X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=c2a7299d66a176a36d722a794166421d507c21e9;hb=3412b273e964fb1a9d22564b04a5f0c827ec2461;hp=dcca874286f0cd78afc91108171a829c4d368fa0;hpb=f8456d4c0b253ae32a4b569e12bb8bf7f7096d65;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index dcca874..c2a7299 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,155 +1,315 @@ /* - * 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 . + * 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.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 java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +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.PrintWriter; +import java.util.Enumeration; +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.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; +import javax.swing.event.MenuEvent; +import javax.swing.event.MenuListener; -import jalview.jbgui.GStructureViewer; -import jalview.api.SequenceStructureBinding; import jalview.bin.Cache; -import jalview.datamodel.*; -import jalview.gui.*; -import jalview.structure.*; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; -import jalview.io.*; -import jalview.schemes.*; -import jalview.ws.ebi.EBIFetchClient; - -import org.jmol.api.*; -import org.jmol.adapter.smarter.SmarterJmolAdapter; -import org.jmol.popup.*; -import org.jmol.viewer.JmolConstants; - -public class AppJmol extends GStructureViewer implements StructureListener, - JmolStatusListener, Runnable, SequenceStructureBinding - +import jalview.datamodel.SequenceI; +import jalview.gui.StructureViewer.ViewerType; +import jalview.io.AppletFormatAdapter; +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.MessageManager; +import jalview.util.Platform; + +public class AppJmol extends StructureViewerBase { - JmolViewer viewer; - - JmolPopup jmolpopup; - - ScriptWindow scriptWindow; - - PDBEntry pdbentry; - - SequenceI[] sequence; + AppJmolBinding jmb; - String[] chains; - - StructureSelectionManager ssm; + JPanel scriptWindow; JSplitPane splitPane; RenderPanel renderPanel; - AlignmentPanel ap; - - String fileLoadingError; - - boolean colourBySequence = true; - - boolean loadingFromArchive = false; - Vector atomsPicked = new Vector(); + private boolean addingStructures = false; + + /** + * + * @param file + * @param id + * @param seq + * @param ap + * @param loadStatus + * @param bounds + * @deprecated defaults to AppJmol(String[] files, ... , viewid); + */ + @Deprecated public AppJmol(String file, String id, SequenceI[] seq, AlignmentPanel ap, String loadStatus, Rectangle bounds) { this(file, id, seq, ap, loadStatus, bounds, null); } + /** + * @deprecated + */ + @Deprecated public AppJmol(String file, String id, SequenceI[] seq, AlignmentPanel ap, String loadStatus, Rectangle bounds, String viewid) { - loadingFromArchive = true; - pdbentry = new PDBEntry(); - pdbentry.setFile(file); - pdbentry.setId(id); - this.sequence = seq; - this.ap = ap; + this(new String[] + { file }, new String[] + { id }, new SequenceI[][] + { seq }, ap, true, true, false, loadStatus, bounds, viewid); + } + + ViewSelectionMenu seqColourBy; + + /** + * + * @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(String[] files, String[] ids, SequenceI[][] seqs, + AlignmentPanel ap, boolean usetoColour, boolean useToAlign, + boolean leaveColouringToJmol, String loadStatus, + Rectangle bounds, String viewid) + { + PDBEntry[] pdbentrys = new PDBEntry[files.length]; + for (int i = 0; i < pdbentrys.length; i++) + { + // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]); + PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB, + files[i]); + pdbentrys[i] = pdbentry; + } + // / TODO: check if protocol is needed to be set, and if chains are + // autodiscovered. + jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), + pdbentrys, seqs, null, null); + + jmb.setLoadingFromArchive(true); + addAlignmentPanel(ap); + if (useToAlign) + { + useAlignmentPanelForSuperposition(ap); + } + 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(bounds); - colourBySequence = false; - seqColour.setSelected(false); - viewId = viewid; + initMenus(); + setViewId(viewid); // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); - initJmol(loadStatus); - this.addInternalFrameListener(new InternalFrameAdapter() { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); + initJmol(loadStatus); // pdbentry, seq, JBPCHECK! + } - public synchronized void addSequence(SequenceI[] seq) + private void initMenus() { - Vector v = new Vector(); - for (int i = 0; i < sequence.length; i++) - v.addElement(sequence[i]); + seqColour.setSelected(jmb.isColourBySequence()); + viewerColour.setSelected(!jmb.isColourBySequence()); + if (_colourwith == null) + { + _colourwith = new Vector(); + } + if (_alignwith == null) + { + _alignwith = new Vector(); + } + + seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith, + new ItemListener() + { + + @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() + { + + @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 + + } - for (int i = 0; i < seq.length; i++) - if (!v.contains(seq[i])) - v.addElement(seq[i]); + @Override + public void menuCanceled(MenuEvent e) + { + // TODO Auto-generated method stub - SequenceI[] tmp = new SequenceI[v.size()]; - v.copyInto(tmp); - sequence = tmp; + } + }); } + IProgressIndicator progressBar = null; + + /** + * add a single PDB structure to a new or existing Jmol view + * + * @param pdbentry + * @param seq + * @param chains + * @param ap + */ public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, - AlignmentPanel ap) + final AlignmentPanel ap) { + progressBar = ap.alignFrame; // //////////////////////////////// // Is the pdb file already loaded? - String