X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=24604ed30a7eee9b31c738605b8ce4affae0f386;hb=853624fb32058cccc544ae7d13af6ad4b0800b6c;hp=a5006143922ff27bac244569bc4181f113252f61;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index a500614..24604ed 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,45 +1,88 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * Copyright (C) 2014 The Jalview Authors + * 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.*; -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.ViewSelectionMenu.ViewSetProvider; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; -import jalview.io.*; -import jalview.schemes.*; +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.MessageManager; import jalview.util.Platform; +import jalview.ws.dbsources.Pdb; + +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.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 +{ + private static final String SPACE = " "; -public class AppJmol extends GStructureViewer implements Runnable, - SequenceStructureBinding, ViewSetProvider + private static final String BACKSLASH = "\""; -{ AppJmolBinding jmb; JPanel scriptWindow; @@ -48,41 +91,6 @@ public class AppJmol extends GStructureViewer implements Runnable, RenderPanel renderPanel; - AlignmentPanel ap; - - 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); - */ - public AppJmol(String file, String id, SequenceI[] seq, - AlignmentPanel ap, String loadStatus, Rectangle bounds) - { - this(file, id, seq, ap, loadStatus, bounds, null); - } - - /** - * @deprecated - */ - public AppJmol(String file, String id, SequenceI[] seq, - AlignmentPanel ap, String loadStatus, Rectangle bounds, - String viewid) - { - this(new String[] - { file }, new String[] - { id }, new SequenceI[][] - { seq }, ap, true, true, false, loadStatus, bounds, viewid); - } - ViewSelectionMenu seqColourBy; /** @@ -112,9 +120,9 @@ public class AppJmol extends GStructureViewer implements Runnable, PDBEntry[] pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < pdbentrys.length; i++) { - PDBEntry pdbentry = new PDBEntry(); - pdbentry.setFile(files[i]); - pdbentry.setId(ids[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 @@ -132,26 +140,27 @@ public class AppJmol extends GStructureViewer implements Runnable, { jmb.setColourBySequence(false); seqColour.setSelected(false); - jmolColour.setSelected(true); + viewerColour.setSelected(true); } - if (usetoColour) + else if (usetoColour) { useAlignmentPanelForColourbyseq(ap); jmb.setColourBySequence(true); seqColour.setSelected(true); - jmolColour.setSelected(false); + viewerColour.setSelected(false); } this.setBounds(bounds); initMenus(); - viewId = viewid; + setViewId(viewid); // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); initJmol(loadStatus); // pdbentry, seq, JBPCHECK! @@ -161,7 +170,7 @@ public class AppJmol extends GStructureViewer implements Runnable, private void initMenus() { seqColour.setSelected(jmb.isColourBySequence()); - jmolColour.setSelected(!jmb.isColourBySequence()); + viewerColour.setSelected(!jmb.isColourBySequence()); if (_colourwith == null) { _colourwith = new Vector(); @@ -171,7 +180,8 @@ public class AppJmol extends GStructureViewer implements Runnable, _alignwith = new Vector(); } - seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith, + seqColourBy = new ViewSelectionMenu( + MessageManager.getString("label.colour_by"), this, _colourwith, new ItemListener() { @@ -191,7 +201,8 @@ public class AppJmol extends GStructureViewer implements Runnable, }); viewMenu.add(seqColourBy); final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this, + JMenu alpanels = new ViewSelectionMenu( + MessageManager.getString("label.superpose_with"), this, _alignwith, handler = new ItemListener() { @@ -199,13 +210,16 @@ public class AppJmol extends GStructureViewer implements Runnable, public void itemStateChanged(ItemEvent e) { alignStructs.setEnabled(_alignwith.size() > 0); - alignStructs.setToolTipText("Align structures using " - + _alignwith.size() + " linked alignment views"); + alignStructs.setToolTipText(MessageManager + .formatMessage( + "label.align_structures_using_linked_alignment_views", + new String[] { new Integer(_alignwith + .size()).toString() })); } }); handler.itemStateChanged(null); - jmolActionMenu.add(alpanels); - jmolActionMenu.addMenuListener(new MenuListener() + viewerActionMenu.add(alpanels); + viewerActionMenu.addMenuListener(new MenuListener() { @Override @@ -244,89 +258,39 @@ public class AppJmol extends GStructureViewer implements Runnable, final AlignmentPanel ap) { progressBar = ap.alignFrame; - // //////////////////////////////// - // Is the pdb file already loaded? - String alreadyMapped = ap.getStructureSelectionManager() - .alreadyMappedToFile(pdbentry.getId()); + String pdbId = pdbentry.getId(); - if (alreadyMapped != null) + /* + * If the PDB file is already loaded, the user may just choose to add to an + * existing viewer (or cancel) + */ + if (addAlreadyLoadedFile(seq, chains, ap, pdbId)) { - 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) - { - // TODO : Fix multiple seq to one chain issue here. - ap.getStructureSelectionManager().setMapping(seq, chains, - alreadyMapped, AppletFormatAdapter.FILE); - if (ap.seqPanel.seqCanvas.fr != null) - { - ap.seqPanel.seqCanvas.fr.featuresAdded(); - ap.paintAlignment(true); - } - - // Now this AppJmol is mapped to new sequences. We must add them to - // the exisiting array - JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (int i = 0; i < frames.length; i++) - { - if (frames[i] instanceof AppJmol) - { - 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.pdbentry.length; pe++) - { - if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped)) - { - topJmol.jmb.addSequence(pe, seq); - topJmol.addAlignmentPanel(ap); - // add it to the set used for colouring - topJmol.useAlignmentPanelForColourbyseq(ap); - topJmol.buildJmolActionMenu(); - ap.getStructureSelectionManager() - .sequenceColoursChanged(ap); - break; - } - } - } - } - - return; - } + return; } - // ///////////////////////////////// - // 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) + + /* + * Check if there are other Jmol views involving this alignment and prompt + * user about adding this molecule to one of them + */ + if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId)) { - Enumeration jm = existingViews.elements(); - while (jm.hasMoreElements()) - { - AppJmol topJmol = (AppJmol) jm.nextElement(); - // TODO: highlight topJmol in view somehow - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - "Do you want to add " + pdbentry.getId() - + " to the view called\n'" + topJmol.getTitle() - + "'\n", "Align to existing structure view", - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) - { - topJmol.useAlignmentPanelForSuperposition(ap); - topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); - return; - } - } + return; } - // ///////////////////////////////// - openNewJmol(ap, new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }); + + /* + * If the options above are declined or do not apply, open a new viewer + */ + 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, @@ -353,9 +317,10 @@ public class AppJmol extends GStructureViewer implements Runnable, } this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); @@ -375,212 +340,27 @@ public class AppJmol extends GStructureViewer implements Runnable, } /** - * list of sequenceSet ids associated with the view - */ - ArrayList _aps = new ArrayList(); - - public AlignmentPanel[] getAllAlignmentPanels() - { - AlignmentPanel[] t, list = new AlignmentPanel[0]; - for (String setid : _aps) - { - AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid); - if (panels != null) - { - t = new AlignmentPanel[list.length + panels.length]; - System.arraycopy(list, 0, t, 0, list.length); - System.arraycopy(panels, 0, t, list.length, panels.length); - list = t; - } - } - - return list; - } - - /** - * list of alignment panels to use for superposition - */ - Vector _alignwith = new Vector(); - - /** - * list of alignment panels that are used for colouring structures by aligned - * sequences - */ - Vector _colourwith = new Vector(); - - /** - * set the primary alignmentPanel reference and add another alignPanel to the - * list of ones to use for colouring and aligning - * - * @param nap - */ - public void addAlignmentPanel(AlignmentPanel nap) - { - if (ap == null) - { - ap = nap; - } - if (!