-/*
- * 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 <http://www.gnu.org/licenses/>.
- * 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<PDBEntry> pdbe = new ArrayList<PDBEntry>();
- List<String> fileids = new ArrayList<String>();
- SequenceI[] sq = ap.av.getAlignment().getSequencesArray();
- for (int s = 0; s < sq.length; s++)
- {
- Vector<PDBEntry> 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<String, Object> getJSpecViewProperty(String arg0)
- {
- // TODO Auto-generated method stub
- return null;
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.api.AlignmentViewPanel;\r
+import jalview.api.FeatureRenderer;\r
+import jalview.api.SequenceRenderer;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.ext.jmol.JalviewJmolBinding;\r
+\r
+import java.awt.Container;\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+import java.util.Map;\r
+import java.util.Vector;\r
+\r
+import org.jmol.api.JmolAppConsoleInterface;\r
+import org.jmol.java.BS;\r
+import org.jmol.viewer.Viewer;\r
+\r
+/**\r
+ * bind an alignment view to an external Jmol instance.\r
+ * \r
+ * @author JimP\r
+ * \r
+ */\r
+public class ExtJmol extends JalviewJmolBinding\r
+{\r
+\r
+ private AlignmentPanel ap;\r
+\r
+ protected ExtJmol(jalview.appletgui.AlignFrame alframe,\r
+ PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,\r
+ String protocol)\r
+ {\r
+ super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,\r
+ chains, protocol);\r
+ }\r
+\r
+ public ExtJmol(Viewer viewer, AlignmentPanel alignPanel,\r
+ SequenceI[][] seqs)\r
+ {\r
+ super(alignPanel.getStructureSelectionManager(), seqs, viewer);\r
+ ap = alignPanel;\r
+ notifyFileLoaded(null, null, null, null, 0);\r
+ }\r
+\r
+ private void notifyFileLoaded(Object object, Object object2, Object object3,\r
+ Object object4, int i) {\r
+ // TODO Auto-generated method stub\r
+ \r
+ }\r
+\r
+ public void updateColours(Object source)\r
+ {\r
+\r
+ // TODO Auto-generated method stub\r
+\r
+ }\r
+\r
+ public void showUrl(String arg0)\r
+ {\r
+ showUrl(arg0, "jmol");\r
+ }\r
+\r
+ @Override\r
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)\r
+ {\r
+ AlignmentPanel ap = (AlignmentPanel) alignment;\r
+ if (ap.av.isShowSequenceFeatures())\r
+ {\r
+ return ap.getFeatureRenderer();\r
+ }\r
+ else\r
+ {\r
+ return null;\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)\r
+ {\r
+ return ((AlignmentPanel) alignment).getSequenceRenderer();\r
+ }\r
+\r
+ @Override\r
+ public void notifyScriptTermination(String strStatus, int msWalltime)\r
+ {\r
+ // ignore\r
+ }\r
+\r
+ @Override\r
+ public void sendConsoleEcho(String strEcho)\r
+ {\r
+ // ignore\r
+ }\r
+\r
+ @Override\r
+ public void sendConsoleMessage(String strStatus)\r
+ {\r
+ // ignore\r
+ }\r
+\r
+ @Override\r
+ public void showUrl(String url, String target)\r
+ {\r
+ ap.alignFrame.showURL(url, target);\r
+ }\r
+\r
+ @Override\r
+ public void refreshGUI()\r
+ {\r
+ // ignore\r
+ }\r
+\r
+ public void selectionChanged(BS arg0)\r
+ {\r
+ System.out.println(arg0);\r
+ }\r
+\r
+ @Override\r
+ public void refreshPdbEntries()\r
+ {\r
+ List<PDBEntry> pdbe = new ArrayList<PDBEntry>();\r
+ List<String> fileids = new ArrayList<String>();\r
+ SequenceI[] sq = ap.av.getAlignment().getSequencesArray();\r
+ for (int s = 0; s < sq.length; s++)\r
+ {\r
+ Vector<PDBEntry> pdbids = sq[s].getPDBId();\r
+ if (pdbids != null)\r
+ {\r
+ for (int pe = 0, peSize = pdbids.size(); pe < peSize; pe++)\r
+ {\r
+ PDBEntry pentry = pdbids.elementAt(pe);\r
+ if (!fileids.contains(pentry.getId()))\r
+ {\r
+ pdbe.add(pentry);\r
+ }\r
+ else\r
+ {\r
+ fileids.add(pentry.getId());\r
+ }\r
+ }\r
+ }\r
+ }\r
+ PDBEntry[] newEntries = new PDBEntry[pdbe.size()];\r
+ for (int pe = 0; pe < pdbe.size(); pe++)\r
+ {\r
+ newEntries[pe] = pdbe.get(pe);\r
+ }\r
+ setPdbentry(newEntries);\r
+ }\r
+\r
+ @Override\r
+ public void showConsole(boolean show)\r
+ {\r
+ // This never gets called because we haven't overriden the associated Jmol's\r
+ // console\r
+ System.err\r
+ .println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="\r
+ + show);\r
+ }\r
+\r
+ @Override\r
+ protected JmolAppConsoleInterface createJmolConsole(\r
+ Container consolePanel, String buttonsToShow)\r
+ {\r
+ // TODO Auto-generated method stub\r
+ return null;\r
+ }\r
+\r
+ @Override\r
+ protected void releaseUIResources()\r
+ {\r
+ ap = null;\r
+ closeConsole();\r
+\r
+ }\r
+\r
+ @Override\r
+ public void releaseReferences(Object svl)\r
+ {\r
+ // TODO Auto-generated method stub\r
+\r
+ }\r
+\r
+ @Override\r
+ public Map<String, Object> getJSpecViewProperty(String arg0)\r
+ {\r
+ // TODO Auto-generated method stub\r
+ return null;\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff