.setThreshold(null);
}
if (annotation.getLinkCount()>0) {
Cache.log.warn("Ignoring "+annotation.getLinkCount()+"links added to AlignmentAnnotation.");
}
if (annotation.getLinkCount()>0) {
Cache.log.warn("Ignoring "+annotation.getLinkCount()+"links added to AlignmentAnnotation.");