_aps.contains(nap.av.getSequenceSetId())) - { - _aps.add(nap.av.getSequenceSetId()); - } - } - - /** - * remove any references held to the given alignment panel - * - * @param nap - */ - public void removeAlignmentPanel(AlignmentPanel nap) - { - try - { - _alignwith.remove(nap); - _colourwith.remove(nap); - if (ap == nap) - { - ap = null; - for (AlignmentPanel aps : getAllAlignmentPanels()) - { - if (aps != nap) - { - ap = aps; - break; - } - } - } - } catch (Exception ex) - { - } - if (ap != null) - { - buildJmolActionMenu(); - } - } - - public void useAlignmentPanelForSuperposition(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_alignwith.contains(nap)) - { - _alignwith.add(nap); - } - } - - public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap) - { - if (_alignwith.contains(nap)) - { - _alignwith.remove(nap); - } - } - - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, - boolean enableColourBySeq) - { - useAlignmentPanelForColourbyseq(nap); - jmb.setColourBySequence(enableColourBySeq); - seqColour.setSelected(enableColourBySeq); - jmolColour.setSelected(!enableColourBySeq); - } - - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_colourwith.contains(nap)) - { - _colourwith.add(nap); - } - } - - public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - if (_colourwith.contains(nap)) - { - _colourwith.remove(nap); - } - } - - /** - * pdb retrieval thread. - */ - private Thread worker = 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 + * Returns a list of any Jmol viewers. The list is restricted to those linked + * to the given alignment panel if it is not null. */ - private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq, - final String[] chains, final boolean b, - final IProgressIndicator alignFrame) - { - if (pdbentry.getFile() == null) - { - if (worker != null && worker.isAlive()) - { - // 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; - } - } - // 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 ap2) + @Override + protected List getViewersFor(AlignmentPanel apanel) { - Vector otherJmols = new Vector(); - // Now this AppJmol is mapped to new sequences. We must add them to - // the exisiting array + List result = new ArrayList(); JInternalFrame[] frames = Desktop.instance.getAllFrames(); - for (int i = 0; i < frames.length; i++) + for (JInternalFrame frame : frames) { - if (frames[i] instanceof AppJmol) + if (frame instanceof AppJmol) { - AppJmol topJmol = ((AppJmol) frames[i]); - if (topJmol.isLinkedWith(ap2)) + if (apanel == null + || ((StructureViewerBase) frame).isLinkedWith(apanel)) { - otherJmols.addElement(topJmol); + result.add((StructureViewerBase) frame); } } } - return otherJmols; + return result; } void initJmol(String command) @@ -600,35 +380,43 @@ public class AppJmol extends GStructureViewer implements Runnable, scriptWindow = new JPanel(bl); scriptWindow.setVisible(false); } - ; - jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, - null); - jmb.newJmolPopup(true, "Jmol", true); + + /* + * -i for no info logging (less verbose) + */ + jmb.allocateViewer(renderPanel, true, "", null, null, "-i", + scriptWindow, null); + // jmb.newJmolPopup("Jmol"); if (command == null) { command = ""; } jmb.evalStateCommand(command); + jmb.evalStateCommand("set hoverDelay=0.1"); jmb.setFinishedInit(true); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(Vector chains) { chainMenu.removeAll(); if (chains == null) { return; } - JMenuItem menuItem = new JMenuItem("All"); + 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; @@ -637,15 +425,18 @@ public class AppJmol extends GStructureViewer implements Runnable, chainMenu.add(menuItem); - for (int c = 0; c < chains.size(); c++) + for (String chain : chains) { - menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true); + menuItem = new JCheckBoxMenuItem(chain, true); menuItem.