X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=unused%2Fappletgui%2FExtJmol.java;fp=unused%2Fappletgui%2FExtJmol.java;h=06ad83b97465cd83df948160f8a99823c2fae7e7;hb=6319110ce33faa76ee6cf9832e78faa224510fed;hp=15f99a23dff9417b24daa85c99237ed266eeb2da;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44;p=jalviewjs.git
diff --git a/unused/appletgui/ExtJmol.java b/unused/appletgui/ExtJmol.java
index 15f99a2..06ad83b 100644
--- a/unused/appletgui/ExtJmol.java
+++ b/unused/appletgui/ExtJmol.java
@@ -1,213 +1,213 @@
-/*
- * 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.
- *
- * 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 .
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.appletgui;
-
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.ext.jmol.JalviewJmolBinding;
-
-import java.awt.Container;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
-import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.java.BS;
-import org.jmol.viewer.Viewer;
-
-/**
- * bind an alignment view to an external Jmol instance.
- *
- * @author JimP
- *
- */
-public class ExtJmol extends JalviewJmolBinding
-{
-
- private AlignmentPanel ap;
-
- protected ExtJmol(jalview.appletgui.AlignFrame alframe,
- PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
- String protocol)
- {
- super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
- chains, protocol);
- }
-
- public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
- SequenceI[][] seqs)
- {
- super(alignPanel.getStructureSelectionManager(), seqs, viewer);
- ap = alignPanel;
- notifyFileLoaded(null, null, null, null, 0);
- }
-
- private void notifyFileLoaded(Object object, Object object2, Object object3,
- Object object4, int i) {
- // TODO Auto-generated method stub
-
- }
-
- public void updateColours(Object source)
- {
-
- // TODO Auto-generated method stub
-
- }
-
- public void showUrl(String arg0)
- {
- showUrl(arg0, "jmol");
- }
-
- @Override
- public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
- {
- AlignmentPanel ap = (AlignmentPanel) alignment;
- if (ap.av.isShowSequenceFeatures())
- {
- return ap.getFeatureRenderer();
- }
- else
- {
- return null;
- }
- }
-
- @Override
- public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
- {
- return ((AlignmentPanel) alignment).getSequenceRenderer();
- }
-
- @Override
- public void notifyScriptTermination(String strStatus, int msWalltime)
- {
- // ignore
- }
-
- @Override
- public void sendConsoleEcho(String strEcho)
- {
- // ignore
- }
-
- @Override
- public void sendConsoleMessage(String strStatus)
- {
- // ignore
- }
-
- @Override
- public void showUrl(String url, String target)
- {
- ap.alignFrame.showURL(url, target);
- }
-
- @Override
- public void refreshGUI()
- {
- // ignore
- }
-
- public void selectionChanged(BS arg0)
- {
- System.out.println(arg0);
- }
-
- @Override
- public void refreshPdbEntries()
- {
- List pdbe = new ArrayList();
- List fileids = new ArrayList();
- SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
- for (int s = 0; s < sq.length; s++)
- {
- Vector pdbids = sq[s].getPDBId();
- if (pdbids != null)
- {
- for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
- {
- PDBEntry pentry = pdbids.elementAt(pe);
- if (!fileids.contains(pentry.getId()))
- {
- pdbe.add(pentry);
- }
- else
- {
- fileids.add(pentry.getId());
- }
- }
- }
- }
- PDBEntry[] newEntries = new PDBEntry[pdbe.size()];
- for (int pe = 0; pe < pdbe.size(); pe++)
- {
- newEntries[pe] = pdbe.get(pe);
- }
- setPdbentry(newEntries);
- }
-
- @Override
- public void showConsole(boolean show)
- {
- // This never gets called because we haven't overriden the associated Jmol's
- // console
- System.err
- .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
- + show);
- }
-
- @Override
- protected JmolAppConsoleInterface createJmolConsole(
- Container consolePanel, String buttonsToShow)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected void releaseUIResources()
- {
- ap = null;
- closeConsole();
-
- }
-
- @Override
- public void releaseReferences(Object svl)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public Map getJSpecViewProperty(String arg0)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
-}
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+
+import java.awt.Container;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.Vector;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.java.BS;
+import org.jmol.viewer.Viewer;
+
+/**
+ * bind an alignment view to an external Jmol instance.
+ *
+ * @author JimP
+ *
+ */
+public class ExtJmol extends JalviewJmolBinding
+{
+
+ private AlignmentPanel ap;
+
+ protected ExtJmol(jalview.appletgui.AlignFrame alframe,
+ PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
+ String protocol)
+ {
+ super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
+ chains, protocol);
+ }
+
+ public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,
+ SequenceI[][] seqs)
+ {
+ super(alignPanel.getStructureSelectionManager(), seqs, viewer);
+ ap = alignPanel;
+ notifyFileLoaded(null, null, null, null, 0);
+ }
+
+ private void notifyFileLoaded(Object object, Object object2, Object object3,
+ Object object4, int i) {
+ // TODO Auto-generated method stub
+
+ }
+
+ public void updateColours(Object source)
+ {
+
+ // TODO Auto-generated method stub
+
+ }
+
+ public void showUrl(String arg0)
+ {
+ showUrl(arg0, "jmol");
+ }
+
+ @Override
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ {
+ AlignmentPanel ap = (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
+ {
+ return ap.getFeatureRenderer();
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ @Override
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+ {
+ return ((AlignmentPanel) alignment).getSequenceRenderer();
+ }
+
+ @Override
+ public void notifyScriptTermination(String strStatus, int msWalltime)
+ {
+ // ignore
+ }
+
+ @Override
+ public void sendConsoleEcho(String strEcho)
+ {
+ // ignore
+ }
+
+ @Override
+ public void sendConsoleMessage(String strStatus)
+ {
+ // ignore
+ }
+
+ @Override
+ public void showUrl(String url, String target)
+ {
+ ap.alignFrame.showURL(url, target);
+ }
+
+ @Override
+ public void refreshGUI()
+ {
+ // ignore
+ }
+
+ public void selectionChanged(BS arg0)
+ {
+ System.out.println(arg0);
+ }
+
+ @Override
+ public void refreshPdbEntries()
+ {
+ List pdbe = new ArrayList();
+ List fileids = new ArrayList();
+ SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
+ for (int s = 0; s < sq.length; s++)
+ {
+ Vector pdbids = sq[s].getPDBId();
+ if (pdbids != null)
+ {
+ for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)
+ {
+ PDBEntry pentry = pdbids.elementAt(pe);
+ if (!fileids.contains(pentry.getId()))
+ {
+ pdbe.add(pentry);
+ }
+ else
+ {
+ fileids.add(pentry.getId());
+ }
+ }
+ }
+ }
+ PDBEntry[] newEntries = new PDBEntry[pdbe.size()];
+ for (int pe = 0; pe < pdbe.size(); pe++)
+ {
+ newEntries[pe] = pdbe.get(pe);
+ }
+ setPdbentry(newEntries);
+ }
+
+ @Override
+ public void showConsole(boolean show)
+ {
+ // This never gets called because we haven't overriden the associated Jmol's
+ // console
+ System.err
+ .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="
+ + show);
+ }
+
+ @Override
+ protected JmolAppConsoleInterface createJmolConsole(
+ Container consolePanel, String buttonsToShow)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ protected void releaseUIResources()
+ {
+ ap = null;
+ closeConsole();
+
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ @Override
+ public Map getJSpecViewProperty(String arg0)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+}