package jalview.gui;
import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.Pdb;
import java.awt.Graphics;
import java.awt.Rectangle;
import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.io.BufferedReader;
import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
-import javax.swing.JMenu;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
import javax.swing.SwingUtilities;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
-import javax.swing.event.MenuEvent;
-import javax.swing.event.MenuListener;
public class AppJmol extends StructureViewerBase
{
+ // ms to wait for Jmol to load files
+ private static final int JMOL_LOAD_TIMEOUT = 20000;
+
private static final String SPACE = " ";
private static final String BACKSLASH = "\"";
RenderPanel renderPanel;
- ViewSelectionMenu seqColourBy;
-
/**
*
* @param files
// / TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
- pdbentrys, seqs, null, null);
+ pdbentrys, seqs, null);
jmb.setLoadingFromArchive(true);
addAlignmentPanel(ap);
{
useAlignmentPanelForSuperposition(ap);
}
+ initMenus();
if (leaveColouringToJmol || !usetoColour)
{
jmb.setColourBySequence(false);
viewerColour.setSelected(false);
}
this.setBounds(bounds);
- initMenus();
setViewId(viewid);
// jalview.gui.Desktop.addInternalFrame(this, "Loading File",
// bounds.width,bounds.height);
}
});
initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
-
}
- private void initMenus()
+ @Override
+ protected void initMenus()
{
- seqColour.setSelected(jmb.isColourBySequence());
- viewerColour.setSelected(!jmb.isColourBySequence());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
-
- seqColourBy = new ViewSelectionMenu(
- MessageManager.getString("label.colour_by"), this, _colourwith,
- new ItemListener()
- {
+ super.initMenus();
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- if (!seqColour.isSelected())
- {
- seqColour.doClick();
- }
- else
- {
- // update the jmol display now.
- seqColour_actionPerformed(null);
- }
- }
- });
- viewMenu.add(seqColourBy);
- final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu(
- MessageManager.getString("label.superpose_with"), this,
- _alignwith, handler = new ItemListener()
- {
+ viewerActionMenu.setText(MessageManager.getString("label.jmol"));
- @Override
- public void itemStateChanged(ItemEvent e)
- {
- alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText(MessageManager
- .formatMessage(
- "label.align_structures_using_linked_alignment_views",
- new String[] { new Integer(_alignwith
- .size()).toString() }));
- }
- });
- handler.itemStateChanged(null);
- viewerActionMenu.add(alpanels);
- viewerActionMenu.addMenuListener(new MenuListener()
- {
-
- @Override
- public void menuSelected(MenuEvent e)
- {
- handler.itemStateChanged(null);
- }
-
- @Override
- public void menuDeselected(MenuEvent e)
- {
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void menuCanceled(MenuEvent e)
- {
- // TODO Auto-generated method stub
-
- }
- });
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_jmol"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
}
IProgressIndicator progressBar = null;
openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
}
- /**
- * Answers true if this viewer already involves the given PDB ID
- */
- @Override
- protected boolean hasPdbId(String pdbId)
- {
- return jmb.hasPdbId(pdbId);
- }
-
private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
SequenceI[][] seqs)
{
progressBar = ap.alignFrame;
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
- pdbentrys, seqs, null, null);
+ pdbentrys, seqs, null);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
+
if (pdbentrys.length > 1)
{
alignAddedStructures = true;
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
initMenus();
- worker = null;
- {
- addingStructures = false;
- worker = new Thread(this);
- worker.start();
- }
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
+
this.addInternalFrameListener(new InternalFrameAdapter()
{
@Override
jmb.setFinishedInit(true);
}
- void setChainMenuItems(Vector<String> chains)
- {
- chainMenu.removeAll();
- if (chains == null)
- {
- return;
- }
- JMenuItem menuItem = new JMenuItem(
- MessageManager.getString("label.all"));
- menuItem.addActionListener(new ActionListener()
- {
- @Override
- public void actionPerformed(ActionEvent evt)
- {
- allChainsSelected = true;
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- {
- ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true);
- }
- }
- centerViewer();
- allChainsSelected = false;
- }
- });
- chainMenu.add(menuItem);
-
- for (String chain : chains)
- {
- menuItem = new JCheckBoxMenuItem(chain, true);
- menuItem.addItemListener(new ItemListener()
- {
- @Override
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- {
- centerViewer();
- }
- }
- });
-
- chainMenu.add(menuItem);
- }
- }
boolean allChainsSelected = false;
- void centerViewer()
+ @Override
+ void showSelectedChains()
{
Vector<String> toshow = new Vector<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
}
// need to wait around until script has finished
- int waitMax = 5000; // give up after 5 seconds
+ int waitMax = JMOL_LOAD_TIMEOUT;
int waitFor = 35;
int waitTotal = 0;
while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
}
if (waitTotal > waitMax)
{
- System.err.println("Timed out waiting for Jmol to load files");
+ System.err
+ .println("Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
+// System.err.println("finished: " + jmb.isFinishedInit()
+// + "; loaded: " + Arrays.toString(jmb.getPdbFile())
+// + "; files: " + files.toString());
+ jmb.getPdbFile();
break;
}
}
}
if (errormsgs.length() > 0)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
