/*
- * 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 ($$Version-Rel$$)
+ * 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.
- *
+ * 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/>.
+ * 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.regex.*;
-import java.util.*;
-import java.awt.*;
-import javax.swing.*;
-import javax.swing.event.*;
-import java.awt.event.*;
-import java.io.*;
-
-import jalview.jbgui.GStructureViewer;
-import jalview.api.SequenceStructureBinding;
-import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.structure.*;
+import java.util.Locale;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.io.File;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JPanel;
+import javax.swing.JSplitPane;
+import javax.swing.SwingUtilities;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
-import jalview.io.*;
-import jalview.schemes.*;
-import jalview.ws.ebi.EBIFetchClient;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.fts.service.alphafold.AlphafoldRestClient;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.structure.StructureCommand;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
+public class AppJmol extends StructureViewerBase
+{
+ // ms to wait for Jmol to load files
+ private static final int JMOL_LOAD_TIMEOUT = 20000;
-import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
+ private static final String SPACE = " ";
-public class AppJmol extends GStructureViewer implements Runnable,
- SequenceStructureBinding
+ private static final String QUOTE = "\"";
-{
AppJmolBinding jmb;
- ScriptWindow scriptWindow;
+ JPanel scriptWindow;
JSplitPane splitPane;
RenderPanel renderPanel;
- AlignmentPanel ap;
-
- Vector atomsPicked = new Vector();
-
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds)
+ /**
+ *
+ * @param files
+ * @param ids
+ * @param seqs
+ * @param ap
+ * @param usetoColour
+ * - add the alignment panel to the list used for colouring these
+ * structures
+ * @param useToAlign
+ * - add the alignment panel to the list used for aligning these
+ * structures
+ * @param leaveColouringToJmol
+ * - do not update the colours from any other source. Jmol is
+ * handling them
+ * @param loadStatus
+ * @param bounds
+ * @param viewid
+ */
+ public AppJmol(StructureViewerModel viewerModel, AlignmentPanel ap,
+ String sessionFile, String viewid)
{
- this(file, id, seq, ap, loadStatus, bounds, null);
- }
+ Map<File, StructureData> pdbData = viewerModel.getFileData();
+ PDBEntry[] pdbentrys = new PDBEntry[pdbData.size()];
+ SequenceI[][] seqs = new SequenceI[pdbData.size()][];
+ int i = 0;
+ for (StructureData data : pdbData.values())
+ {
+ PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
+ PDBEntry.Type.PDB, data.getFilePath());
+ pdbentrys[i] = pdbentry;
+ List<SequenceI> sequencesForPdb = data.getSeqList();
+ seqs[i] = sequencesForPdb
+ .toArray(new SequenceI[sequencesForPdb.size()]);
+ i++;
+ }
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds,
- String viewid)
- {
- PDBEntry pdbentry = new PDBEntry();
- pdbentry.setFile(file);
- pdbentry.setId(id);
- // / TODO: check if protocol is needed to be set, and if chains are
+ // TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
- jmb = new AppJmolBinding(this, new PDBEntry[]
- { pdbentry }, seq, null, null);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null);
jmb.setLoadingFromArchive(true);
- this.ap = ap;
- this.setBounds(bounds);
- jmb.setColourBySequence(false);
- seqColour.setSelected(false);
- viewId = viewid;
- // jalview.gui.Desktop.addInternalFrame(this, "Loading File",
- // bounds.width,bounds.height);
+ addAlignmentPanel(ap);
+ if (viewerModel.isAlignWithPanel())
+ {
+ useAlignmentPanelForSuperposition(ap);
+ }
+ initMenus();
+ boolean useToColour = viewerModel.isColourWithAlignPanel();
+ boolean leaveColouringToJmol = viewerModel.isColourByViewer();
+ if (leaveColouringToJmol || !useToColour)
+ {
+ jmb.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
+ }
+ else if (useToColour)
+ {
+ useAlignmentPanelForColourbyseq(ap);
+ jmb.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
+ }
+
+ this.setBounds(viewerModel.getX(), viewerModel.getY(),
+ viewerModel.getWidth(), viewerModel.getHeight());
+ setViewId(viewid);
this.addInternalFrameListener(new InternalFrameAdapter()
{
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ @Override
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
- initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
-
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("load FILES ").append(QUOTE)
+ .append(Platform.escapeBackslashes(sessionFile)).append(QUOTE);
+ initJmol(cmd.toString());
}
- public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
- AlignmentPanel ap)
+ @Override
+ protected void initMenus()
{
- // ////////////////////////////////
- // Is the pdb file already loaded?