alreadyMapped = StructureSelectionManager - .getStructureSelectionManager().alreadyMappedToFile( - pdbentry.getId()); + String alreadyMapped = ap.getStructureSelectionManager() + .alreadyMappedToFile(pdbentry.getId()); if (alreadyMapped != null) { - int option = JOptionPane - .showInternalConfirmDialog( - Desktop.desktop, - pdbentry.getId() - + " is already displayed." - + "\nDo you want to map sequences to the visible structure?", - "Map Sequences to Visible Window: " - + pdbentry.getId(), JOptionPane.YES_NO_OPTION); - + int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.pdb_entry_is_already_displayed", new String[] + { pdbentry.getId() }), MessageManager.formatMessage( + "label.map_sequences_to_visible_window", new String[] + { pdbentry.getId() }), + JOptionPane.YES_NO_CANCEL_OPTION); + + if (option == JOptionPane.CANCEL_OPTION) + { + return; + } if (option == JOptionPane.YES_OPTION) { - StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, chains, alreadyMapped, - AppletFormatAdapter.FILE); - if (ap.seqPanel.seqCanvas.fr != null) + // TODO : Fix multiple seq to one chain issue here. + ap.getStructureSelectionManager().setMapping(seq, chains, + alreadyMapped, AppletFormatAdapter.FILE); + if (ap.getSeqPanel().seqCanvas.fr != null) { - ap.seqPanel.seqCanvas.fr.featuresAdded(); + ap.getSeqPanel().seqCanvas.fr.featuresAdded(); ap.paintAlignment(true); } @@ -161,11 +321,23 @@ public class AppJmol extends GStructureViewer implements StructureListener, { if (frames[i] instanceof AppJmol) { - AppJmol topJmol = ((AppJmol) frames[i]); - if (topJmol.pdbentry.getFile().equals(alreadyMapped)) + final AppJmol topJmol = ((AppJmol) frames[i]); + // JBPNOTE: this looks like a binding routine, rather than a gui + // routine + for (int pe = 0; pe < topJmol.jmb.getPdbCount(); pe++) { - topJmol.addSequence(seq); - break; + if (topJmol.jmb.getPdbEntry(pe).getFile() + .equals(alreadyMapped)) + { + topJmol.jmb.addSequence(pe, seq); + topJmol.addAlignmentPanel(ap); + // add it to the set used for colouring + topJmol.useAlignmentPanelForColourbyseq(ap); + topJmol.buildActionMenu(); + ap.getStructureSelectionManager() + .sequenceColoursChanged(ap); + break; + } } } } @@ -174,76 +346,205 @@ public class AppJmol extends GStructureViewer implements StructureListener, } } // ///////////////////////////////// + // Check if there are other Jmol views involving this alignment + // and prompt user about adding this molecule to one of them + Vector existingViews = getJmolsFor(ap); + if (existingViews.size() > 0) + { + Enumeration jm = existingViews.elements(); + while (jm.hasMoreElements()) + { + AppJmol topJmol = (AppJmol) jm.nextElement(); + // TODO: highlight topJmol in view somehow + int option = JOptionPane + .showInternalConfirmDialog( + Desktop.desktop, + MessageManager.formatMessage( + "label.add_pdbentry_to_view", new String[] + { pdbentry.getId(), topJmol.getTitle() }), + MessageManager + .getString("label.align_to_existing_structure_view"), + JOptionPane.YES_NO_CANCEL_OPTION); + if (option == JOptionPane.CANCEL_OPTION) + { + return; + } + if (option == JOptionPane.YES_OPTION) + { + topJmol.useAlignmentPanelForSuperposition(ap); + topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); + return; + } + } + } + // ///////////////////////////////// + openNewJmol(ap, new PDBEntry[] + { pdbentry }, new SequenceI[][] + { seq }); + } - this.ap = ap; - this.pdbentry = pdbentry; - this.sequence = seq; - this.setSize(400, 400); - // jalview.gui.Desktop.addInternalFrame(this, "Jmol - // View"+(pdbentry.getId()!=null ? "for "+pdbentry.getId() - // : ""), 400, 400); - - if (pdbentry.getFile() != null) + private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, + SequenceI[][] seqs) + { + progressBar = ap.alignFrame; + jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), + pdbentrys, seqs, null, null); + addAlignmentPanel(ap); + useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length > 1) { - initJmol("load \"" + pdbentry.getFile() + "\""); + alignAddedStructures = true; + useAlignmentPanelForSuperposition(ap); } - else + jmb.setColourBySequence(true); + setSize(400, 400); // probably should be a configurable/dynamic default here + initMenus(); + worker = null; { - Thread worker = new Thread(this); + addingStructures = false; + worker = new Thread(this); worker.start(); } - this.addInternalFrameListener(new InternalFrameAdapter() { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); + } - void initJmol(String command) + /** + * create a new Jmol containing several structures superimposed using the + * given alignPanel. + * + * @param ap + * @param pe + * @param seqs + */ + public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs) { - renderPanel = new RenderPanel(); - - this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER); + openNewJmol(ap, pe, seqs); + } - StringBuffer title = new StringBuffer(sequence[0].getName() + ":" - + pdbentry.getId()); + /** + * pdb retrieval thread. + */ + private Thread worker = null; - if (pdbentry.getProperty() != null) + /** + * add a new structure (with associated sequences and chains) to this viewer, + * retrieving it if necessary first. + * + * @param pdbentry + * @param seq + * @param chains + * @param alignFrame + * @param align + * if true, new structure(s) will be align using associated alignment + */ + private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq, + final String[] chains, final boolean b, + final IProgressIndicator alignFrame) + { + if (pdbentry.getFile() == null) { - if (pdbentry.getProperty().get("method") != null) + if (worker != null && worker.isAlive()) { - title.append(" Method: "); - title.append(pdbentry.getProperty().get("method")); + // a retrieval