/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.structure.*;
import jalview.io.*;
-import org.jmol.api.*;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-
import jalview.schemes.*;
public class AppletJmol extends EmbmenuFrame implements
CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
+ CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false);
+
MenuItem chain = new MenuItem("By Chain");
MenuItem charge = new MenuItem("Charge & Cysteine");
MenuItem buried = new MenuItem("Buried Index");
+ MenuItem purinepyrimidine = new MenuItem("Purine/Pyrimidine");
+
MenuItem user = new MenuItem("User Defined Colours");
MenuItem jmolHelp = new MenuItem("Jmol Help");
AlignmentPanel ap;
+ ArrayList _aps = new ArrayList();
+
String fileLoadingError;
boolean loadedInline;
* datasource protocol for access to PDBEntry
*/
String protocol = null;
+
/**
- * Load a bunch of pdb entries associated with sequences in the alignment and display them - aligning them if necessary.
- * @param pdbentries each pdb file (at least one needed)
- * @param boundseqs each set of sequences for each pdb file (must match number of pdb files)
- * @param boundchains the target pdb chain corresponding with each sequence associated with each pdb file (may be null at any level)
- * @param align true/false
- * @param ap associated alignment
- * @param protocol how to get pdb data
+ * Load a bunch of pdb entries associated with sequences in the alignment and
+ * display them - aligning them if necessary.
+ *
+ * @param pdbentries
+ * each pdb file (at least one needed)
+ * @param boundseqs
+ * each set of sequences for each pdb file (must match number of pdb
+ * files)
+ * @param boundchains
+ * the target pdb chain corresponding with each sequence associated
+ * with each pdb file (may be null at any level)
+ * @param align
+ * true/false
+ * @param ap
+ * associated alignment
+ * @param protocol
+ * how to get pdb data
*/
- public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs, String[][] boundchains, boolean align, AlignmentPanel ap, String protocol)
+ public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs,
+ String[][] boundchains, boolean align, AlignmentPanel ap,
+ String protocol)
{
throw new Error("Not yet implemented.");
}
+
public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
AlignmentPanel ap, String protocol)
{
this.ap = ap;
- jmb = new AppletJmolBinding(this, new PDBEntry[]
- { pdbentry }, new SequenceI[][]{seq}, new String[][]{ chains }, protocol);
+ jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
+ new PDBEntry[]
+ { pdbentry }, new SequenceI[][]
+ { seq }, new String[][]
+ { chains }, protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
}
String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
- pdbentry.getId());
+ .getStructureSelectionManager(ap.av.applet)
+ .alreadyMappedToFile(pdbentry.getId());
MCview.PDBfile reader = null;
if (alreadyMapped != null)
{
- reader = StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, pdbentry.getFile(), protocol);
+ reader = StructureSelectionManager.getStructureSelectionManager(
+ ap.av.applet).setMapping(seq, chains, pdbentry.getFile(),
+ protocol);
// PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW?