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent evt) { if (!allChainsSelected) + { centerViewer(); + } } }); @@ -655,13 +446,9 @@ public class AppJmol extends GStructureViewer implements Runnable, boolean allChainsSelected = false; - private boolean alignAddedStructures = false; - void centerViewer() { - Vector toshow = new Vector(); - String lbl; - int mlength, p, mnum; + Vector toshow = new Vector(); for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) @@ -676,10 +463,15 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.centerViewer(toshow); } - void closeViewer() + @Override + public void closeViewer(boolean closeExternalViewer) { - jmb.closeViewer(); - ap = null; + // Jmol does not use an external viewer + if (jmb != null) + { + jmb.closeViewer(); + } + setAlignmentPanel(null); _aps.clear(); _alignwith.clear(); _colourwith.clear(); @@ -688,75 +480,221 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb = null; } + @Override + public void run() + { + _started = true; + try + { + List files = fetchPdbFiles(); + if (files.size() > 0) + { + showFilesInViewer(files); + } + } finally + { + _started = false; + worker = null; + } + } + /** - * state flag for PDB retrieval thread + * 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 */ - private boolean _started = false; + void showFilesInViewer(List files) + { + long lastnotify = jmb.getLoadNotifiesHandled(); + StringBuilder fileList = new StringBuilder(); + for (String s : files) + { + fileList.append(SPACE).append(BACKSLASH) + .append(Platform.escapeString(s)).append(BACKSLASH); + } + String filesString = fileList.toString(); - public void run() + if (!addingStructures) + { + try + { + initJmol("load FILES " + filesString); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("When trying to open the Jmol viewer!", oomerror); + Cache.log.debug("File locations are " + filesString); + } catch (Exception ex) + { + Cache.log.error("Couldn't open Jmol viewer!", ex); + } + } + else + { + StringBuilder cmd = new StringBuilder(); + cmd.append("loadingJalviewdata=true\nload APPEND "); + cmd.append(filesString); + cmd.append("\nloadingJalviewdata=null"); + final String command = cmd.toString(); + 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 " + filesString); + } catch (Exception ex) + { + Cache.log.error("Couldn't add files to Jmol viewer!", ex); + } + } + + // need to wait around until script has finished + int waitMax = 5000; // give up after 5 seconds + int waitFor = 35; + int waitTotal = 0; + while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() + : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb + .getPdbFile().length == files.size())) + { + try + { + Cache.log.debug("Waiting around for jmb notify."); + Thread.sleep(waitFor); + waitTotal += waitFor; + } catch (Exception e) + { + } + if (waitTotal > waitMax) + { + System.err.println("Timed out waiting for Jmol to load files"); + break; + } + } + + // refresh the sequence colours for the new structure(s) + for (AlignmentPanel ap : _colourwith) + { + jmb.updateColours(ap); + } + // do superposition if asked to + if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures) + { + alignAddedStructures(); + } + addingStructures = false; + } + + /** + * Queues a thread to align structures with Jalview alignments + */ + void alignAddedStructures() { - _started = true; + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + if (jmb.viewer.isScriptExecuting()) + { + SwingUtilities.invokeLater(this); + try + { + Thread.sleep(5); + } catch (InterruptedException q) + { + } + return; + } + else + { + alignStructs_withAllAlignPanels(); + } + } + }); + alignAddedStructures = false; + } + + /** + * Retrieves and saves as file any modelled PDB entries for which we do not + * already have a file saved. Returns a list of absolute paths to structure + * files which were either retrieved, or already stored but not modelled in + * the structure viewer (i.e. files to add to the viewer display). + * + * @return + */ + List fetchPdbFiles() + { + // todo - record which pdbids were successfully imported. + StringBuilder errormsgs = new StringBuilder(); + + List files = new ArrayList(); 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 + String[] filesInViewer = jmb.getPdbFile(); // 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++) + Pdb pdbclient = new Pdb(); + for (int pi = 0; pi < jmb.getPdbCount(); pi++) { - String file = jmb.pdbentry[pi].getFile(); + String file = jmb.getPdbEntry(pi).getFile(); if (file == null) { // retrieve the pdb and store it locally AlignmentI pdbseq = null; - pdbid = jmb.pdbentry[pi].getId(); + pdbid = jmb.getPdbEntry(pi).getId(); long hdl = pdbid.hashCode() - System.currentTimeMillis(); if (progressBar != null) { - progressBar.setProgressBar("Fetching PDB " + pdbid, hdl); + progressBar.setProgressBar(MessageManager.formatMessage( + "status.fetching_pdb", new String[] { pdbid }), hdl); } try { - pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi] - .getId()); + 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) + errormsgs.append("'").append(pdbid).append("'"); + } finally { - progressBar.setProgressBar("Finished.", hdl); + 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(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() - .elementAt(0)).getFile()).getAbsolutePath(); - jmb.pdbentry[pi].setFile(file); - - files.append(" \"" + Platform.escapeString(file) + "\""); + file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries() + .elementAt(0).getFile()).getAbsolutePath(); + jmb.getPdbEntry(pi).setFile(file); + files.add(file); } else { - errormsgs.append("'" + pdbid + "' "); + errormsgs.append("'").append(pdbid).append("' "); } } else { - if (curfiles != null && curfiles.length > 0) + if (filesInViewer != null && filesInViewer.length > 0) { addingStructures = true; // already files loaded. - for (int c = 0; c < curfiles.length; c++) + for (int c = 0; c < filesInViewer.length; c++) { - if (curfiles[c].equals(file)) + if (filesInViewer[c].equals(file)) { file = null; break; @@ -765,7 +703,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } if (file != null) { - files.append(" \"" + Platform.escapeString(file) + "\""); + files.add(file); } } } @@ -775,117 +713,39 @@ public class AppJmol extends GStructureViewer implements Runnable, } catch (Exception ex) { ex.printStackTrace(); - errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid - + "'"); + errormsgs.append("When retrieving pdbfiles : current was: '") + .append(pdbid).append("'"); } if (errormsgs.length() > 0) { - - 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); - + 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().length != jmb.pdbentry.length)) - { - 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; + 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("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); if (value == JalviewFileChooser.APPROVE_OPTION) { + BufferedReader in = null; try { // TODO: cope with multiple PDB files in view - BufferedReader in = new BufferedReader(new FileReader( - jmb.getPdbFile()[0])); + in = new BufferedReader(new FileReader(jmb.getPdbFile()[0])); File outFile = chooser.getSelectedFile(); PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); @@ -901,20 +761,29 @@ public class AppJmol extends GStructureViewer implements Runnable, } 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 { - for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) - { - cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile())); - cap.appendText("\n"); - } + cap.appendText(jmb.printMappings()); } catch (OutOfMemoryError e) { new OOMWarning( @@ -923,68 +792,68 @@ public class AppJmol extends GStructureViewer implements Runnable, cap.dispose(); return; } - jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", - 550, 600); + 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.TYPE.PNG, "Make PNG image from view", + width, height, null, null, null, 0, false); + } + else if (type == jalview.util.ImageMaker.TYPE.EPS) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, - "Make PNG image from view", width, height, null, null); + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view", + width, height, null, this.getTitle(), null, 0, false); } 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(), null, 0, false); } if (im.getGraphics() != null) { - Rectangle rect = new Rectangle(width, height); - jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect); + jmb.viewer.renderScreenImage(im.getGraphics(), width, height); im.writeImage(); } } - public void jmolColour_actionPerformed(ActionEvent actionEvent) + @Override + public void viewerColour_actionPerformed(ActionEvent actionEvent) { - if (jmolColour.isSelected()) + if (viewerColour.isSelected()) { // disable automatic sequence colouring. jmb.setColourBySequence(false); } } + @Override public void seqColour_actionPerformed(ActionEvent actionEvent) { jmb.setColourBySequence(seqColour.isSelected()); @@ -996,96 +865,110 @@ public class AppJmol extends GStructureViewer implements Runnable, { if (!jmb.isLoadingFromArchive()) { - if (_colourwith.size() == 0 && ap != null) + if (_colourwith.size() == 0 && getAlignmentPanel() != null) { // Make the currently displayed alignment panel the associated view - _colourwith.add(ap.alignFrame.alignPanel); + _colourwith.add(getAlignmentPanel().alignFrame.alignPanel); } } // Set the colour using the current view for the associated alignframe for (AlignmentPanel ap : _colourwith) { - jmb.colourBySequence(ap.av.showSequenceFeatures, ap); + 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, - "Select Background Colour", null); + java.awt.Color col = JColorChooser + .showDialog(this, MessageManager + .getString("label.select_backgroud_colour"), null); if (col != null) { jmb.setBackgroundColour(col); } } - public void jmolHelp_actionPerformed(ActionEvent actionEvent) + @Override + public void showHelp_actionPerformed(ActionEvent actionEvent) { try { @@ -1133,31 +1016,30 @@ public class AppJmol extends GStructureViewer implements Runnable, { 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.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("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++) + 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 @@ -1171,26 +1053,17 @@ public class AppJmol extends GStructureViewer implements Runnable, 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.retrieving_pdb_data"), + 20, currentSize.height / 2); } else { - jmb.viewer.renderScreenImage(g, currentSize, rectClip); + jmb.viewer.renderScreenImage(g, currentSize.width, + currentSize.height); } } } - String viewId = null; - - public String getViewId() - { - if (viewId == null) - { - viewId = System.currentTimeMillis() + "." + this.hashCode(); - } - return viewId; - } - public void updateTitleAndMenus() { if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) @@ -1201,9 +1074,9 @@ public class AppJmol extends GStructureViewer implements Runnable, setChainMenuItems(jmb.chainNames); this.setTitle(jmb.getViewerTitle()); - if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1) + if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) { - jmolActionMenu.setVisible(true); + viewerActionMenu.setVisible(true); } if (!jmb.isLoadingFromArchive()) { @@ -1211,27 +1084,6 @@ public class AppJmol extends GStructureViewer implements Runnable, } } - protected void buildJmolActionMenu() - { - if (_alignwith == null) - { - _alignwith = new Vector(); - } - if (_alignwith.size() == 0 && ap != null) - { - _alignwith.add(ap); - } - ; - for (Component c : jmolActionMenu.getMenuComponents()) - { - if (c != alignStructs) - { - jmolActionMenu.remove((JMenuItem) c); - } - } - final ItemListener handler; - } - /* * (non-Javadoc) * @@ -1247,14 +1099,14 @@ public class AppJmol extends GStructureViewer implements Runnable, private void alignStructs_withAllAlignPanels() { - if (ap == null) + if (getAlignmentPanel() == null) { return; } ; if (_alignwith.size() == 0) { - _alignwith.add(ap); + _alignwith.add(getAlignmentPanel()); } ; try @@ -1285,6 +1137,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } + @Override public void setJalviewColourScheme(ColourSchemeI ucs) { jmb.setJalviewColourScheme(ucs); @@ -1306,37 +1159,31 @@ public class AppJmol extends GStructureViewer implements Runnable, return ap; } } - return ap; + return getAlignmentPanel(); } - /** - * - * @param ap2 - * @return true if this Jmol instance is linked with the given alignPanel - */ - public boolean isLinkedWith(AlignmentPanel ap2) + @Override + public AAStructureBindingModel getBinding() { - return _aps.contains(ap2.av.getSequenceSetId()); + return this.jmb; } - public boolean isUsedforaligment(AlignmentPanel ap2) + @Override + public String getStateInfo() { - - return (_alignwith != null) && _alignwith.contains(ap2); + return jmb == null ? null : jmb.viewer.getStateInfo(); } - public boolean isUsedforcolourby(AlignmentPanel ap2) + @Override + public ViewerType getViewerType() { - return (_colourwith != null) && _colourwith.contains(ap2); + return ViewerType.JMOL; } - /** - * - * @return TRUE if the view is NOT being coloured by sequence associations. - */ - public boolean isColouredByJmol() + @Override + protected AAStructureBindingModel getBindingModel() { - return !jmb.isColourBySequence(); + return jmb; } }