- String alreadyMapped = StructureSelectionManager
- .getStructureSelectionManager().alreadyMappedToFile(
- pdbentry.getId());
+ super.initMenus();
- if (alreadyMapped != null)
- {
- int option = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- pdbentry.getId()
- + " is already displayed."
- + "\nDo you want to re-use this viewer ?",
- "Map Sequences to Visible Window: "
- + pdbentry.getId(), JOptionPane.YES_NO_OPTION);
-
- if (option == JOptionPane.YES_OPTION)
- {
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, chains, alreadyMapped,
- AppletFormatAdapter.FILE);
- if (ap.seqPanel.seqCanvas.fr != null)
- {
- ap.seqPanel.seqCanvas.fr.featuresAdded();
- ap.paintAlignment(true);
- }
+ viewerColour
+ .setText(MessageManager.getString("label.colour_with_jmol"));
+ viewerColour.setToolTipText(MessageManager
+ .getString("label.let_jmol_manage_structure_colours"));
+ }
- // Now this AppJmol is mapped to new sequences. We must add them to
- // the exisiting array
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
+ /**
+ * display a single PDB structure in a new Jmol view
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param ap
+ */
+ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
+ final AlignmentPanel ap)
+ {
+ setProgressIndicator(ap.alignFrame);
- for (int i = 0; i < frames.length; i++)
- {
- if (frames[i] instanceof AppJmol)
- {
- AppJmol topJmol = ((AppJmol) frames[i]);
- // JBPNOTE: this looks like a binding routine, rather than a gui
- // routine
- for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++)
- {
- if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped))
- {
- topJmol.jmb.addSequence(seq);
- break;
- }
- }
- }
- }
+ openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+ new SequenceI[][]
+ { seq });
+ }
- return;
- }
+ private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
+ PDBEntry[] pdbentrys,
+ SequenceI[][] seqs)
+ {
+ setProgressIndicator(ap.alignFrame);
+ jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
+ pdbentrys, seqs, null);
+ addAlignmentPanel(ap);
+ useAlignmentPanelForColourbyseq(ap);
+
+ alignAddedStructures = alignAdded;
+ if (pdbentrys.length > 1)
+ {
+ useAlignmentPanelForSuperposition(ap);
}
- // /////////////////////////////////
- jmb = new AppJmolBinding(this, new PDBEntry[]
- { pdbentry }, seq, null, null);
- this.ap = ap;
+ jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
-
- if (pdbentry.getFile() != null)
- {
- initJmol("load \"" + pdbentry.getFile() + "\"");
- }
- else
- {
- Thread worker = new Thread(this);
- worker.start();
- }
+ initMenus();
+ addingStructures = false;
+ worker = new Thread(this);
+ worker.start();
this.addInternalFrameListener(new InternalFrameAdapter()
{
- public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
+ @Override
+ public void internalFrameClosing(
+ InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
}
+ /**
+ * create a new Jmol containing several structures optionally superimposed
+ * using the given alignPanel.
