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JAL-4366 allow a 3di alignment to be loaded and shown as a split frame with existing...
[jalview.git]
/
src
/
jalview
/
gui
/
CrossRefAction.java
diff --git
a/src/jalview/gui/CrossRefAction.java
b/src/jalview/gui/CrossRefAction.java
index
b04661e
..
93a4006
100644
(file)
--- a/
src/jalview/gui/CrossRefAction.java
+++ b/
src/jalview/gui/CrossRefAction.java
@@
-115,7
+115,8
@@
public class CrossRefAction implements Runnable
if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
{
if (dna && AlignmentUtils.looksLikeEnsembl(alignment))
{
- // override default featureColourScheme so products have Ensembl variant colours
+ // override default featureColourScheme so products have Ensembl variant
+ // colours
featureColourScheme = new SequenceFetcher()
.getFeatureColourScheme(DBRefSource.ENSEMBL);
}
featureColourScheme = new SequenceFetcher()
.getFeatureColourScheme(DBRefSource.ENSEMBL);
}
@@
-206,7
+207,8
@@
public class CrossRefAction implements Runnable
* and for JAL-3330 also to original alignFrame view(s)
* this currently trashes any original settings.
*/
* and for JAL-3330 also to original alignFrame view(s)
* this currently trashes any original settings.
*/
- for (AlignmentViewPanel origpanel: alignFrame.getAlignPanels()) {
+ for (AlignmentViewPanel origpanel : alignFrame.getAlignPanels())
+ {
origpanel.getAlignViewport()
.mergeFeaturesStyle(featureColourScheme);
}
origpanel.getAlignViewport()
.mergeFeaturesStyle(featureColourScheme);
}
@@
-293,9
+295,9
@@
public class CrossRefAction implements Runnable
{
return;
}
{
return;
}
-
+
Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
Set<String> ensemblDivisions = new EnsemblInfo().getDivisions();
-
+
/*
* first look for direct dbrefs from sequence to Ensembl
*/
/*
* first look for direct dbrefs from sequence to Ensembl
*/
@@
-430,7
+432,7
@@
public class CrossRefAction implements Runnable
MessageManager.getString("label.cant_map_cds"),
MessageManager.getString("label.operation_failed"),
JvOptionPane.OK_OPTION);
MessageManager.getString("label.cant_map_cds"),
MessageManager.getString("label.operation_failed"),
JvOptionPane.OK_OPTION);
- System.err.println("Failed to make CDS alignment");
+ jalview.bin.Console.errPrintln("Failed to make CDS alignment");
return null;
}
return null;
}
@@
-451,8
+453,7
@@
public class CrossRefAction implements Runnable
copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
xrefs.getSequencesArray(), dataset);
}
copyAlignment = AlignmentUtils.makeCopyAlignment(sel,
xrefs.getSequencesArray(), dataset);
}
- copyAlignment
- .setGapCharacter(alignFrame.viewport.getGapCharacter());
+ copyAlignment.setGapCharacter(alignFrame.viewport.getGapCharacter());
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
@@
-465,8
+466,8
@@
public class CrossRefAction implements Runnable
if (copyAlignment.getHeight() <= 0)
{
if (copyAlignment.getHeight() <= 0)
{
- System.err.println(
- "No Sequences generated for xRef type " + source);
+ jalview.bin.Console
+ .errPrintln("No Sequences generated for xRef type " + source);
return null;
}
return null;
}