X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=3a376b89b96e74dd5657e5e827511270e36933e0;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=80a7b9e8d14363894979f31b0381daa44c7fbe52;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 80a7b9e..3a376b8 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,45 +1,46 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* 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.
+ * 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
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.awt.Container;
-import java.util.BitSet;
-
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
import jalview.structure.StructureSelectionManager;
+import java.awt.Container;
+import java.util.BitSet;
+
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolViewer;
import org.jmol.popup.JmolPopup;
import org.openscience.jmol.app.jmolpanel.AppConsole;
-public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
{
-
- /**
- *
- */
private AppJmol appJmolWindow;
+ private FeatureRenderer fr = null;
+
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
String protocol)
@@ -48,19 +49,17 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
appJmolWindow = appJmol;
}
- FeatureRenderer fr = null;
-
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer(
+ public FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
: (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
+ if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
{
- fr = ap.cloneFeatureRenderer();
+ fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
}
else
{
@@ -72,7 +71,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer(
+ public SequenceRenderer getSequenceRenderer(
AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
@@ -128,10 +127,12 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
AlignmentPanel ap = (AlignmentPanel) source, topap;
// ignore events from panels not used to colour this view
if (!appJmolWindow.isUsedforcolourby(ap))
+ {
return;
+ }
if (!isLoadingFromArchive())
{
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
}
@@ -151,7 +152,6 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
public void newJmolPopup(boolean translateLocale, String menuName,
boolean asPopup)
{
-
jmolpopup = new JmolPopup();
jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
}
@@ -173,25 +173,6 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
appJmolWindow.showConsole(b);
}
- /**
- * add the given sequences to the mapping scope for the given pdb file handle
- *
- * @param pdbFile
- * - pdbFile identifier
- * @param seq
- * - set of sequences it can be mapped to
- */
- public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
- {
- for (int pe = 0; pe < pdbentry.length; pe++)
- {
- if (pdbentry[pe].getFile().equals(pdbFile))
- {
- addSequence(pe, seq);
- }
- }
- }
-
@Override
protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
Container consolePanel, String buttonsToShow)
@@ -203,20 +184,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
protected void releaseUIResources()
{
appJmolWindow = null;
- if (console != null)
- {
- try
- {
- console.setVisible(false);
- } catch (Error e)
- {
- } catch (Exception x)
- {
- }
- ;
- console = null;
- }
-
+ closeConsole();
}
@Override
@@ -225,8 +193,6 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
if (svl instanceof SeqPanel)
{
appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-
}
- ;
}
}