.formatMessage("label.pdb_entries_couldnt_be_retrieved",
new String[] { errormsgs.toString() }),
MessageManager.getString("label.couldnt_load_file"),
- JOptionPane.ERROR_MESSAGE);
+ JvOptionPane.ERROR_MESSAGE);
}
return files;
}
@Override
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
-
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
- chooser.setToolTipText(MessageManager.getString("action.save"));
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
- {
- BufferedReader in = null;
- try
- {
- // TODO: cope with multiple PDB files in view
- in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
- File outFile = chooser.getSelectedFile();
-
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
- while ((data = in.readLine()) != null)
- {
- if (!(data.indexOf("<PRE>") > -1 || data.indexOf("</PRE>") > -1))
- {
- out.println(data);
- }
- }
- out.close();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- } finally
- {
- if (in != null)
- {
- try
- {
- in.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- }
- }
-
- @Override
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try
- {
- cap.appendText(jmb.printMappings());
- } catch (OutOfMemoryError e)
- {
- new OOMWarning(
- "composing sequence-structure alignments for display in text box.",
- e);
- cap.dispose();
- return;
- }
- jalview.gui.Desktop.addInternalFrame(cap,
- MessageManager.getString("label.pdb_sequence_mapping"), 550,
- 600);
- }
-
- @Override
public void eps_actionPerformed(ActionEvent e)
{
makePDBImage(jalview.util.ImageMaker.TYPE.EPS);
}
@Override
- public void viewerColour_actionPerformed(ActionEvent actionEvent)
- {
- if (viewerColour.isSelected())
- {
- // disable automatic sequence colouring.
- jmb.setColourBySequence(false);
- }
- }
-
- @Override
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- if (_colourwith == null)
- {
- _colourwith = new Vector<AlignmentPanel>();
- }
- if (jmb.isColourBySequence())
- {
- if (!jmb.isLoadingFromArchive())
- {
- if (_colourwith.size() == 0 && getAlignmentPanel() != null)
- {
- // Make the currently displayed alignment panel the associated view
- _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
- }
- }
- // Set the colour using the current view for the associated alignframe
- for (AlignmentPanel ap : _colourwith)
- {
- jmb.colourBySequence(ap);
- }
- }
- }
-
- @Override
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- @Override
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- @Override
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- @Override
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- @Override
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- @Override
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
- }
-
- @Override
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
- }
-
- @Override
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
-
- @Override
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
-
- @Override
- public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
- {
- setJalviewColourScheme(new PurinePyrimidineColourScheme());
- }
-
- @Override
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- @Override
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser
- .showDialog(this, MessageManager
- .getString("label.select_backgroud_colour"), null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
- }
-
- @Override
public void showHelp_actionPerformed(ActionEvent actionEvent)
{
try
{
- jalview.util.BrowserLauncher
+ BrowserLauncher
.openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
{
getSize(currentSize);
- if (jmb != null && jmb.fileLoadingError != null)
+ if (jmb != null && jmb.hasFileLoadingError())
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
}
}
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.chainNames);
-
- this.setTitle(jmb.getViewerTitle());
- if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)
- {
- viewerActionMenu.setVisible(true);
- }
- if (!jmb.isLoadingFromArchive())
- {
- seqColour_actionPerformed(null);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event
- * .ActionEvent)
- */
- @Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
- {
- alignStructs_withAllAlignPanels();
- }
-
- private void alignStructs_withAllAlignPanels()
- {
- if (getAlignmentPanel() == null)
- {
- return;
- }
- ;
- if (_alignwith.size() == 0)
- {
- _alignwith.add(getAlignmentPanel());
- }
- ;
- try
- {
- AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
- int[] alm = new int[_alignwith.size()];
- int a = 0;
-
- for (AlignmentPanel ap : _alignwith)
- {
- als[a] = ap.av.getAlignment();
- alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
- }
- jmb.superposeStructures(als, alm, alc);
- } catch (Exception e)
- {
- StringBuffer sp = new StringBuffer();
- for (AlignmentPanel ap : _alignwith)
- {
- sp.append("'" + ap.alignFrame.getTitle() + "' ");
- }
- Cache.log.info("Couldn't align structures with the " + sp.toString()
- + "associated alignment panels.", e);
-
- }
-
- }
-
- @Override
- public void setJalviewColourScheme(ColourSchemeI ucs)
- {
- jmb.setJalviewColourScheme(ucs);
-
- }
-
- /**
- *
- * @param alignment
- * @return first alignment panel displaying given alignment, or the default
- * alignment panel
- */
- public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)
- {
- for (AlignmentPanel ap : getAllAlignmentPanels())
- {
- if (ap.av.getAlignment() == alignment)
- {
- return ap;
- }
- }
- return getAlignmentPanel();
- }
-
@Override
public AAStructureBindingModel getBinding()
{
}
@Override
- protected AAStructureBindingModel getBindingModel()
+ protected String getViewerName()
{
- return jmb;
+ return "Jmol";
}
-
}
git://source.jalview.org / jalview.git / blobdiff