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JAL-3390 new View menu option to hide hidden regions in structure
[jalview.git]
/
src
/
jalview
/
ext
/
rbvi
/
chimera
/
JalviewChimeraBinding.java
diff --git
a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index
1731a05
..
fc6dd26
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@
-22,7
+22,6
@@
package jalview.ext.rbvi.chimera;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.api.SequenceRenderer;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
@@
-667,16
+666,15
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
/**
* @param files
/**
* @param files
- * @param sr
* @param viewPanel
* @return
*/
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
* @param viewPanel
* @return
*/
@Override
protected StructureMappingcommandSet[] getColourBySequenceCommands(
- String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
+ String[] files, AlignmentViewPanel viewPanel)
{
return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
{
return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
- getSequence(), sr, viewPanel);
+ this, viewPanel);
}
/**
}
/**
@@
-1350,7
+1348,7
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
continue;
}
Iterator<int[]> visible;
continue;
}
Iterator<int[]> visible;
- if (isShowAlignmentOnly())
+ if (isShowAlignmentOnly() && isHideHiddenRegions())
{
visible = alignment.getHiddenColumns()
.getVisContigsIterator(0, width, true);
{
visible = alignment.getHiddenColumns()
.getVisContigsIterator(0, width, true);