/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
*/
private AppJmol appJmolWindow;
- public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ String protocol)
{
super(sSm, pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
FeatureRenderer fr = null;
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ public jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
+ : (AlignmentPanel) alignment;
if (ap.av.showSequenceFeatures)
{
- if (fr==null)
+ if (fr == null)
+ {
+ fr = ap.cloneFeatureRenderer();
+ }
+ else
{
- fr=ap.cloneFeatureRenderer();
- } else {
ap.updateFeatureRenderer(fr);
}
}
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+ public jalview.api.SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
{
- return new SequenceRenderer(((AlignmentPanel)alignment).av);
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
public void sendConsoleEcho(String strEcho)
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source,topap;
+ AlignmentPanel ap = (AlignmentPanel) source, topap;
// ignore events from panels not used to colour this view
if (!appJmolWindow.isUsedforcolourby(ap))
return;
- if (!isLoadingFromArchive()) {
+ if (!isLoadingFromArchive())
+ {
colourBySequence(ap.av.getShowSequenceFeatures(), ap);
}
}
{
jmolpopup = new JmolPopup();
- jmolpopup.initialize(viewer, translateLocale, menuName,
- asPopup);
+ jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
}
public void selectionChanged(BitSet arg0)
@Override
public void releaseReferences(Object svl)
{
- if (svl instanceof SeqPanel) {
+ if (svl instanceof SeqPanel)
+ {
appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-
- };
+
+ }
+ ;
}
}