+ *
+ * @param ap
+ * @param alignAdded
+ * - true to superimpose
+ * @param pe
+ * @param seqs
+ */
+ public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+ SequenceI[][] seqs)
+ {
+ openNewJmol(ap, alignAdded, pe, seqs);
+ }
+
+
void initJmol(String command)
{
jmb.setFinishedInit(false);
this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER);
jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(),
getBounds().width, getBounds().height);
- jmb.allocateViewer(renderPanel, true, "", null, null, "");
- jmb.newJmolPopup(true, "Jmol", true);
- jmb.evalStateCommand(command);
- jmb.setFinishedInit(true);
- }
-
- void setChainMenuItems(Vector chains)
- {
- chainMenu.removeAll();
- if (chains==null)
+ if (scriptWindow == null)
{
- return;
+ BorderLayout bl = new BorderLayout();
+ bl.setHgap(0);
+ bl.setVgap(0);
+ scriptWindow = new JPanel(bl);
+ scriptWindow.setVisible(false);
}
- JMenuItem menuItem = new JMenuItem("All");
- menuItem.addActionListener(new ActionListener()
- {
- 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 (int c = 0; c < chains.size(); c++)
+ jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
+ null);
+ // jmb.newJmolPopup("Jmol");
+ if (command == null)
{
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
- menuItem.addItemListener(new ItemListener()
- {
- public void itemStateChanged(ItemEvent evt)
- {
- if (!allChainsSelected)
- centerViewer();
- }
- });
-
- chainMenu.add(menuItem);
+ command = "";
}
+ jmb.executeCommand(new StructureCommand(command), false);
+ jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
+ jmb.setFinishedInit(true);
}
- boolean allChainsSelected = false;
-
- void centerViewer()
+ @Override
+ public void run()
{
- Vector toshow = new Vector();
- String lbl;
- int mlength, p, mnum;
- for (int i = 0; i < chainMenu.getItemCount(); i++)
+ _started = true;
+ try
{
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+ List<String> files = jmb.fetchPdbFiles(this);
+ if (files.size() > 0)
{
- JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
- if (item.isSelected())
- {
- toshow.addElement(item.getText());
- }
+ showFilesInViewer(files);
}
+ } finally
+ {
+ _started = false;
+ worker = null;
}
- jmb.centerViewer(toshow);
}
- void closeViewer()
+ /**
+ * Either adds the given files to a structure viewer or opens a new viewer to
+ * show them
+ *
+ * @param files
+ * list of absolute paths to structure files
+ */
+ void showFilesInViewer(List<String> files)
{
- jmb.closeViewer();
- // TODO: check for memory leaks where instance isn't finalised because jmb
- // holds a reference to the window
- jmb = null;
- }
+ long lastnotify = jmb.getLoadNotifiesHandled();
+ StringBuilder fileList = new StringBuilder();
+ for (String s : files)
+ {
+ fileList.append(SPACE).append(QUOTE)
+ .append(Platform.escapeBackslashes(s)).append(QUOTE);
+ }
+ String filesString = fileList.toString();
- public void run()
- {
- String pdbid = "";
- // todo - record which pdbids were successfuly imported.
- StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer();
- try
+ if (!addingStructures)
{
- // TODO: replace with reference fetching/transfer code (validate PDBentry
- // as a DBRef?)
- jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb();
- for (int pi = 0; pi < jmb.pdbentry.length; pi++)
+ try
{
- AlignmentI pdbseq;
- if ((pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi]
- .getId())) != null)
- {
- String file;
- // just transfer the file name from the first sequence's first
- // PDBEntry
- jmb.pdbentry[pi].setFile(file = ((PDBEntry) pdbseq.getSequenceAt(
- 0).getPDBId().elementAt(0)).getFile());
- files.append("\"" + file + "\"");
- }
- else
- {
- errormsgs.append("'" + pdbid + "' ");
- }
+ initJmol("load FILES " + filesString);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("When trying to open the Jmol viewer!", oomerror);
+ Console.debug("File locations are " + filesString);
+ } catch (Exception ex)
+ {
+ Console.error("Couldn't open Jmol viewer!", ex);
+ ex.printStackTrace();
+ return;
}
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("'" + pdbid + "'");
}
- if (errormsgs.length() > 0)
+ else
{
+ StringBuilder cmd = new StringBuilder();
+ cmd.append("loadingJalviewdata=true\nload APPEND ");
+ cmd.append(filesString);
+ cmd.append("\nloadingJalviewdata=null");
+ final StructureCommand command = new StructureCommand(cmd.toString());
+ lastnotify = jmb.getLoadNotifiesHandled();
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "The following pdb entries could not be retrieved from the PDB:\n"
- + errormsgs.toString()
- + "\nPlease try downloading them manually.",
- "Couldn't load file", JOptionPane.ERROR_MESSAGE);
-
- }
- if (files.length() > 0)
- {
try
{
- initJmol("load FILES " + files.toString());
+ jmb.executeCommand(command, false);
} catch (OutOfMemoryError oomerror)
{
- new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + files);
+ new OOMWarning("When trying to add structures to the Jmol viewer!",
+ oomerror);
+ Console.debug("File locations are " + filesString);
+ return;
} catch (Exception ex)
{
- Cache.log.error("Couldn't open Jmol viewer!", ex);
+ Console.error("Couldn't add files to Jmol viewer!", ex);
+ ex.printStackTrace();
+ return;
}
}
- }
-
- public void pdbFile_actionPerformed(ActionEvent actionEvent)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ // need to wait around until script has finished
+ int waitMax = JMOL_LOAD_TIMEOUT;
+ int waitFor = 35;
+ int waitTotal = 0;
+ while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
+ : !(jmb.isFinishedInit() && jmb.getStructureFiles() != null
+ && jmb.getStructureFiles().length == files.size()))
{
try
{
- // TODO: cope with multiple PDB files in view
- BufferedReader in = new BufferedReader(new FileReader(jmb.getPdbFile()[0]));
- File outFile = chooser.getSelectedFile();
+ Console.debug("Waiting around for jmb notify.");
+ waitTotal += waitFor;
- 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)
+ // Thread.sleep() throws an exception in JS
+ Thread.sleep(waitFor);
+ } catch (Exception e)
{
- ex.printStackTrace();
+ }
+ if (waitTotal > waitMax)
+ {
+ 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.getStructureFiles();
+ break;
}
}
- }
- public void viewMapping_actionPerformed(ActionEvent actionEvent)
- {
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- try {for (int pdbe = 0; pdbe<jmb.pdbentry.length; pdbe++) {
- cap.appendText(StructureSelectionManager.getStructureSelectionManager()
- .printMapping(jmb.pdbentry[pdbe].getFile()));
- cap.appendText("\n");
- }} catch (OutOfMemoryError e)
+ // refresh the sequence colours for the new structure(s)
+ for (AlignmentViewPanel ap : _colourwith)
+ {
+ jmb.updateColours(ap);
+ }
+ // do superposition if asked to
+ if (alignAddedStructures)
{
- new OOMWarning("composing sequence-structure alignments for display in text box.", e);
- cap.dispose();
- return;
+ alignAddedStructures();
}
- jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping",
- 550, 600);
+ addingStructures = false;
}
/**
- * DOCUMENT ME!
- *
- * @param e
- * DOCUMENT ME!
+ * Queues a thread to align structures with Jalview alignments
*/
- public void eps_actionPerformed(ActionEvent e)
+ void alignAddedStructures()
{
- makePDBImage(jalview.util.ImageMaker.EPS);
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ if (jmb.jmolViewer.isScriptExecuting())
+ {
+ SwingUtilities.invokeLater(this);
+ try
+ {
+ Thread.sleep(5);
+ } catch (InterruptedException q)
+ {
+ }
+ return;
+ }
+ else
+ {
+ alignStructsWithAllAlignPanels();
+ }
+ }
+ });
+
}
/**
- * DOCUMENT ME!
