git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-1925 update source version in license
[jalview.git]
/
src
/
jalview
/
ext
/
jmol
/
JalviewJmolBinding.java
diff --git
a/src/jalview/ext/jmol/JalviewJmolBinding.java
b/src/jalview/ext/jmol/JalviewJmolBinding.java
index
729780c
..
94b10d8
100644
(file)
--- a/
src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/
src/jalview/ext/jmol/JalviewJmolBinding.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-231,10
+231,9
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
public void superposeStructures(AlignmentI alignment, int refStructure,
ColumnSelection hiddenCols)
{
public void superposeStructures(AlignmentI alignment, int refStructure,
ColumnSelection hiddenCols)
{
- superposeStructures(new AlignmentI[]
- { alignment }, new int[]
- { refStructure }, new ColumnSelection[]
- { hiddenCols });
+ superposeStructures(new AlignmentI[] { alignment },
+ new int[] { refStructure },
+ new ColumnSelection[] { hiddenCols });
}
/**
}
/**
@@
-458,8
+457,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
+ selectioncom.toString() + "); cartoons; ");
// selcom.append("; ribbons; ");
String cmdString = command.toString();
+ selectioncom.toString() + "); cartoons; ");
// selcom.append("; ribbons; ");
String cmdString = command.toString();
- System.out
-.println("Superimpose command(s):\n" + cmdString);
+ System.out.println("Superimpose command(s):\n" + cmdString);
evalStateCommand(cmdString);
}
evalStateCommand(cmdString);
}
@@
-516,7
+514,8
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
}
AlignmentI alignment = alignmentv.getAlignment();
}
AlignmentI alignment = alignmentv.getAlignment();
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(files, sr, fr, alignment))
+ for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+ files, sr, fr, alignment))
{
for (String cbyseq : cpdbbyseq.commands)
{
{
for (String cbyseq : cpdbbyseq.commands)
{
@@
-536,10
+535,8
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
String[] files, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
String[] files, SequenceRenderer sr, FeatureRenderer fr,
AlignmentI alignment)
{
- return JmolCommands
- .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
- fr,
- alignment);
+ return JmolCommands.getColourBySequenceCommand(getSsm(), files,
+ getSequence(), sr, fr, alignment);
}
/**
}
/**
@@
-592,8
+589,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
}
// TODO: verify atomIndex is selecting correct model.
// return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
}
// TODO: verify atomIndex is selecting correct model.
// return new Color(viewer.getAtomArgb(atomIndex)); Jmol 12.2.4
- int colour = viewer.ms.at[atomIndex]
- .atomPropertyInt(T.color);
+ int colour = viewer.ms.at[atomIndex].atomPropertyInt(T.color);
return new Color(colour);
}
return new Color(colour);
}
@@
-891,8
+887,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
pdbfilename = modelFileNames[_mp];
if (pdbfilename == null)
{
pdbfilename = modelFileNames[_mp];
if (pdbfilename == null)
{
- pdbfilename = new File(
- viewer.ms.getModelFileName(mnumber))
+ pdbfilename = new File(viewer.ms.getModelFileName(mnumber))
.getAbsolutePath();
}
.getAbsolutePath();
}
@@
-1135,8
+1130,8
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+ ".0", "PDB");
}
pdbfile = viewer.getData("" + (1 + _modelFileNameMap[modelnum])
+ ".0", "PDB");
}
- // search pdbentries and sequences to find correct pdbentry for this
- // model
+ // search pdbentries and sequences to find correct pdbentry for this
+ // model
for (int pe = 0; pe < getPdbCount(); pe++)
{
boolean matches = false;
for (int pe = 0; pe < getPdbCount(); pe++)
{
boolean matches = false;
@@
-1460,4
+1455,3
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
showConsole(false);
}
}
showConsole(false);
}
}
-