X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=b0722c084a30cacb609f8f3bb4d3a4f2b04e3d38;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=bf82bcad97a41b840e2fbbbd4468072230785a95;hpb=ecfc49bc5a7e416c0f967677651923993f105dd8;p=jalview.git diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index bf82bca..b0722c0 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * 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. * @@ -20,20 +20,52 @@ */ 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 jalview.schemes.*; +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.List; +import java.util.Vector; + +import jalview.bin.JalviewLite; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; +import jalview.io.FileParse; +import jalview.io.StructureFile; +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; public class AppletJmol extends EmbmenuFrame implements -// StructureListener, + // StructureListener, KeyListener, ActionListener, ItemListener { @@ -56,32 +88,35 @@ public class AppletJmol extends EmbmenuFrame implements CheckboxMenuItem jmolColour = new CheckboxMenuItem( MessageManager.getString("action.using_jmol"), false); - MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain")); + MenuItem chain = new MenuItem( + MessageManager.getString("action.by_chain")); MenuItem charge = new MenuItem( MessageManager.getString("label.charge_cysteine")); - MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo")); + MenuItem zappo = new MenuItem( + MessageManager.getString("label.colourScheme_zappo")); - MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor")); + MenuItem taylor = new MenuItem( + MessageManager.getString("label.colourScheme_taylor")); MenuItem hydro = new MenuItem( - MessageManager.getString("label.hydrophobicity")); + MessageManager.getString("label.colourScheme_hydrophobic")); MenuItem helix = new MenuItem( - MessageManager.getString("label.helix_propensity")); + MessageManager.getString("label.colourScheme_helixpropensity")); MenuItem strand = new MenuItem( - MessageManager.getString("label.strand_propensity")); + MessageManager.getString("label.colourScheme_strandpropensity")); MenuItem turn = new MenuItem( - MessageManager.getString("label.turn_propensity")); + MessageManager.getString("label.colourScheme_turnpropensity")); MenuItem buried = new MenuItem( - MessageManager.getString("label.buried_index")); + MessageManager.getString("label.colourScheme_buriedindex")); MenuItem purinepyrimidine = new MenuItem( - MessageManager.getString("label.purine_pyrimidine")); + MessageManager.getString("label.colourScheme_purine/pyrimidine")); MenuItem user = new MenuItem( MessageManager.getString("label.user_defined_colours")); @@ -99,7 +134,8 @@ public class AppletJmol extends EmbmenuFrame implements AlignmentPanel ap; - ArrayList _aps = new ArrayList(); + List _aps = new ArrayList<>(); // remove? never + // added to String fileLoadingError; @@ -139,25 +175,23 @@ public class AppletJmol extends EmbmenuFrame implements String[][] boundchains, boolean align, AlignmentPanel ap, String protocol) { - throw new Error("Not yet implemented."); + throw new Error(MessageManager.getString("error.not_yet_implemented")); } public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, - AlignmentPanel ap, String protocol) + AlignmentPanel ap, DataSourceType protocol) { this.ap = ap; jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(), new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }, new String[][] - { chains }, protocol); + { pdbentry }, new SequenceI[][] { seq }, protocol); jmb.setColourBySequence(true); if (pdbentry.getId() == null || pdbentry.getId().length() < 1) { - if (protocol.equals(AppletFormatAdapter.PASTE)) + if (protocol == DataSourceType.PASTE) { - pdbentry.setId("PASTED PDB" - + (chains == null ? "_" : chains.toString())); + pdbentry.setId( + "PASTED PDB" + (chains == null ? "_" : chains.toString())); } else { @@ -165,7 +199,7 @@ public class AppletJmol extends EmbmenuFrame implements } } - if (jalview.bin.JalviewLite.debug) + if (JalviewLite.debug) { System.err .