/* * 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 * * 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 . */ package jalview.appletgui; import java.awt.Container; import java.util.BitSet; import java.util.Hashtable; import java.util.Vector; import org.jmol.api.JmolAppConsoleInterface; import org.jmol.api.JmolViewer; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.ext.jmol.JalviewJmolBinding; /** * 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(JmolViewer viewer, AlignmentPanel alignPanel, SequenceI[][] seqs) { super(alignPanel.getStructureSelectionManager(), viewer); ap = alignPanel; this.sequence = seqs; notifyFileLoaded(null, null, null, null, 0); } public void updateColours(Object source) { // TODO Auto-generated method stub } public void showUrl(String arg0) { showUrl(arg0, "jmol"); } public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) { AlignmentPanel ap = (AlignmentPanel)alignment; if (ap.av.showSequenceFeatures) { return ap.getFeatureRenderer(); } else { return null; } } public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) { return ((AlignmentPanel)alignment).getSequenceRenderer(); } public void notifyScriptTermination(String strStatus, int msWalltime) { // ignore } public void sendConsoleEcho(String strEcho) { // ignore } public void sendConsoleMessage(String strStatus) { // ignore } public void showUrl(String url, String target) { ap.alignFrame.showURL(url, target); } public void refreshGUI() { // ignore } public void selectionChanged(BitSet arg0) { System.out.println(arg0); } public void refreshPdbEntries() { Vector pdbe = new Vector(); Hashtable fileids = new Hashtable(); 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 = (PDBEntry) pdbids.elementAt(pe); if (!fileids.containsKey(pentry.getId())) { pdbe.addElement(pentry); } } } } pdbentry = new PDBEntry[pdbe.size()]; for (int pe = 0; pe < pdbe.size(); pe++) { pdbentry[pe] = (PDBEntry) pdbe.elementAt(pe); } } @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(JmolViewer viewer2, Container consolePanel, String buttonsToShow) { // TODO Auto-generated method stub return null; } @Override protected void releaseUIResources() { ap = null; if (console != null) { try { console.setVisible(false); } catch (Error e) { } catch (Exception x) { } ; console = null; } } @Override public void releaseReferences(Object svl) { // TODO Auto-generated method stub } }