+ * Outputs the Jmol viewer image as an image file, after prompting the user to
+ * choose a file and (for EPS) choice of Text or Lineart character rendering
+ * (unless a preference for this is set)
*
- * @param e
- * DOCUMENT ME!
+ * @param type
*/
- public void png_actionPerformed(ActionEvent e)
- {
- makePDBImage(jalview.util.ImageMaker.PNG);
- }
-
- void makePDBImage(int type)
+ @Override
+ public void makePDBImage(ImageMaker.TYPE type)
{
int width = getWidth();
int height = getHeight();
-
- jalview.util.ImageMaker im;
-
- if (type == jalview.util.ImageMaker.PNG)
+ ImageWriterI writer = new ImageWriterI()
{
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
- "Make PNG image from view", width, height, null, null);
- }
- else
- {
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Make EPS file from view", width, height, null, this
- .getTitle());
- }
-
- if (im.getGraphics() != null)
- {
- Rectangle rect = new Rectangle(width, height);
- jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
- im.writeImage();
- }
- }
-
- public void seqColour_actionPerformed(ActionEvent actionEvent)
- {
- jmb.setColourBySequence(seqColour.isSelected());
- // Set the colour using the current view for the associated alignframe
- jmb.colourBySequence(ap.alignFrame.viewport.showSequenceFeatures, ap.alignFrame.viewport.alignment);
- }
-
- public void chainColour_actionPerformed(ActionEvent actionEvent)
- {
- chainColour.setSelected(true);
- jmb.colourByChain();
- }
-
- public void chargeColour_actionPerformed(ActionEvent actionEvent)
- {
- chargeColour.setSelected(true);
- jmb.colourByCharge();
- }
-
- public void zappoColour_actionPerformed(ActionEvent actionEvent)
- {
- zappoColour.setSelected(true);
- jmb.setJalviewColourScheme(new ZappoColourScheme());
- }
-
- public void taylorColour_actionPerformed(ActionEvent actionEvent)
- {
- taylorColour.setSelected(true);
- jmb.setJalviewColourScheme(new TaylorColourScheme());
- }
-
- public void hydroColour_actionPerformed(ActionEvent actionEvent)
- {
- hydroColour.setSelected(true);
- jmb.setJalviewColourScheme(new HydrophobicColourScheme());
- }
-
- public void helixColour_actionPerformed(ActionEvent actionEvent)
- {
- helixColour.setSelected(true);
- jmb.setJalviewColourScheme(new HelixColourScheme());
- }
-
- public void strandColour_actionPerformed(ActionEvent actionEvent)
- {
- strandColour.setSelected(true);
- jmb.setJalviewColourScheme(new StrandColourScheme());
- }
-
- public void turnColour_actionPerformed(ActionEvent actionEvent)
- {
- turnColour.setSelected(true);
- jmb.setJalviewColourScheme(new TurnColourScheme());
- }
-
- public void buriedColour_actionPerformed(ActionEvent actionEvent)
- {
- buriedColour.setSelected(true);
- jmb.setJalviewColourScheme(new BuriedColourScheme());
- }
-
-
- public void userColour_actionPerformed(ActionEvent actionEvent)
- {
- userColour.setSelected(true);
- new UserDefinedColours(this, null);
- }
-
- public void backGround_actionPerformed(ActionEvent actionEvent)
- {
- java.awt.Color col = JColorChooser.showDialog(this,
- "Select Background Colour", null);
- if (col != null)
- {
- jmb.setBackgroundColour(col);
- }
+ @Override
+ public void exportImage(Graphics g) throws Exception
+ {
+ jmb.jmolViewer.renderScreenImage(g, width, height);
+ }
+ };
+ String view = MessageManager.getString("action.view").toLowerCase(Locale.ROOT);
+ ImageExporter exporter = new ImageExporter(writer,
+ getProgressIndicator(), type, getTitle());
+ exporter.doExport(null, this, width, height, view);
}
