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[jalview.git]
/
src
/
jalview
/
gui
/
AppJmol.java
diff --git
a/src/jalview/gui/AppJmol.java
b/src/jalview/gui/AppJmol.java
index
8d9d9f0
..
e942b88
100644
(file)
--- a/
src/jalview/gui/AppJmol.java
+++ b/
src/jalview/gui/AppJmol.java
@@
-1,6
+1,6
@@
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-35,6
+35,7
@@
import jalview.structure.*;
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
import jalview.datamodel.PDBEntry;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.util.Platform;
public class AppJmol extends GStructureViewer implements Runnable,
SequenceStructureBinding, ViewSetProvider
public class AppJmol extends GStructureViewer implements Runnable,
SequenceStructureBinding, ViewSetProvider
@@
-722,10
+723,11
@@
public class AppJmol extends GStructureViewer implements Runnable,
{
// just transfer the file name from the first sequence's first
// PDBEntry
{
// just transfer the file name from the first sequence's first
// PDBEntry
- jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq
- .getSequenceAt(0).getPDBId().elementAt(0)).getFile());
+ file = new File(((PDBEntry) pdbseq
+ .getSequenceAt(0).getPDBId().elementAt(0)).getFile()).getAbsolutePath();
+ jmb.pdbentry[pi].setFile(file);
- files.append(" \"" + jalview.util.Platform.escapeString(file) + "\"");
+ files.append(" \"" + Platform.escapeString(file) + "\"");
}
else
{
}
else
{
@@
-748,7
+750,7
@@
public class AppJmol extends GStructureViewer implements Runnable,
}
if (file != null)
{
}
if (file != null)
{
- files.append(" \"" + jalview.util.Platform.escapeString(file) + "\"");
+ files.append(" \"" + Platform.escapeString(file) + "\"");
}
}
}
}
}
}
@@
-1043,7
+1045,12
@@
public class AppJmol extends GStructureViewer implements Runnable,
buriedColour.setSelected(true);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
buriedColour.setSelected(true);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
-
+
+ public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+ {
+ setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
+
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);
public void userColour_actionPerformed(ActionEvent actionEvent)
{
userColour.setSelected(true);