is in progress, wait around and add ourselves to the + // queue. + new Thread(new Runnable() + { + public void run() + { + while (worker != null && worker.isAlive() && _started) + { + try + { + Thread.sleep(100 + ((int) Math.random() * 100)); + + } catch (Exception e) + { + } + + } + // and call ourselves again. + addStructure(pdbentry, seq, chains, b, alignFrame); + } + }).start(); + return; } - if (pdbentry.getProperty().get("chains") != null) + } + // otherwise, start adding the structure. + jmb.addSequenceAndChain(new PDBEntry[] + { pdbentry }, new SequenceI[][] + { seq }, new String[][] + { chains }); + addingStructures = true; + _started = false; + alignAddedStructures = b; + progressBar = alignFrame; // visual indication happens on caller frame. + (worker = new Thread(this)).start(); + return; + } + + private Vector getJmolsFor(AlignmentPanel apanel) + { + Vector result = new Vector(); + JInternalFrame[] frames = Desktop.instance.getAllFrames(); + + for (JInternalFrame frame : frames) + { + if (frame instanceof AppJmol) { - title.append(" Chain:"); - title.append(pdbentry.getProperty().get("chains")); + if (((StructureViewerBase) frame).isLinkedWith(apanel)) + { + result.addElement(frame); + } } } + return result; + } - this.setTitle(title.toString()); - jalview.gui.Desktop.addInternalFrame(this, title.toString(), + void initJmol(String command) + { + jmb.setFinishedInit(false); + renderPanel = new RenderPanel(); + // TODO: consider waiting until the structure/view is fully loaded before + // displaying + this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER); + jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(), getBounds().width, getBounds().height); - // * OK, but safer to assign htmlName, URL bases, comandOptions, and - // statusListener now. - - viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel, - new SmarterJmolAdapter(), "", null, null, "", this); - - jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true); - - viewer.evalStringQuiet(command); + if (scriptWindow == null) + { + BorderLayout bl = new BorderLayout(); + bl.setHgap(0); + bl.setVgap(0); + scriptWindow = new JPanel(bl); + scriptWindow.setVisible(false); + } + ; + jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, + null); + jmb.newJmolPopup(true, "Jmol", true); + if (command == null) + { + command = ""; + } + jmb.evalStateCommand(command); + jmb.setFinishedInit(true); } void setChainMenuItems(Vector chains) { chainMenu.removeAll(); - - JMenuItem menuItem = new JMenuItem("All"); + if (chains == null) + { + return; + } + JMenuItem menuItem = new JMenuItem( + MessageManager.getString("label.all")); menuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent evt) @@ -252,7 +553,9 @@ public class AppJmol extends GStructureViewer implements StructureListener, for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) + { ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); + } } centerViewer(); allChainsSelected = false; @@ -269,7 +572,9 @@ public class AppJmol extends GStructureViewer implements StructureListener, public void itemStateChanged(ItemEvent evt) { if (!allChainsSelected) + { centerViewer(); + } } }); @@ -279,114 +584,230 @@ public class AppJmol extends GStructureViewer implements StructureListener, boolean allChainsSelected = false; + private boolean alignAddedStructures = false; + void centerViewer() { - jmolHistory(false); - StringBuffer cmd = new StringBuffer(); + Vector toshow = new Vector(); String lbl; - int mlength, p,mnum; + int mlength, p, mnum; for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) { JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i); if (item.isSelected()) - { lbl = item.getText(); - mlength = 0; - do { - p = mlength; - mlength = lbl.indexOf(":", p); - } while (p < mlength && mlength < (lbl.length() - 2)); - if (pdbentry.getId().equals(lbl.substring(0,mlength))) - { - mnum = 1+getModelNum(pdbentry.getFile()); - if (mnum>0) - {cmd.append(":" + lbl.substring(mlength + 1) + " /" - + mnum + " or "); - } - } + toshow.addElement(item.getText()); } } } - - if (cmd.length() > 0) - cmd.setLength(cmd.length() - 4); - - viewer.evalStringQuiet("select *;restrict " + cmd + ";cartoon;center " - + cmd); - jmolHistory(true); - } - private int getModelNum(String modelFileName) - { - String[] mfn = getPdbFile(); - if (mfn == null) - { - return -1; - } - for (int i = 0; i < mfn.length; i++) - { - if (mfn[i].equalsIgnoreCase(modelFileName)) - return i; - } - return -1; + jmb.centerViewer(toshow); } - void closeViewer() + public void closeViewer(boolean closeExternalViewer) { - viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE); - // remove listeners for all structures in viewer - StructureSelectionManager.getStructureSelectionManager() - .removeStructureViewerListener(this, getPdbFile()); - // and shut down jmol - viewer.evalStringQuiet("zap"); - viewer.setJmolStatusListener(null); - viewer = null; + // JMol does not use an external viewer + jmb.closeViewer(); + setAlignmentPanel(null); + _aps.clear(); + _alignwith.clear(); + _colourwith.clear(); + // TODO: check for memory leaks where instance isn't finalised because jmb + // holds a reference to the window + jmb = null; } + /** + * state flag for PDB retrieval thread + */ + private boolean _started = false; + public void run() { + _started = true; + String pdbid = ""; + // todo - record which pdbids were successfuly imported. + StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer(); try { + String[] curfiles = jmb.getPdbFile(); // files currently in viewer // TODO: replace with reference fetching/transfer code (validate PDBentry // as a DBRef?) jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb(); - AlignmentI pdbseq; - if ((pdbseq = pdbclient.getSequenceRecords(pdbentry.getId())) != null) - { - // just transfer the file name from the first seuqence's first PDBEntry - pdbentry.setFile(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() - .elementAt(0)).getFile()); - initJmol("load " + pdbentry.getFile()); - } - else + for (int pi = 0; pi < jmb.getPdbCount(); pi++) { - JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - pdbentry.getId() - + " could not be retrieved. Please try downloading the file manually.", - "Couldn't load file", JOptionPane.ERROR_MESSAGE); + String file = jmb.getPdbEntry(pi).getFile(); + if (file == null) + { + // retrieve the pdb and store it locally + AlignmentI pdbseq = null; + pdbid = jmb.getPdbEntry(pi).getId(); + long hdl = pdbid.hashCode() - System.currentTimeMillis(); + if (progressBar != null) + { + progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl); + } + try + { + pdbseq = pdbclient.getSequenceRecords(pdbid); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("Retrieving PDB id " + pdbid, oomerror); + } catch (Exception ex) + { + ex.printStackTrace(); + errormsgs.append("'" + pdbid + "'"); + } + if (progressBar != null) + { + progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl); + } + if (pdbseq != null) + { + // just transfer the file name from the first sequence's first + // PDBEntry + file = new File(pdbseq.getSequenceAt(0).getPDBId() + .elementAt(0).getFile()).getAbsolutePath(); + jmb.getPdbEntry(pi).setFile(file); + files.append(" \"" + Platform.escapeString(file) + "\""); + } + else + { + errormsgs.append("'" + pdbid + "' "); + } + } + else + { + if (curfiles != null && curfiles.length > 0) + { + addingStructures = true; // already files loaded. + for (int c = 0; c < curfiles.length; c++) + { + if (curfiles[c].equals(file)) + { + file = null; + break; + } + } + } + if (file != null) + { + files.append(" \"" + Platform.escapeString(file) + "\""); + } + } } } catch (OutOfMemoryError oomerror) { - new OOMWarning("Retrieving PDB id " + pdbentry.getId() + " from MSD", - oomerror); + new OOMWarning("Retrieving PDB files: " + pdbid, oomerror); } catch (Exception ex) { ex.printStackTrace(); + errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid + + "'"); + } + if (errormsgs.length() > 0) + { + + JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .formatMessage("label.pdb_entries_couldnt_be_retrieved", + new String[] + { errormsgs.toString() }), MessageManager + .getString("label.couldnt_load_file"), + JOptionPane.ERROR_MESSAGE); + + } + long lastnotify = jmb.getLoadNotifiesHandled(); + if (files.length() > 0) + { + if (!addingStructures) + { + + try + { + initJmol("load FILES " + files.toString()); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("When trying to open the Jmol viewer!", oomerror); + Cache.log.debug("File locations are " + files); + } catch (Exception ex) + { + Cache.log.error("Couldn't open Jmol viewer!", ex); + } + } + else + { + StringBuffer cmd = new StringBuffer(); + cmd.append("loadingJalviewdata=true\nload APPEND "); + cmd.append(files.toString()); + cmd.append("\nloadingJalviewdata=null"); + final String command = cmd.toString(); + cmd = null; + lastnotify = jmb.getLoadNotifiesHandled(); + + try + { + jmb.evalStateCommand(command); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning( + "When trying to add structures to the Jmol viewer!", + oomerror); + Cache.log.debug("File locations are " + files); + } catch (Exception ex) + { + Cache.log.error("Couldn't add files to Jmol viewer!", ex); + } + } + + // need to wait around until script has finished + while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() + : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb + .getPdbFile().length != jmb.getPdbCount())) + { + try + { + Cache.log.debug("Waiting around for jmb notify."); + Thread.sleep(35); + } catch (Exception e) + { + } + } + // refresh the sequence colours for the new structure(s) + for (AlignmentPanel ap : _colourwith) + { + jmb.updateColours(ap); + } + // do superposition if asked to + if (alignAddedStructures) + { + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + alignStructs_withAllAlignPanels(); + // jmb.superposeStructures(ap.av.getAlignment(), -1, null); + } + }); + alignAddedStructures = false; + } + addingStructures = false; + } + _started = false; + worker = null; } + @Override public void pdbFile_actionPerformed(ActionEvent actionEvent) { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache - .getProperty("LAST_DIRECTORY")); + JalviewFileChooser chooser = new JalviewFileChooser( + jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save PDB File"); - chooser.setToolTipText("Save"); + chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file")); + chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -394,8 +815,9 @@ public class AppJmol extends GStructureViewer implements StructureListener, { try { - BufferedReader in = new BufferedReader(new FileReader(pdbentry - .getFile())); + // TODO: cope with multiple PDB files in view + BufferedReader in = new BufferedReader(new FileReader( + jmb.getPdbFile()[0])); File outFile = chooser.getSelectedFile(); PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); @@ -415,181 +837,199 @@ public class AppJmol extends GStructureViewer implements StructureListener, } } + @Override public void viewMapping_actionPerformed(ActionEvent actionEvent) { jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); - jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", - 550, 600); - cap.setText(StructureSelectionManager.getStructureSelectionManager() - .printMapping(pdbentry.getFile())); + 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); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ + @Override public void eps_actionPerformed(ActionEvent e) { - makePDBImage(jalview.util.ImageMaker.EPS); + makePDBImage(jalview.util.ImageMaker.TYPE.EPS); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ + @Override public void png_actionPerformed(ActionEvent e) { - makePDBImage(jalview.util.ImageMaker.PNG); + makePDBImage(jalview.util.ImageMaker.TYPE.PNG); } - void makePDBImage(int type) + void makePDBImage(jalview.util.ImageMaker.TYPE type) { int width = getWidth(); int height = getHeight(); jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + if (type == jalview.util.ImageMaker.TYPE.PNG) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view", width, height, null, null); } + else if (type == jalview.util.ImageMaker.TYPE.EPS) + { + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.EPS, + "Make EPS file from view", width, height, null, + this.getTitle()); + } else { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Make EPS file from view", width, height, null, this - .getTitle()); + + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", + width, height, null, this.getTitle()); } if (im.getGraphics() != null) { Rectangle rect = new Rectangle(width, height); - viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect); + jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect); im.writeImage(); } } + @Override + public void viewerColour_actionPerformed(ActionEvent actionEvent) + { + if (viewerColour.isSelected()) + { + // disable automatic sequence colouring. + jmb.setColourBySequence(false); + } + } + + @Override public void seqColour_actionPerformed(ActionEvent actionEvent) { - lastCommand = null; - colourBySequence = seqColour.isSelected(); - colourBySequence(ap.alignFrame.alignPanel); + jmb.setColourBySequence(seqColour.isSelected()); + if (_colourwith == null) + { + _colourwith = new Vector(); + } + 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.av.isShowSequenceFeatures(), ap); + } + } } + @Override public void chainColour_actionPerformed(ActionEvent actionEvent) { - colourBySequence = false; - seqColour.setSelected(false); - jmolHistory(false); - viewer.evalStringQuiet("select *;color chain"); - jmolHistory(true); + chainColour.setSelected(true); + jmb.colourByChain(); } + @Override public void chargeColour_actionPerformed(ActionEvent actionEvent) { - colourBySequence = false; - seqColour.setSelected(false); - jmolHistory(false); - viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;" - + "select LYS,ARG;color blue;select CYS;color yellow"); - jmolHistory(true); + chargeColour.setSelected(true); + jmb.colourByCharge(); } + @Override public void zappoColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new ZappoColourScheme()); + zappoColour.setSelected(true); + jmb.setJalviewColourScheme(new ZappoColourScheme()); } + @Override public void taylorColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new TaylorColourScheme()); + taylorColour.setSelected(true); + jmb.setJalviewColourScheme(new TaylorColourScheme()); } + @Override public void hydroColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new HydrophobicColourScheme()); + hydroColour.setSelected(true); + jmb.setJalviewColourScheme(new HydrophobicColourScheme()); } + @Override public void helixColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new HelixColourScheme()); + helixColour.setSelected(true); + jmb.setJalviewColourScheme(new HelixColourScheme()); } + @Override public void strandColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new StrandColourScheme()); + strandColour.setSelected(true); + jmb.setJalviewColourScheme(new StrandColourScheme()); } + @Override public void turnColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new TurnColourScheme()); + turnColour.setSelected(true); + jmb.setJalviewColourScheme(new TurnColourScheme()); } + @Override public void buriedColour_actionPerformed(ActionEvent actionEvent) { - setJalviewColourScheme(new BuriedColourScheme()); + buriedColour.setSelected(true); + jmb.setJalviewColourScheme(new BuriedColourScheme()); } - public void setJalviewColourScheme(ColourSchemeI cs) + @Override + public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) { - jmolHistory(false); - colourBySequence = false; - seqColour.setSelected(false); - - if (cs == null) - return; - - String res; - int index; - Color col; - - Enumeration en = ResidueProperties.aa3Hash.keys(); - StringBuffer command = new StringBuffer("select *;color white;"); - while (en.hasMoreElements()) - { - res = en.nextElement().toString(); - index = ((Integer) ResidueProperties.aa3Hash.get(res)).intValue(); - if (index > 20) - continue; - - col = cs.findColour(ResidueProperties.aa[index].charAt(0)); - - command.append("select " + res + ";color[" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); - } - - viewer.evalStringQuiet(command.toString()); - jmolHistory(true); - } + 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, - "Select Background Colour", null); - + MessageManager.getString("label.select_backgroud_colour"), null); if (col != null) { - jmolHistory(false); - viewer.evalStringQuiet("background [" + col.getRed() + "," - + col.getGreen() + "," + col.getBlue() + "];"); - jmolHistory(true); + jmb.setBackgroundColour(col); } } - private void jmolHistory(boolean enable) - { - viewer.setBooleanProperty("history", enable); - } - public void jmolHelp_actionPerformed(ActionEvent actionEvent) + @Override + public void showHelp_actionPerformed(ActionEvent actionEvent) { try { @@ -599,514 +1039,9 @@ public class AppJmol extends GStructureViewer implements StructureListener, { } } - String[] modelFileNames = null; - - // //////////////////////////////// - // /StructureListener - public String[] getPdbFile() - { - if (modelFileNames == null) - { - String mset[] = new String[viewer.getModelCount()]; - for (int i = 0; i < mset.length; i++) - { - try { - String mname = viewer.getModelFileName(i); - if (mname==null) - { - System.err.println("Model "+i+" has no filename!"); - continue; - } - File fpath = new File(mname); - mset[i] = fpath.toString(); - } catch (Exception e) - { - System.err.println("Couldn't parse "+viewer.getModelFileName(i)+" as a file!"); - } - } - modelFileNames = mset; - } - return modelFileNames; - } - - Pattern pattern = Pattern - .compile("\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+).