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Merge branch 'features/JAL-2295setChimeraAttributes' into
[jalview.git]
/
src
/
jalview
/
ext
/
rbvi
/
chimera
/
ChimeraCommands.java
diff --git
a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index
07c0015
..
c4aa2e7
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@
-60,13
+60,13
@@
public class ChimeraCommands
* @param alignment
* @return
*/
* @param alignment
* @return
*/
- public static StructureMappingcommandSet getColourBySequenceCommand(
+ public static StructureMappingcommandSet[] getColourBySequenceCommand(
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
StructureSelectionManager ssm, String[] files,
SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
- Map<Object, AtomSpecModel> colourMap = buildColoursMap(
- ssm, files, sequence, sr, fr, alignment);
+ Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
+ sequence, sr, fr, alignment);
List<String> colourCommands = buildColourCommands(colourMap);
List<String> colourCommands = buildColourCommands(colourMap);
@@
-74,7
+74,7
@@
public class ChimeraCommands
ChimeraCommands.class, null,
colourCommands.toArray(new String[colourCommands.size()]));
ChimeraCommands.class, null,
colourCommands.toArray(new String[colourCommands.size()]));
- return cs;
+ return new StructureMappingcommandSet[] { cs };
}
/**
}
/**
@@
-113,8
+113,7
@@
public class ChimeraCommands
}
sb.append("color ").append(colourCode).append(" ");
firstColour = false;
}
sb.append("color ").append(colourCode).append(" ");
firstColour = false;
- final AtomSpecModel colourData = colourMap
- .get(colour);
+ final AtomSpecModel colourData = colourMap.get(colour);
sb.append(colourData.getAtomSpec());
}
commands.add(sb.toString());
sb.append(colourData.getAtomSpec());
}
commands.add(sb.toString());
@@
-240,7
+239,7
@@
public class ChimeraCommands
{
if (startPos != -1)
{
{
if (startPos != -1)
{
- addRange(colourMap, lastColour, pdbfnum, startPos,
+ addColourRange(colourMap, lastColour, pdbfnum, startPos,
lastPos, lastChain);
}
startPos = pos;
lastPos, lastChain);
}
startPos = pos;
@@
-252,8
+251,8
@@
public class ChimeraCommands
// final colour range
if (lastColour != null)
{
// final colour range
if (lastColour != null)
{
- addRange(colourMap, lastColour, pdbfnum, startPos,
- lastPos, lastChain);
+ addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos,
+ lastChain);
}
// break;
}
}
// break;
}
@@
-273,7
+272,7
@@
public class ChimeraCommands
* @param endPos
* @param chain
*/
* @param endPos
* @param chain
*/
- protected static void addRange(Map<Object, AtomSpecModel> map,
+ protected static void addColourRange(Map<Object, AtomSpecModel> map,
Object key, int model, int startPos, int endPos, String chain)
{
/*
Object key, int model, int startPos, int endPos, String chain)
{
/*
@@
-341,7
+340,7
@@
public class ChimeraCommands
{
return theMap;
}
{
return theMap;
}
-
+
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
@@
-432,7
+431,7
@@
public class ChimeraCommands
}
for (int[] range : mappedRanges)
{
}
for (int[] range : mappedRanges)
{
- addRange(featureValues, value, modelNumber, range[0], range[1],
+ addColourRange(featureValues, value, modelNumber, range[0], range[1],
mapping.getChain());
}
}
mapping.getChain());
}
}