// FOR NOW, LETS JUST OPEN A NEW WINDOW
}
hydro.addActionListener(this);
chain.addActionListener(this);
seqColour.addItemListener(this);
+ jmolColour.addItemListener(this);
zappo.addActionListener(this);
taylor.addActionListener(this);
helix.addActionListener(this);
strand.addActionListener(this);
turn.addActionListener(this);
buried.addActionListener(this);
+ purinepyrimidine.addActionListener(this);
user.addActionListener(this);
jmolHelp.addActionListener(this);
coloursMenu.add(strand);
coloursMenu.add(turn);
coloursMenu.add(buried);
+ coloursMenu.add(purinepyrimidine);
coloursMenu.add(user);
-
+ coloursMenu.add(jmolColour);
helpMenu.add(jmolHelp);
+ this.setLayout(new BorderLayout());
setMenuBar(menuBar);
renderPanel = new RenderPanel();
embedMenuIfNeeded(renderPanel);
this.add(renderPanel, BorderLayout.CENTER);
+ scriptWindow = new Panel();
+ scriptWindow.setVisible(false);
+ // this.add(scriptWindow, BorderLayout.SOUTH);
+
try
{
- jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()+"_jmol_",
- ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(),
- "-applet");
+ jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
+ + "_jmol_", ap.av.applet.getDocumentBase(),
+ ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
} catch (Exception e)
{
System.err
closeViewer();
}
});
- if (pdbentry.getProperty()==null)
+ if (pdbentry.getProperty() == null)
{
pdbentry.setProperty(new Hashtable());
pdbentry.getProperty().put("protocol", protocol);
frame.add(cap);
StringBuffer sb = new StringBuffer();
- try {
- for (int s = 0; s < jmb.pdbentry.length; s++)
+ try
{
- sb.append(StructureSelectionManager.getStructureSelectionManager()
- .printMapping(jmb.pdbentry[s].getFile()));
- sb.append("\n");
- }
- cap.setText(sb.toString());
- }
- catch (OutOfMemoryError ex)
+ for (int s = 0; s < jmb.pdbentry.length; s++)
+ {
+ sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
+ sb.append("\n");
+ }
+ cap.setText(sb.toString());
+ } catch (OutOfMemoryError ex)
{
frame.dispose();
- System.err.println("Out of memory when trying to create dialog box with sequence-structure mapping.");
+ System.err
+ .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
return;
}
jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
setEnabled(buried);
jmb.setJalviewColourScheme(new BuriedColourScheme());
}
+ else if (evt.getSource() == purinepyrimidine)
+ {
+ jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme());
+ }
else if (evt.getSource() == user)
{
setEnabled(user);
}
/**
- * tick or untick the seqColour menu entry depending upon if it was selected
- * or not.
+ * tick or untick the seqColour menu entry or jmoColour entry depending upon
+ * if it was selected or not.
*
* @param itm
*/
private void setEnabled(MenuItem itm)
{
+ jmolColour.setState(itm == jmolColour);
seqColour.setState(itm == seqColour);
jmb.setColourBySequence(itm == seqColour);
}
public void itemStateChanged(ItemEvent evt)
{
- if (evt.getSource() == seqColour)
+ if (evt.getSource() == jmolColour)
+ {
+ setEnabled(jmolColour);
+ jmb.setColourBySequence(false);
+ }
+ else if (evt.getSource() == seqColour)
{
setEnabled(seqColour);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
}
else if (!allChainsSelected)
centerViewer();
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
}
public void updateTitleAndMenus()
return;
}
setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
setTitle(jmb.getViewerTitle());
}
}
}
+ Panel splitPane = null;
+
public void showConsole(boolean showConsole)
{
- if (scriptWindow == null)
- {
- scriptWindow = new Panel(new BorderLayout());
- inputLine = new TextField();
- history = new TextArea(5, 40);
- scriptWindow.add(history, BorderLayout.CENTER);
- scriptWindow.add(inputLine, BorderLayout.SOUTH);
- add(scriptWindow, BorderLayout.SOUTH);
+ if (showConsole)
+ {
+ remove(renderPanel);
+ splitPane = new Panel();
+
+ splitPane.setLayout(new java.awt.GridLayout(2, 1));
+ splitPane.add(renderPanel);
+ splitPane.add(scriptWindow);
+ scriptWindow.setVisible(true);
+ this.add(splitPane, BorderLayout.CENTER);
+ splitPane.setVisible(true);
+ splitPane.validate();
+ }
+ else
+ {
scriptWindow.setVisible(false);
- history.setEditable(false);
- inputLine.addKeyListener(this);
+ remove(splitPane);
+ add(renderPanel, BorderLayout.CENTER);
+ splitPane = null;
}
-
- scriptWindow.setVisible(!scriptWindow.isVisible());
validate();
}
{
jmb.setJalviewColourScheme(ucs);
}
+
+ public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
+ {
+ for (int i = 0; i < _aps.size(); i++)
+ {
+ if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
+ {
+ return ((AlignmentPanel) _aps.get(i));
+ }
+ }
+ return ap;
+ }
}
git://source.jalview.org / jalview.git / blobdiff