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; + } + +}