X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=c9f275b56d87ef1c7c2dac1c8be98b96198ed1ad;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=103d8cbdbdc3ddd39b5b8d5d9455ac803b93095c;hpb=fa43d97147c913accb1559c07980991cea6025f0;p=jalview.git diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index 103d8cb..c9f275b 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -1,78 +1,124 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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.appletgui; -import java.util.*; -import java.awt.*; -import java.awt.event.*; - -import jalview.api.SequenceStructureBinding; -import jalview.datamodel.*; -import jalview.structure.*; -import jalview.io.*; - -import org.jmol.api.*; - -import org.jmol.popup.*; -import org.jmol.viewer.JmolConstants; - -import jalview.schemes.*; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; +import jalview.io.FileParse; +import jalview.schemes.BuriedColourScheme; +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.UserColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.Menu; +import java.awt.MenuBar; +import java.awt.MenuItem; +import java.awt.Panel; +import java.awt.TextArea; +import java.awt.TextField; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.KeyEvent; +import java.awt.event.KeyListener; +import java.awt.event.WindowAdapter; +import java.awt.event.WindowEvent; +import java.util.ArrayList; +import java.util.Hashtable; +import java.util.List; +import java.util.Vector; public class AppletJmol extends EmbmenuFrame implements // StructureListener, - KeyListener, ActionListener, ItemListener, SequenceStructureBinding + KeyListener, ActionListener, ItemListener { - Menu fileMenu = new Menu("File"); + Menu fileMenu = new Menu(MessageManager.getString("action.file")); + + Menu viewMenu = new Menu(MessageManager.getString("action.view")); + + Menu coloursMenu = new Menu(MessageManager.getString("action.colour")); - Menu viewMenu = new Menu("View"); + Menu chainMenu = new Menu(MessageManager.getString("action.show_chain")); - Menu coloursMenu = new Menu("Colours"); + Menu helpMenu = new Menu(MessageManager.getString("action.help")); - Menu chainMenu = new Menu("Show Chain"); + MenuItem mappingMenuItem = new MenuItem( + MessageManager.getString("label.view_mapping")); - Menu helpMenu = new Menu("Help"); + CheckboxMenuItem seqColour = new CheckboxMenuItem( + MessageManager.getString("action.by_sequence"), true); - MenuItem mappingMenuItem = new MenuItem("View Mapping"); + CheckboxMenuItem jmolColour = new CheckboxMenuItem( + MessageManager.getString("action.using_jmol"), false); - CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true); + MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain")); - MenuItem chain = new MenuItem("By Chain"); + MenuItem charge = new MenuItem( + MessageManager.getString("label.charge_cysteine")); - MenuItem charge = new MenuItem("Charge & Cysteine"); + MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo")); - MenuItem zappo = new MenuItem("Zappo"); + MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor")); - MenuItem taylor = new MenuItem("Taylor"); + MenuItem hydro = new MenuItem( + MessageManager.getString("label.hydrophobicity")); - MenuItem hydro = new MenuItem("Hydrophobicity"); + MenuItem helix = new MenuItem( + MessageManager.getString("label.helix_propensity")); - MenuItem helix = new MenuItem("Helix Propensity"); + MenuItem strand = new MenuItem( + MessageManager.getString("label.strand_propensity")); - MenuItem strand = new MenuItem("Strand Propensity"); + MenuItem turn = new MenuItem( + MessageManager.getString("label.turn_propensity")); - MenuItem turn = new MenuItem("Turn Propensity"); + MenuItem buried = new MenuItem( + MessageManager.getString("label.buried_index")); - MenuItem buried = new MenuItem("Buried Index"); + MenuItem purinepyrimidine = new MenuItem( + MessageManager.getString("label.purine_pyrimidine")); - MenuItem user = new MenuItem("User Defined Colours"); + MenuItem user = new MenuItem( + MessageManager.getString("label.user_defined_colours")); - MenuItem jmolHelp = new MenuItem("Jmol Help"); + MenuItem jmolHelp = new MenuItem( + MessageManager.getString("label.jmol_help")); Panel scriptWindow; @@ -84,6 +130,9 @@ public class AppletJmol extends EmbmenuFrame implements AlignmentPanel ap; + List _aps = new ArrayList(); // remove? never + // added to + String fileLoadingError; boolean loadedInline; @@ -99,12 +148,39 @@ public class AppletJmol extends EmbmenuFrame implements */ String protocol = null; + /** + * Load a bunch of pdb entries associated with sequences in the alignment and + * display them - aligning them if necessary. + * + * @param pdbentries + * each pdb file (at least one needed) + * @param boundseqs + * each set of sequences for each pdb file (must match number of pdb + * files) + * @param boundchains + * the target pdb chain corresponding with each sequence associated + * with each pdb file (may be null at any level) + * @param align + * true/false + * @param ap + * associated alignment + * @param protocol + * how to get pdb data + */ + public