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JAL-1957 enabled multi-chain mapping and highlight for Chimera viewer
[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
fa1b7e2
..
a551ca2
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@
-67,8
+67,7
@@
public class ChimeraCommands
ChimeraCommands.class, null,
colourCommands.toArray(new String[0]));
ChimeraCommands.class, null,
colourCommands.toArray(new String[0]));
- return new StructureMappingcommandSet[]
- { cs };
+ return new StructureMappingcommandSet[] { cs };
}
/**
}
/**
@@
-79,7
+78,7
@@
public class ChimeraCommands
* <blockquote> color colorname #modelnumber:range.chain e.g. color #00ff00
* #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
*
* <blockquote> color colorname #modelnumber:range.chain e.g. color #00ff00
* #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
*
- * @see http
+ * @see http
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
* .html </pre>
*
* ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
* .html </pre>
*
@@
-107,7
+106,8
@@
public class ChimeraCommands
sb.append("color ").append(colourCode).append(" ");
firstColour = false;
boolean firstModelForColour = true;
sb.append("color ").append(colourCode).append(" ");
firstColour = false;
boolean firstModelForColour = true;
- final Map<Integer, Map<String, List<int[]>>> colourData = colourMap.get(colour);
+ final Map<Integer, Map<String, List<int[]>>> colourData = colourMap
+ .get(colour);
for (Integer model : colourData.keySet())
{
boolean firstPositionForModel = true;
for (Integer model : colourData.keySet())
{
boolean firstPositionForModel = true;
@@
-121,6
+121,7
@@
public class ChimeraCommands
final Map<String, List<int[]>> modelData = colourData.get(model);
for (String chain : modelData.keySet())
{
final Map<String, List<int[]>> modelData = colourData.get(model);
for (String chain : modelData.keySet())
{
+ boolean hasChain = !"".equals(chain.trim());
for (int[] range : modelData.get(chain))
{
if (!firstPositionForModel)
for (int[] range : modelData.get(chain))
{
if (!firstPositionForModel)
@@
-135,7
+136,10
@@
public class ChimeraCommands
{
sb.append(range[0]).append("-").append(range[1]);
}
{
sb.append(range[0]).append("-").append(range[1]);
}
- sb.append(".").append(chain);
+ if (hasChain)
+ {
+ sb.append(".").append(chain);
+ }
firstPositionForModel = false;
}
}
firstPositionForModel = false;
}
}
@@
-228,7
+232,7
@@
public class ChimeraCommands
addColourRange(colourMap, lastColour, pdbfnum, startPos,
lastPos, lastChain);
}
addColourRange(colourMap, lastColour, pdbfnum, startPos,
lastPos, lastChain);
}
- break;
+ // break;
}
}
}
}
}
}
@@
-283,8
+287,7
@@
public class ChimeraCommands
/*
* Add the start/end positions
*/
/*
* Add the start/end positions
*/
- chainData.add(new int[]
- { startPos, endPos });
+ chainData.add(new int[] { startPos, endPos });
}
}
}
}