-/**
+/*
+ * 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.gui;
-import java.util.BitSet;
-import java.util.Vector;
-
+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 org.jmol.popup.JmolPopup;
+import java.awt.Container;
+import java.util.Map;
-class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
-{
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.java.BS;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
- /**
- *
- */
+public class AppJmolBinding extends JalviewJmolBinding
+{
private AppJmol appJmolWindow;
- public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ private FeatureRenderer fr = null;
+
+ public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ String protocol)
{
- super(pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
}
- FeatureRenderer fr = null;
-
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer()
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- if (appJmolWindow.ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow
+ .getAlignmentPanel() : (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
{
- fr = new FeatureRenderer(appJmolWindow.ap);
+ fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
+ }
+ else
+ {
+ ap.updateFeatureRenderer(fr);
}
-
- fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
}
return fr;
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer()
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
- return new SequenceRenderer(appJmolWindow.ap.av);
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
- if (appJmolWindow.scriptWindow != null)
+ if (console != null)
{
- appJmolWindow.scriptWindow.sendConsoleEcho(strEcho);
+ console.sendConsoleEcho(strEcho);
}
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
- if (appJmolWindow.scriptWindow != null && strStatus != null)
+ if (console != null && strStatus != null)
// && !strStatus.equals("Script completed"))
// should we squash the script completed string ?
{
- appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
+ console.sendConsoleMessage(strStatus);
}
}
public void refreshGUI()
{
// appJmolWindow.repaint();
- appJmolWindow.updateTitleAndMenus();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ appJmolWindow.updateTitleAndMenus();
+ appJmolWindow.revalidate();
+ }
+ });
}
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
+ // ignore events from panels not used to colour this view
+ if (!appJmolWindow.isUsedforcolourby(ap))
+ {
return;
-
- colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ }
+ if (!isLoadingFromArchive())
+ {
+ colourBySequence(ap);
+ }
}
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
- if (appJmolWindow.scriptWindow != null)
- appJmolWindow.scriptWindow.notifyScriptTermination(strStatus,
- msWalltime);
+ // todo - script termination doesn't happen ?
+ // if (console != null)
+ // console.notifyScriptTermination(strStatus,
+ // msWalltime);
}
public void showUrl(String url)
showUrl(url, "jmol");
}
- public void newJmolPopup(boolean translateLocale, String menuName,
- boolean asPopup)
+ public void newJmolPopup(String menuName)
{
-
- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
- asPopup);
+ // jmolpopup = new JmolAwtPopup();
+ // jmolpopup.jpiInitialize((viewer), menuName);
}
- /**
- * add structures and any known sequence associations
- *
- * @returns the pdb entries added to the current set.
- */
- private PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
- SequenceI[][] seq, String[][] chns)
+ @Override
+ public void selectionChanged(BS arg0)
{
- int pe = -1;
- Vector v = new Vector();
- Vector rtn = new Vector();
- for (int i = 0; i < pdbentry.length; i++)
- {
- v.addElement(pdbentry[i]);
- }
- for (int i = 0; i < pdbe.length; i++)
- {
- int r = v.indexOf(pdbe[i]);
- if (r == -1 || r >= pdbentry.length)
- {
- rtn.addElement(new int[]
- { v.size(), i });
- v.addElement(pdbe[i]);
- }
- else
- {
- // just make sure the sequence/chain entries are all up to date
- addSequenceAndChain(r, seq[i], chns[i]);
- }
- }
- pdbe = new PDBEntry[v.size()];
- v.copyInto(pdbe);
- pdbentry = pdbe;
- if (rtn.size() > 0)
- {
- // expand the tied seuqence[] and string[] arrays
- SequenceI[][] sqs = new SequenceI[pdbentry.length][];
- String[][] sch = new String[pdbentry.length][];
- System.arraycopy(sequence, 0, sqs, 0, sequence.length);
- System.arraycopy(chains, 0, sch, 0, this.chains.length);
- sequence = sqs;
- chains = sch;
- pdbe = new PDBEntry[rtn.size()];
- for (int r = 0; r < pdbe.length; r++)
- {
- int[] stri = ((int[]) rtn.elementAt(r));
- // record the pdb file as a new addition
- pdbe[r] = pdbentry[stri[0]];
- // and add the new sequence/chain entries
- addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
- }
- }
- else
- {
- pdbe = null;
- }
- return pdbe;
+ // TODO Auto-generated method stub
+
}
- void addSequence(int pe, SequenceI[] seq)
+ @Override
+ public void refreshPdbEntries()
{
- // add sequences to the pe'th pdbentry's seuqence set.
