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Merge branch 'develop' into features/JAL-1705_ensembl
[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
148f252
..
5342dc8
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@
-20,13
+20,6
@@
*/
package jalview.ext.rbvi.chimera;
*/
package jalview.ext.rbvi.chimera;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
@@
-37,6
+30,13
@@
import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
*
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
*
@@
-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;
@@
-287,8
+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 });
}
}
}
}