AppletJmol(PDBEntry[] pdbentries, SequenceI[][] boundseqs, + String[][] boundchains, boolean align, AlignmentPanel ap, + String protocol) + { + throw new Error(MessageManager.getString("error.not_yet_implemented")); + } + public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, AlignmentPanel ap, String protocol) { this.ap = ap; - jmb = new AppletJmolBinding(this, new PDBEntry[] - { pdbentry }, seq, chains, protocol); + jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(), + new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }, + new String[][] { chains }, protocol); jmb.setColourBySequence(true); if (pdbentry.getId() == null || pdbentry.getId().length() < 1) { @@ -126,13 +202,14 @@ public class AppletJmol extends EmbmenuFrame implements } String alreadyMapped = StructureSelectionManager - .getStructureSelectionManager().alreadyMappedToFile( - pdbentry.getId()); + .getStructureSelectionManager(ap.av.applet) + .alreadyMappedToFile(pdbentry.getId()); MCview.PDBfile reader = null; if (alreadyMapped != null) { - reader = StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, chains, pdbentry.getFile(), protocol); + reader = StructureSelectionManager.getStructureSelectionManager( + ap.av.applet).setMapping(seq, chains, pdbentry.getFile(), + protocol); // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW? // FOR NOW, LETS JUST OPEN A NEW WINDOW } @@ -149,12 +226,14 @@ public class AppletJmol extends EmbmenuFrame implements hydro.addActionListener(this); chain.addActionListener(this); seqColour.addItemListener(this); + jmolColour.addItemListener(this); zappo.addActionListener(this); taylor.addActionListener(this); helix.addActionListener(this); strand.addActionListener(this); turn.addActionListener(this); buried.addActionListener(this); + purinepyrimidine.addActionListener(this); user.addActionListener(this); jmolHelp.addActionListener(this); @@ -169,20 +248,26 @@ public class AppletJmol extends EmbmenuFrame implements coloursMenu.add(strand); coloursMenu.add(turn); coloursMenu.add(buried); + coloursMenu.add(purinepyrimidine); coloursMenu.add(user); - + coloursMenu.add(jmolColour); helpMenu.add(jmolHelp); + this.setLayout(new BorderLayout()); setMenuBar(menuBar); renderPanel = new RenderPanel(); embedMenuIfNeeded(renderPanel); this.add(renderPanel, BorderLayout.CENTER); + scriptWindow = new Panel(); + scriptWindow.setVisible(false); + // this.add(scriptWindow, BorderLayout.SOUTH); + try { - jmb.allocateViewer(renderPanel, "jalviewJmol", - ap.av.applet.getDocumentBase(), ap.av.applet.getCodeBase(), - ""); + jmb.allocateViewer(renderPanel, true, ap.av.applet.getName() + + "_jmol_", ap.av.applet.getDocumentBase(), + ap.av.applet.getCodeBase(), "-applet", scriptWindow, null); } catch (Exception e) { System.err @@ -194,7 +279,7 @@ public class AppletJmol extends EmbmenuFrame implements dispose(); return; } - jmb.newJmolPopup(true, "Jmol", true); + // jmb.newJmolPopup(true, "Jmol", true); this.addWindowListener(new WindowAdapter() { @@ -203,12 +288,18 @@ public class AppletJmol extends EmbmenuFrame implements closeViewer(); } }); - + if (pdbentry.getProperty() == null) + { + pdbentry.setProperty(new Hashtable()); + pdbentry.getProperty().put("protocol", protocol); + } if (pdbentry.getFile() != null) { // import structure data from pdbentry.getFile based on given protocol if (protocol.equals(AppletFormatAdapter.PASTE)) { + // TODO: JAL-623 : correctly record file contents for matching up later + // pdbentry.getProperty().put("pdbfilehash",""+pdbentry.getFile().hashCode()); loadInline(pdbentry.getFile()); } else if (protocol.equals(AppletFormatAdapter.FILE) @@ -255,7 +346,8 @@ public class AppletJmol extends EmbmenuFrame implements if (freader == null) { throw new Exception( - "Invalid datasource. Could not obtain Reader."); + MessageManager + .getString("exception.invalid_datasource_couldnt_obtain_reader")); } jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader); @@ -276,23 +368,22 @@ public class AppletJmol extends EmbmenuFrame implements public void loadInline(String string) { loadedInline = true; - jmb.viewer.openStringInline(string); + jmb.loadInline(string); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(Vector chains) { chainMenu.removeAll(); - MenuItem menuItem = new MenuItem("All"); + MenuItem menuItem = new MenuItem(MessageManager.getString("label.all")); menuItem.addActionListener(this); chainMenu.add(menuItem); CheckboxMenuItem menuItemCB; - for (int c = 0; c < chains.size(); c++) + for (String ch : chains) { - menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(), - true); + menuItemCB = new CheckboxMenuItem(ch, true); menuItemCB.addItemListener(this); chainMenu.add(menuItemCB); } @@ -302,9 +393,7 @@ public class AppletJmol extends EmbmenuFrame implements 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 CheckboxMenuItem) @@ -336,23 +425,19 @@ public class AppletJmol extends EmbmenuFrame implements frame.add(cap); StringBuffer sb = new StringBuffer(); - try { - for (int s = 0; s < jmb.pdbentry.length; s++) + try { - sb.append(StructureSelectionManager.getStructureSelectionManager() - .printMapping(jmb.pdbentry[s].getFile())); - sb.append("\n"); - } - cap.setText(sb.toString()); - } - catch (OutOfMemoryError ex) + cap.setText(jmb.printMappings()); + } catch (OutOfMemoryError ex) { frame.dispose(); - System.err.println("Out of memory when trying to create dialog box with sequence-structure mapping."); + System.err + .println("Out of memory when trying to create dialog box with sequence-structure mapping."); return; } - jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", - 550, 600); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.pdb_sequence_mapping"), 550, + 600); } else if (evt.getSource() == charge) { @@ -400,6 +485,10 @@ public class AppletJmol extends EmbmenuFrame implements setEnabled(buried); jmb.setJalviewColourScheme(new BuriedColourScheme()); } + else if (evt.getSource() == purinepyrimidine) + { + jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme()); + } else if (evt.getSource() == user) { setEnabled(user); @@ -423,7 +512,9 @@ public class AppletJmol extends EmbmenuFrame implements for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof CheckboxMenuItem) + { ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true); + } } centerViewer(); @@ -432,26 +523,34 @@ public class AppletJmol extends EmbmenuFrame implements } /** - * tick or untick the seqColour menu entry depending upon if it was selected - * or not. + * tick or untick the seqColour menu entry or jmoColour entry depending upon + * if it was selected or not. * * @param itm */ private void setEnabled(MenuItem itm) { + jmolColour.setState(itm == jmolColour); seqColour.setState(itm == seqColour); jmb.setColourBySequence(itm == seqColour); } public void itemStateChanged(ItemEvent evt) { - if (evt.getSource() == seqColour) + if (evt.getSource() == jmolColour) + { + setEnabled(jmolColour); + jmb.setColourBySequence(false); + } + else if (evt.getSource() == seqColour) { setEnabled(seqColour); - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment); + jmb.colourBySequence(ap); } else if (!allChainsSelected) + { centerViewer(); + } } public void keyPressed(KeyEvent evt) @@ -459,7 +558,7 @@ public class AppletJmol extends EmbmenuFrame implements if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible()) { jmb.eval(inputLine.getText()); - history.append("\n$ " + inputLine.getText()); + addToHistory("$ " + inputLine.getText()); inputLine.setText(""); } @@ -475,8 +574,8 @@ public class AppletJmol extends EmbmenuFrame implements public void updateColours(Object source) { - AlignmentPanel ap = (AlignmentPanel) source; - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment); + AlignmentPanel panel = (AlignmentPanel) source; + jmb.colourBySequence(panel); } public void updateTitleAndMenus() @@ -487,7 +586,7 @@ public class AppletJmol extends EmbmenuFrame implements return; } setChainMenuItems(jmb.chainNames); - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment); + jmb.colourBySequence(ap); setTitle(jmb.getViewerTitle()); } @@ -503,22 +602,30 @@ public class AppletJmol extends EmbmenuFrame implements } } + Panel splitPane = null; + public void showConsole(boolean showConsole) { - if (scriptWindow == null) - { - scriptWindow = new Panel(new BorderLayout()); - inputLine = new TextField(); - history = new TextArea(5, 40); - scriptWindow.add(history, BorderLayout.CENTER); - scriptWindow.add(inputLine, BorderLayout.SOUTH); - add(scriptWindow, BorderLayout.SOUTH); + if (showConsole) + { + remove(renderPanel); + splitPane = new Panel(); + + splitPane.setLayout(new java.awt.GridLayout(2, 1)); + splitPane.add(renderPanel); + splitPane.add(scriptWindow); + scriptWindow.setVisible(true); + this.add(splitPane, BorderLayout.CENTER); + splitPane.setVisible(true); + splitPane.validate(); + } + else + { scriptWindow.setVisible(false); - history.setEditable(false); - inputLine.addKeyListener(this); + remove(splitPane); + add(renderPanel, BorderLayout.CENTER); + splitPane = null; } - - scriptWindow.setVisible(!scriptWindow.isVisible()); validate(); } @@ -534,8 +641,6 @@ public class AppletJmol extends EmbmenuFrame implements { Dimension currentSize = new Dimension(); - Rectangle rectClip = new Rectangle(); - public void update(Graphics g) { paint(g); @@ -544,7 +649,6 @@ public class AppletJmol extends EmbmenuFrame implements public void paint(Graphics g) { currentSize = this.getSize(); - rectClip = g.getClipBounds(); if (jmb.viewer == null) { @@ -552,11 +656,13 @@ public class AppletJmol extends EmbmenuFrame implements 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); } } } @@ -583,4 +689,30 @@ public class AppletJmol extends EmbmenuFrame implements { jmb.setJalviewColourScheme(ucs); } + + public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) + { + for (int i = 0; i < _aps.size(); i++) + { + if (_aps.get(i).av.getAlignment() == alignment) + { + return (_aps.get(i)); + } + } + return ap; + } + + /** + * Append the given text to the history object + * + * @param text + */ + public void addToHistory(String text) + { + // actually currently never initialised + if (history != null) + { + history.append("\n" + text); + } + } }