- public void jmolHelp_actionPerformed(ActionEvent actionEvent)
+ @Override
+ public void showHelp_actionPerformed()
{
try
{
- jalview.util.BrowserLauncher
- .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ BrowserLauncher // BH 2018
+ .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
+ System.err.println("Show Jmol help failed with: " + ex.getMessage());
}
}
+ @Override
public void showConsole(boolean showConsole)
{
- if (scriptWindow == null)
- scriptWindow = new ScriptWindow(this);
-
if (showConsole)
{
if (splitPane == null)
splitPane.setTopComponent(renderPanel);
splitPane.setBottomComponent(scriptWindow);
this.getContentPane().add(splitPane, BorderLayout.CENTER);
+ splitPane.setDividerLocation(getHeight() - 200);
+ scriptWindow.setVisible(true);
+ scriptWindow.validate();
+ splitPane.validate();
}
- splitPane.setDividerLocation(getHeight() - 200);
- splitPane.validate();
}
else
{
if (splitPane != null)
+ {
splitPane.setVisible(false);
+ }
splitPane = null;
{
final Dimension currentSize = new Dimension();
- final Rectangle rectClip = new Rectangle();
-
+ @Override
public void paintComponent(Graphics g)
{
getSize(currentSize);
- g.getClipBounds(rectClip);
- if (jmb.fileLoadingError != null)
+ if (jmb != null && jmb.hasFileLoadingError())
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Error loading file...", 20,
- currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_file")
+ + "...", 20, currentSize.height / 2);
StringBuffer sb = new StringBuffer();
- int lines=0;
- for (int e=0;e<jmb.pdbentry.length; e++)
+ int lines = 0;
+ for (int e = 0; e < jmb.getPdbCount(); e++)
{
- sb.append(jmb.pdbentry[e].getId());
- if (e<jmb.pdbentry.length-1) {
+ sb.append(jmb.getPdbEntry(e).getId());
+ if (e < jmb.getPdbCount() - 1)
+ {
sb.append(",");
}
- if (e==jmb.pdbentry.length-1 || sb.length()>20)
+ if (e == jmb.getPdbCount() - 1 || sb.length() > 20)
{
lines++;
- g.drawString(sb.toString(), 20, currentSize.height/2 - lines*g.getFontMetrics().getHeight());
+ g.drawString(sb.toString(), 20, currentSize.height / 2
+ - lines * g.getFontMetrics().getHeight());
}
}
}
+ else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit())
+ {
+ g.setColor(Color.black);
+ g.fillRect(0, 0, currentSize.width, currentSize.height);
+ g.setColor(Color.white);
+ g.setFont(new Font("Verdana", Font.BOLD, 14));
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
+ }
else
- if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit())
- {
- g.setColor(Color.black);
- g.fillRect(0, 0, currentSize.width, currentSize.height);
- g.setColor(Color.white);
- g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
- }
- else
{
- jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+ jmb.jmolViewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
}
}
}
- String viewId = null;
-
- public String getViewId()
+ @Override
+ public AAStructureBindingModel getBinding()
{
- if (viewId == null)
- {
- viewId = System.currentTimeMillis() + "." + this.hashCode();
- }
- return viewId;
+ return this.jmb;
}
- public void updateTitleAndMenus()
- {
- if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0)
- {
- repaint();
- return;
- }
- setChainMenuItems(jmb.chainNames);
- jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
- this.setTitle(jmb.getViewerTitle());
+ @Override
+ public ViewerType getViewerType()
+ {
+ return ViewerType.JMOL;
}
- public void setJalviewColourScheme(ColourSchemeI ucs)
+ @Override
+ protected String getViewerName()
{
- jmb.setJalviewColourScheme(ucs);
-
+ return "Jmol";
}
-
}
git://source.jalview.org / jalview.git / blobdiff