- addSequenceAndChain(pe, seq, null);
+ // TODO Auto-generated method stub
+
}
- private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+ @Override
+ public void showConsole(boolean b)
{
- if (pe < 0 || pe >= pdbentry.length)
- {
- throw new Error(
- "Implementation error - no corresponding pdbentry (for index "
- + pe + ") to add sequences mappings to");
- }
- final String nullChain = "TheNullChain";
- Vector s = new Vector();
- Vector c = new Vector();
- if (chains == null)
- {
- chains = new String[pdbentry.length][];
- }
- if (sequence[pe] != null)
- {
- for (int i = 0; i < sequence[pe].length; i++)
- {
- s.addElement(sequence[pe][i]);
- if (chains[pe] != null)
- {
- if (i < chains[pe].length)
- {
- c.addElement(chains[pe][i]);
- }
- else
- {
- c.addElement(nullChain);
- }
- }
- else
- {
- if (tchain != null && tchain.length > 0)
- {
- c.addElement(nullChain);
- }
- }
- }
- }
- for (int i = 0; i < seq.length; i++)
- {
- if (!s.contains(seq[i]))
- {
- s.addElement(seq[i]);
- if (tchain != null && i < tchain.length)
- {
- c.addElement(tchain[i] == null ? nullChain : tchain[i]);
- }
- }
- }
- SequenceI[] tmp = new SequenceI[s.size()];
- s.copyInto(tmp);
- sequence[pe] = tmp;
- if (c.size() > 0)
- {
- String[] tch = new String[c.size()];
- c.copyInto(tch);
- for (int i = 0; i < tch.length; i++)
- {
- if (tch[i] == nullChain)
- {
- tch[i] = null;
- }
- }
- chains[pe] = tch;
- }
- else
- {
- chains[pe] = null;
- }
+ appJmolWindow.showConsole(b);
}
- public void selectionChanged(BitSet arg0)
+ @Override
+ protected JmolAppConsoleInterface createJmolConsole(
+ Container consolePanel, String buttonsToShow)
{
- // TODO Auto-generated method stub
-
+ viewer.setJmolCallbackListener(this);
+ return new AppConsole(viewer, consolePanel, buttonsToShow);
}
- public void refreshPdbEntries()
+ @Override
+ protected void releaseUIResources()
{
- // TODO Auto-generated method stub
-
+ appJmolWindow = null;
+ closeConsole();
}
- /**
- * add another pdb entry into the view, with associated sequences and chains
- *
- * @param pdbentry
- * @param seq
- * @param chains
- * @param align
- * if true, new structure(s) will be align using associated alignment
- */
- public synchronized void addStructure(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, final boolean align)
+ @Override
+ public void releaseReferences(Object svl)
{
- PDBEntry[] pe = addSequenceAndChain(new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains });
- if (pe != null)
+ if (svl instanceof SeqPanel)
{
- StringBuffer cmd = new StringBuffer();
- cmd.append("load APPEND");
- for (int p = 0; p < pe.length; p++)
- {
- cmd.append(" \"");
- cmd.append(pe[p].getFile());
- cmd.append("\"");
- }
- cmd.append("\n");
- final String command = cmd.toString();
- cmd = null;
- new Thread(new Runnable()
- {
- public void run()
- {
- evalStateCommand(command);
- if (align)
- {
- // may need to wait around until script has finished
- while (viewer.isScriptExecuting())
- {
- try
- {
- Thread.sleep(20);
- } catch (Exception e)
- {
- }
- ;
- }
- superposeStructures(appJmolWindow.ap.av.getAlignment(), -1, null);
- }
- }
- }).start();
+ appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
}
}
- /**
- * 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)
+ @Override
+ public Map<String, Object> getJSpecViewProperty(String arg0)
{
- for (int pe = 0; pe < pdbentry.length; pe++)
- {
- if (pdbentry[pe].getFile().equals(pdbFile))
- {
- addSequence(pe, seq);
- }
- }
+ // TODO Auto-generated method stub
+ return null;
}
-
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff