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JAL-3390 first pass refactoring for JalviewJmolBinding.showStructures
[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
44bcbe4
..
381bbea
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/
src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@
-650,32
+650,32
@@
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
/**
* Sends a set of colour commands to the structure viewer
*
/**
* Sends a set of colour commands to the structure viewer
*
- * @param colourBySequenceCommands
+ * @param commands
*/
@Override
*/
@Override
- protected void colourBySequence(
- StructureMappingcommandSet[] colourBySequenceCommands)
+ protected void colourBySequence(String[] commands)
{
{
- for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
+ for (String command : commands)
{
{
- for (String command : cpdbbyseq.commands)
- {
- sendAsynchronousCommand(command, COLOURING_CHIMERA);
- }
+ sendAsynchronousCommand(command, COLOURING_CHIMERA);
}
}
/**
}
}
/**
+ * Computes and returns a set of commands to colour residues in Chimera the same
+ * as mapped residues in the alignment
+ *
* @param files
* @param viewPanel
* @return
*/
@Override
* @param files
* @param viewPanel
* @return
*/
@Override
- protected StructureMappingcommandSet[] getColourBySequenceCommands(
+ protected String[] getColourBySequenceCommands(
String[] files, AlignmentViewPanel viewPanel)
{
String[] files, AlignmentViewPanel viewPanel)
{
- return ChimeraCommands.getColourBySequenceCommand(files, viewPanel,
- this);
+ Map<Object, AtomSpecModel> colourMap = buildColoursMap(viewPanel);
+
+ return ChimeraCommands.getColourBySequenceCommand(colourMap, this);
}
/**
}
/**