*(/[0-9]*)?"); - - String lastMessage; - - public void mouseOverStructure(int atomIndex, String strInfo) - { - // copied from AppJmol - will be refactored to binding eventually - int pdbResNum; - int mdlSep = strInfo.indexOf("/"); - int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; - - if (chainSeparator == -1) - { - chainSeparator = strInfo.indexOf("."); - if (mdlSep > -1 && mdlSep < chainSeparator) - { - chainSeparator1 = chainSeparator; - chainSeparator = mdlSep; - } - } - pdbResNum = Integer.parseInt(strInfo.substring( - strInfo.indexOf("]") + 1, chainSeparator)); - - String chainId; - - if (strInfo.indexOf(":") > -1) - chainId = strInfo.substring(strInfo.indexOf(":") + 1, strInfo - .indexOf(".")); - else - { - chainId = " "; - } - - String pdbfilename = pdbentry.getFile(); - if (mdlSep > -1) - { - if (chainSeparator1 == -1) - { - chainSeparator1 = strInfo.indexOf(".", mdlSep); - } - String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1, - chainSeparator1) : strInfo.substring(mdlSep + 1); - try - { - // recover PDB filename for the model hovered over. - pdbfilename = viewer - .getModelFileName(new Integer(mdlId).intValue() - 1); - } catch (Exception e) - { - } - ; - } - if (lastMessage == null || !lastMessage.equals(strInfo)) - ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename); - - lastMessage = strInfo; -/* - * Old Implementation based on Pattern regex. - Matcher matcher = pattern.matcher(strInfo); - matcher.find(); - matcher.group(1); - int pdbResNum = Integer.parseInt(matcher.group(2)); - String chainId = matcher.group(3); - - if (chainId != null) - chainId = chainId.substring(1, chainId.length()); - else - { - chainId = " "; - } - String mdlId = matcher.group(4); - String pdbfilename = pdbentry.getFile(); - - if (mdlId!=null && mdlId.length()>0) - { - try { - // recover PDB filename for the model hovered over. - pdbfilename = viewer.getModelFileName(new Integer(mdlId).intValue()-1); - } catch (Exception e) {}; - } - if (lastMessage == null || !lastMessage.equals(strInfo)) - { - ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename); - } - lastMessage = strInfo; */ - } - - StringBuffer resetLastRes = new StringBuffer(); - - StringBuffer eval = new StringBuffer(); - - public void highlightAtom(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - int mdlNum = 1+getModelNum(pdbfile); - if (mdlNum==0) - { - return; - } - - jmolHistory(false); - // if (!pdbfile.equals(pdbentry.getFile())) - // return; - if (resetLastRes.length() > 0) - { - viewer.evalStringQuiet(resetLastRes.toString()); - } - - eval.setLength(0); - eval.append("select " + pdbResNum); // +modelNum - - resetLastRes.setLength(0); - resetLastRes.append("select " + pdbResNum); // +modelNum - - if (!chain.equals(" ")) - { - eval.append(":"); - resetLastRes.append(":"); - eval.append(chain); - resetLastRes.append(chain); - } - // if (mdlNum != 0) - { - eval.append(" /" + (mdlNum)); - resetLastRes.append(" /" + (mdlNum)); - } - eval.append(";wireframe 100;" + eval.toString() + " and not hetero;"); - - resetLastRes.append(";wireframe 0;" + resetLastRes.toString() - + " and not hetero; spacefill 0;"); - - eval.append("spacefill 200;select none"); - - viewer.evalStringQuiet(eval.toString()); - jmolHistory(true); - } - - public Color getColour(int atomIndex, int pdbResNum, String chain, - String pdbfile) - { - if (!pdbfile.equals(pdbentry.getFile())) - return null; - - return new Color(viewer.getAtomArgb(atomIndex)); - } - - public void updateColours(Object source) - { - colourBySequence((AlignmentPanel) source); - } - - // End StructureListener - // ////////////////////////// - - String lastCommand; - - FeatureRenderer fr = null; - - public void colourBySequence(AlignmentPanel sourceap) - { - this.ap = sourceap; - - if (!colourBySequence || ap.alignFrame.getCurrentView() != ap.av) - return; - - String[] files = getPdbFile(); - - SequenceRenderer sr = new SequenceRenderer(ap.av); - - boolean showFeatures = false; - - if (ap.av.showSequenceFeatures) - { - showFeatures = true; - if (fr == null) - { - fr = new jalview.gui.FeatureRenderer(ap); - } - - fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); - } - - StringBuffer command = new StringBuffer(); - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - - if (mapping == null || mapping.length < 1) - continue; - - - int lastPos = -1; - for (int sp, s = 0; s < sequence.length; s++) - { - for (int m = 0; m < mapping.length; m++) - { - if (mapping[m].getSequence() == sequence[s] - && (sp = ap.av.alignment.findIndex(sequence[s])) > -1) - { - SequenceI asp = ap.av.alignment.getSequenceAt(sp); - for (int r = 0; r < asp.getLength(); r++) - { - // No mapping to gaps in sequence. - if (jalview.util.Comparison.isGap(asp.getCharAt(r))) - { - continue; - } - int pos = mapping[m].getPDBResNum(asp.findPosition(r)); - - if (pos < 1 || pos == lastPos) - continue; - - lastPos = pos; - - Color col = sr.getResidueBoxColour(asp, r); - - if (showFeatures) - col = fr.findFeatureColour(col, asp, r); - String newSelcom = (mapping[m].getChain() != " " ? ":" - + mapping[m].getChain() : "") - + "/" - + (pdbfnum + 1) - + ".1" - + ";color[" - + col.getRed() - + "," - + col.getGreen() - + "," - + col.getBlue() + "]"; - if (command.toString().endsWith(newSelcom)) - { - command = condenseCommand(command, pos); - continue; - } - - command.append(";select " + pos); - command.append(newSelcom); - } - break; - } - } - } - } - jmolHistory(false); - - if (lastCommand == null || !lastCommand.equals(command.toString())) - { - viewer.evalStringQuiet(command.toString()); - } - jmolHistory(true); - lastCommand = command.toString(); - } - - StringBuffer condenseCommand(StringBuffer command, int pos) - { - StringBuffer sb = new StringBuffer(command.substring(0, command - .lastIndexOf("select") + 7)); - - command.delete(0, sb.length()); - - String start; - - if (command.indexOf("-") > -1) - { - start = command.substring(0, command.indexOf("-")); - } - else - { - start = command.substring(0, command.indexOf(":")); - } - - sb.append(start + "-" + pos + command.substring(command.indexOf(":"))); - - return sb; - } - - // /////////////////////////////// - // JmolStatusListener - - public String eval(String strEval) - { - // System.out.println(strEval); - // "# 'eval' is implemented only for the applet."; - return null; - } - - public void createImage(String file, String type, int quality) - { - System.out.println("JMOL CREATE IMAGE"); - } - - public void notifyFileLoaded(String fullPathName, String fileName2, - String modelName, String errorMsg, int modelParts) - { - if (errorMsg != null) - { - fileLoadingError = errorMsg; - repaint(); - return; - } - - fileLoadingError = null; - modelFileNames = null; - - String[] modelfilenames = getPdbFile(); - ssm = StructureSelectionManager.getStructureSelectionManager(); - boolean modelsloaded=false; - for (int modelnum = 0; modelnum < modelfilenames.length; modelnum++) - { - String fileName = modelfilenames[modelnum]; - - if (fileName != null) - { - modelsloaded=true; - // search pdbentries and sequences to find correct pdbentry and sequence[] pair for this filename - if (pdbentry.getFile().equals(fileName)) - { - // TODO: do some checking using the modelPts number of parts against our - // own estimate of the number of chains - // FILE LOADED OK - MCview.PDBfile pdbFile = ssm.setMapping(sequence, chains, pdbentry - .getFile(), AppletFormatAdapter.FILE); - Vector chains = new Vector(); - for (int i = 0; i < pdbFile.chains.size(); i++) - { - chains - .addElement(new String(pdbFile.id+":"+((MCview.PDBChain) pdbFile.chains.elementAt(i)).id)); - } - setChainMenuItems(chains); - - if (!loadingFromArchive) - { - viewer - .evalStringQuiet("model 0; select backbone;restrict;cartoon;wireframe off;spacefill off"); - - colourBySequence(ap); - } - if (fr != null) - fr.featuresAdded(); - - loadingFromArchive = false; - } - else { - // this is a foreign pdb file that jalview doesn't know about - add it to the dataset - // and try to find a home - either on a matching sequence or as a new sequence. - String pdbcontent = viewer.getData("/" + (modelnum + 1) + ".1", - "PDB"); - // parse pdb file into a chain, etc. - // locate best match for pdb in associated views and add mapping to - // ssm - modelsloaded=true; - } - } - } - if (modelsloaded) - { - ssm.addStructureViewerListener(this); - jmolpopup.updateComputedMenus(); - } - } - - public void sendConsoleEcho(String strEcho) - { - if (scriptWindow != null) - scriptWindow.sendConsoleEcho(strEcho); - } - - public void sendConsoleMessage(String strStatus) - { - if (scriptWindow != null) - scriptWindow.sendConsoleMessage(strStatus); - } - - public void notifyScriptTermination(String strStatus, int msWalltime) - { - if (scriptWindow != null) - scriptWindow.notifyScriptTermination(strStatus, msWalltime); - } - - public void handlePopupMenu(int x, int y) - { - jmolpopup.show(x, y); - } - - public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) - { - notifyAtomPicked(iatom, strMeasure, null); - } - - public void notifyAtomPicked(int atomIndex, String strInfo, String strData) - { - if (strData != null) - { - Cache.log.info("Non null pick data string: " + strData - + " (other info: '" + strInfo + "' pos " + atomIndex + ")"); - } - /* - Matcher matcher = pattern.matcher(strInfo); - matcher.find(); - - matcher.group(1); - String resnum = new String(matcher.group(2)); - String chainId = matcher.group(3); - - String picked = resnum; - - - if (chainId != null) - picked += (":" + chainId.substring(1, chainId.length())); -*/ - int chainSeparator = strInfo.indexOf(":"); - int p=0; - if (chainSeparator == -1) - chainSeparator = strInfo.indexOf("."); - - String picked = strInfo.substring(strInfo.indexOf("]") + 1, - chainSeparator); - String mdlString=""; - if ((p=strInfo.indexOf(":")) > -1) - picked += strInfo.substring(p + 1, strInfo - .indexOf(".")); - - if ((p=strInfo.indexOf("/"))> -1) - { - mdlString += strInfo.substring(p, strInfo.indexOf(" #")); - } - picked = "((" + picked + ".CA" + mdlString+")|(" + picked + ".P" + mdlString+"))"; - jmolHistory(false); - if (!atomsPicked.contains(picked)) - { - // TODO: re-instate chain ID separator dependent labelling for both applet and application -// if (chainId != null) - viewer.evalString("select " + picked + ";label %n %r:%c"); -// else -// viewer.evalString("select " + picked + ";label %n %r"); - atomsPicked.addElement(picked); - } - else - { - viewer.evalString("select " + picked + ";label off"); - atomsPicked.removeElement(picked); - } - jmolHistory(true); - if (scriptWindow != null) - { - scriptWindow.sendConsoleMessage(strInfo); - scriptWindow.sendConsoleMessage("\n"); - } - } - - public void notifyAtomHovered(int atomIndex, String strInfo, String data) - { - if (data != null) - { - Cache.log.info("Non null