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-1683 replace year/version strings with tokens in source
[jalview.git]
/
src
/
jalview
/
gui
/
AppJmol.java
diff --git
a/src/jalview/gui/AppJmol.java
b/src/jalview/gui/AppJmol.java
index
bd4a393
..
86ab536
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 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-147,9
+147,7
@@
public class AppJmol extends StructureViewerBase
PDBEntry[] pdbentrys = new PDBEntry[files.length];
for (int i = 0; i < pdbentrys.length; i++)
{
PDBEntry[] pdbentrys = new PDBEntry[files.length];
for (int i = 0; i < pdbentrys.length; i++)
{
- PDBEntry pdbentry = new PDBEntry();
- pdbentry.setFile(files[i]);
- pdbentry.setId(ids[i]);
+ PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
pdbentrys[i] = pdbentry;
}
// / TODO: check if protocol is needed to be set, and if chains are
pdbentrys[i] = pdbentry;
}
// / TODO: check if protocol is needed to be set, and if chains are
@@
-169,7
+167,7
@@
public class AppJmol extends StructureViewerBase
seqColour.setSelected(false);
viewerColour.setSelected(true);
}
seqColour.setSelected(false);
viewerColour.setSelected(true);
}
- if (usetoColour)
+ else if (usetoColour)
{
useAlignmentPanelForColourbyseq(ap);
jmb.setColourBySequence(true);
{
useAlignmentPanelForColourbyseq(ap);
jmb.setColourBySequence(true);
@@
-940,7
+938,7
@@
public class AppJmol extends StructureViewerBase
// Set the colour using the current view for the associated alignframe
for (AlignmentPanel ap : _colourwith)
{
// Set the colour using the current view for the associated alignframe
for (AlignmentPanel ap : _colourwith)
{
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
}
}
}
}
}