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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[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
cec9b0c
..
58325fd
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)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-63,11
+63,6
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
- /*
- * state flag used to check if the Jmol viewer's paint method can be called
- */
- private boolean finishedInit = false;
-
boolean allChainsSelected = false;
/*
boolean allChainsSelected = false;
/*
@@
-236,10
+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 });
}
/**
}
/**
@@
-281,7
+275,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
String nSeconds = " ";
if (files.length > 10)
{
String nSeconds = " ";
if (files.length > 10)
{
- nSeconds = " 0.00001 ";
+ nSeconds = " 0.005 ";
}
else
{
}
else
{
@@
-290,7
+284,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
}
// see JAL-1345 - should really automatically turn off the animation for
// large numbers of structures, but Jmol doesn't seem to allow that.
}
// see JAL-1345 - should really automatically turn off the animation for
// large numbers of structures, but Jmol doesn't seem to allow that.
- nSeconds = " ";
+ // nSeconds = " ";
// union of all aligned positions are collected together.
for (int a = 0; a < _alignment.length; a++)
{
// union of all aligned positions are collected together.
for (int a = 0; a < _alignment.length; a++)
{
@@
-463,8
+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);
}
@@
-521,7
+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)
{
@@
-541,10
+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);
}
/**
}
/**
@@
-597,8
+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);
}
@@
-676,6
+667,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
// applet path with docroot - discard as format won't match pdbfile
mset[0] = m;
}
// applet path with docroot - discard as format won't match pdbfile
mset[0] = m;
}
+ _modelFileNameMap[0] = 0; // filename index for first model is always 0.
}
int j = 1;
for (int i = 1; i < mset.length; i++)
}
int j = 1;
for (int i = 1; i < mset.length; i++)
@@
-895,8
+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();
}
@@
-951,7
+942,7
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
String mdlString = "";
if ((p = strInfo.indexOf(":")) > -1)
{
String mdlString = "";
if ((p = strInfo.indexOf(":")) > -1)
{
- picked += strInfo.substring(p + 1, strInfo.indexOf("."));
+ picked += strInfo.substring(p, strInfo.indexOf("."));
}
if ((p = strInfo.indexOf("/")) > -1)
}
if ((p = strInfo.indexOf("/")) > -1)
@@
-1139,8
+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;
@@
-1410,16
+1401,6
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
return null;
}
return null;
}
- public boolean isFinishedInit()
- {
- return finishedInit;
- }
-
- public void setFinishedInit(boolean finishedInit)
- {
- this.finishedInit = finishedInit;
- }
-
/**
*
*/
/**
*
*/
@@
-1474,4
+1455,3
@@
public abstract class JalviewJmolBinding extends AAStructureBindingModel
showConsole(false);
}
}
showConsole(false);
}
}
-