hover data string: " + data - + " (other info: '" + strInfo + "' pos " + atomIndex + ")"); - } - mouseOverStructure(atomIndex, strInfo); - } - - @Override - public void showUrl(String url) - { - try - { - jalview.util.BrowserLauncher.openURL(url); - } catch (IOException e) - { - Cache.log.error("Failed to launch Jmol-associated url " + url, e); - // TODO: 2.6 : warn user if browser was not configured. - } - } public void showConsole(boolean showConsole) { - if (scriptWindow == null) - scriptWindow = new ScriptWindow(this); if (showConsole) { @@ -1116,15 +1051,19 @@ public class AppJmol extends GStructureViewer implements StructureListener, 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; @@ -1134,14 +1073,6 @@ public class AppJmol extends GStructureViewer implements StructureListener, validate(); } - public float[][] functionXY(String functionName, int x, int y) - { - return null; - } - - // /End JmolStatusListener - // ///////////////////////////// - class RenderPanel extends JPanel { final Dimension currentSize = new Dimension(); @@ -1153,137 +1084,161 @@ public class AppJmol extends GStructureViewer implements StructureListener, getSize(currentSize); g.getClipBounds(rectClip); - if (viewer == null) + if (jmb != null && jmb.fileLoadingError != null) { 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); + 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.getPdbCount(); e++) + { + sb.append(jmb.getPdbEntry(e).getId()); + if (e < jmb.getPdbCount() - 1) + { + sb.append(","); + } + + if (e == jmb.getPdbCount() - 1 || sb.length() > 20) + { + lines++; + g.drawString(sb.toString(), 20, currentSize.height / 2 - lines + * g.getFontMetrics().getHeight()); + } + } } - else if (fileLoadingError != null) + 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("Error loading file..." + pdbentry.getId(), 20, - currentSize.height / 2); + g.drawString(MessageManager.getString("label.retrieving_pdb_data"), + 20, currentSize.height / 2); } else { - viewer.renderScreenImage(g, currentSize, rectClip); + jmb.viewer.renderScreenImage(g, currentSize, rectClip); } } } - String viewId = null; - - public String getViewId() + public void updateTitleAndMenus() { - if (viewId == null) + 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()) { - viewId = System.currentTimeMillis() + "." + this.hashCode(); + seqColour_actionPerformed(null); } - return viewId; } + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event + * .ActionEvent) + */ @Override - public String createImage(String fileName, String type, - Object textOrBytes, int quality) + protected void alignStructs_actionPerformed(ActionEvent actionEvent) { - // TODO Auto-generated method stub - return null; + alignStructs_withAllAlignPanels(); } - @Override - public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) + private void alignStructs_withAllAlignPanels() { - // TODO Auto-generated method stub - return null; + 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 Hashtable getRegistryInfo() + public void setJalviewColourScheme(ColourSchemeI ucs) { - // TODO Auto-generated method stub - return null; + jmb.setJalviewColourScheme(ucs); + } - @Override - public void notifyCallback(int type, Object[] data) + /** + * + * @param alignment + * @return first alignment panel displaying given alignment, or the default + * alignment panel + */ + public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) { - try + for (AlignmentPanel ap : getAllAlignmentPanels()) { - switch (type) + if (ap.av.getAlignment() == alignment) { - case JmolConstants.CALLBACK_LOADSTRUCT: - notifyFileLoaded((String) data[1], (String) data[2], - (String) data[3], (String) data[4], ((Integer) data[5]) - .intValue()); - - break; - case JmolConstants.CALLBACK_PICK: - notifyAtomPicked(((Integer) data[2]).intValue(), (String) data[1], - (String) data[0]); - // also highlight in alignment - case JmolConstants.CALLBACK_HOVER: - notifyAtomHovered(((Integer) data[2]).intValue(), (String) data[1], - (String) data[0]); - break; - case JmolConstants.CALLBACK_SCRIPT: - notifyScriptTermination((String) data[2], ((Integer) data[3]) - .intValue()); - break; - case JmolConstants.CALLBACK_ECHO: - sendConsoleEcho((String) data[1]); - break; - case JmolConstants.CALLBACK_MESSAGE: - sendConsoleMessage((data == null) ? ((String) null) - : (String) data[1]); - break; - case JmolConstants.CALLBACK_MEASURE: - case JmolConstants.CALLBACK_CLICK: - default: - System.err.println("Unhandled callback " + type + " " + data); - break; + return ap; } - } catch (Exception e) - { - Cache.log.warn("Squashed Jmol callback handler error: ", e); } + return getAlignmentPanel(); } @Override - public boolean notifyEnabled(int callbackPick) + public AAStructureBindingModel getBinding() { - switch (callbackPick) - { - case JmolConstants.CALLBACK_ECHO: - case JmolConstants.CALLBACK_LOADSTRUCT: - case JmolConstants.CALLBACK_MEASURE: - case JmolConstants.CALLBACK_MESSAGE: - case JmolConstants.CALLBACK_PICK: - case JmolConstants.CALLBACK_SCRIPT: - case JmolConstants.CALLBACK_HOVER: - case JmolConstants.CALLBACK_ERROR: - return true; - case JmolConstants.CALLBACK_CLICK: - case JmolConstants.CALLBACK_ANIMFRAME: - case JmolConstants.CALLBACK_MINIMIZATION: - case JmolConstants.CALLBACK_RESIZE: - case JmolConstants.CALLBACK_SYNC: - } - return false; + return this.jmb; } @Override - public void setCallbackFunction(String callbackType, - String callbackFunction) + public String getStateInfo() { - Cache.log.debug("Ignoring set-callback request to associate " - + callbackType + " with function " + callbackFunction); + return jmb == null ? null : jmb.viewer.getStateInfo(); + } + @Override + public ViewerType getViewerType() + { + return ViewerType.JMOL; } }