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'"); @@ -174,12 +208,12 @@ public class AppletJmol extends EmbmenuFrame implements String alreadyMapped = StructureSelectionManager .getStructureSelectionManager(ap.av.applet) .alreadyMappedToFile(pdbentry.getId()); - MCview.PDBfile reader = null; + StructureFile reader = null; if (alreadyMapped != null) { - reader = StructureSelectionManager.getStructureSelectionManager( - ap.av.applet).setMapping(seq, chains, pdbentry.getFile(), - protocol); + reader = StructureSelectionManager + .getStructureSelectionManager(ap.av.applet) + .setMapping(seq, chains, pdbentry.getFile(), protocol, null); // PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW? // FOR NOW, LETS JUST OPEN A NEW WINDOW } @@ -235,47 +269,45 @@ public class AppletJmol extends EmbmenuFrame implements try { - jmb.allocateViewer(renderPanel, true, ap.av.applet.getName() - + "_jmol_", ap.av.applet.getDocumentBase(), - ap.av.applet.getCodeBase(), "-applet", scriptWindow, null); + 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 - .println("Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase=" - + ap.av.applet.getDocumentBase() - + "\nCodebase=" + System.err.println( + "Couldn't create a jmol viewer. Args to allocate viewer were:\nDocumentBase=" + + ap.av.applet.getDocumentBase() + "\nCodebase=" + ap.av.applet.getCodeBase()); e.printStackTrace(); dispose(); return; } - jmb.newJmolPopup(true, "Jmol", true); + // jmb.newJmolPopup(true, "Jmol", true); this.addWindowListener(new WindowAdapter() { + @Override public void windowClosing(WindowEvent evt) { closeViewer(); } }); - if (pdbentry.getProperty() == null) - { - pdbentry.setProperty(new Hashtable()); - pdbentry.getProperty().put("protocol", protocol); - } + pdbentry.setProperty("protocol", protocol); if (pdbentry.getFile() != null) + { // import structure data from pdbentry.getFile based on given protocol - if (protocol.equals(AppletFormatAdapter.PASTE)) + if (protocol == DataSourceType.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) - || protocol.equals(AppletFormatAdapter.URL)) + else if (protocol == DataSourceType.FILE + || protocol == DataSourceType.URL) { - jmb.viewer.openFile(pdbentry.getFile()); + jmb.jmolViewer.openFile(pdbentry.getFile()); } else { @@ -288,8 +320,8 @@ public class AppletJmol extends EmbmenuFrame implements { if (jalview.bin.JalviewLite.debug) { - System.err - .println("AppletJmol:Trying to reuse existing PDBfile IO parser."); + System.err.println( + "AppletJmol:Trying to reuse existing PDBfile IO parser."); } // re-use the one we opened earlier freader = reader.getReader(); @@ -298,12 +330,12 @@ public class AppletJmol extends EmbmenuFrame implements { if (jalview.bin.JalviewLite.debug) { - System.err - .println("AppletJmol:Creating new PDBfile IO parser."); + System.err.println( + "AppletJmol:Creating new PDBfile IO parser."); } FileParse fp = new FileParse(pdbentry.getFile(), protocol); fp.mark(); - // reader = new MCview.PDBfile(fp); + // reader = new mc_view.PDBfile(fp); // could set ID, etc. // if (!reader.isValid()) // { @@ -315,10 +347,10 @@ public class AppletJmol extends EmbmenuFrame implements } if (freader == null) { - throw new Exception( - "Invalid datasource. Could not obtain Reader."); + throw new Exception(MessageManager.getString( + "exception.invalid_datasource_couldnt_obtain_reader")); } - jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(), + jmb.jmolViewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader); } catch (Exception e) { @@ -340,7 +372,7 @@ public class AppletJmol extends EmbmenuFrame implements jmb.loadInline(string); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(List chains) { chainMenu.removeAll(); @@ -350,10 +382,9 @@ public class AppletJmol extends EmbmenuFrame implements 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); } @@ -363,9 +394,7 @@ 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) @@ -377,16 +406,17 @@ public class AppletJmol extends EmbmenuFrame implements } } } - jmb.centerViewer(toshow); + jmb.showChains(toshow); } void closeViewer() { - jmb.closeViewer(); + jmb.closeViewer(true); jmb = null; this.setVisible(false); } + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == mappingMenuItem) @@ -399,17 +429,12 @@ public class AppletJmol extends EmbmenuFrame implements StringBuffer sb = new StringBuffer(); try { - for (int s = 0; s < jmb.pdbentry.length; s++) - { - sb.append(jmb.printMapping(jmb.pdbentry[s].getFile())); - sb.append("\n"); - } - cap.setText(sb.toString()); + 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, @@ -430,41 +455,41 @@ public class AppletJmol extends EmbmenuFrame implements else if (evt.getSource() == zappo) { setEnabled(zappo); - jmb.setJalviewColourScheme(new ZappoColourScheme()); + jmb.colourByJalviewColourScheme(new ZappoColourScheme()); } else if (evt.getSource() == taylor) { setEnabled(taylor); - jmb.setJalviewColourScheme(new TaylorColourScheme()); + jmb.colourByJalviewColourScheme(new TaylorColourScheme()); } else if (evt.getSource() == hydro) { setEnabled(hydro); - jmb.setJalviewColourScheme(new HydrophobicColourScheme()); + jmb.colourByJalviewColourScheme(new HydrophobicColourScheme()); } else if (evt.getSource() == helix) { setEnabled(helix); - jmb.setJalviewColourScheme(new HelixColourScheme()); + jmb.colourByJalviewColourScheme(new HelixColourScheme()); } else if (evt.getSource() == strand) { setEnabled(strand); - jmb.setJalviewColourScheme(new StrandColourScheme()); + jmb.colourByJalviewColourScheme(new StrandColourScheme()); } else if (evt.getSource() == turn) { setEnabled(turn); - jmb.setJalviewColourScheme(new TurnColourScheme()); + jmb.colourByJalviewColourScheme(new TurnColourScheme()); } else if (evt.getSource() == buried) { setEnabled(buried); - jmb.setJalviewColourScheme(new BuriedColourScheme()); + jmb.colourByJalviewColourScheme(new BuriedColourScheme()); } else if (evt.getSource() == purinepyrimidine) { - jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme()); + jmb.colourByJalviewColourScheme(new PurinePyrimidineColourScheme()); } else if (evt.getSource() == user) { @@ -475,10 +500,10 @@ public class AppletJmol extends EmbmenuFrame implements { try { - ap.av.applet.getAppletContext().showDocument( - new java.net.URL( + ap.av.applet.getAppletContext() + .showDocument(new java.net.URL( "http://jmol.sourceforge.net/docs/JmolUserGuide/"), - "jmolHelp"); + "jmolHelp"); } catch (java.net.MalformedURLException ex) { } @@ -489,7 +514,9 @@ 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(); @@ -510,6 +537,7 @@ public class AppletJmol extends EmbmenuFrame implements jmb.setColourBySequence(itm == seqColour); } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == jmolColour) @@ -520,46 +548,51 @@ public class AppletJmol extends EmbmenuFrame implements else if (evt.getSource() == seqColour) { setEnabled(seqColour); - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap); + jmb.colourBySequence(ap); } else if (!allChainsSelected) + { centerViewer(); + } } + @Override public void keyPressed(KeyEvent evt) { if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible()) { jmb.eval(inputLine.getText()); - history.append("\n$ " + inputLine.getText()); + addToHistory("$ " + inputLine.getText()); inputLine.setText(""); } } + @Override public void keyTyped(KeyEvent evt) { } + @Override public void keyReleased(KeyEvent evt) { } public void updateColours(Object source) { - AlignmentPanel ap = (AlignmentPanel) source; - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap); + AlignmentPanel panel = (AlignmentPanel) source; + jmb.colourBySequence(panel); } public void updateTitleAndMenus() { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) + if (jmb.hasFileLoadingError()) { repaint(); return; } - setChainMenuItems(jmb.chainNames); - jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap); + setChainMenuItems(jmb.getChainNames()); + jmb.colourBySequence(ap); setTitle(jmb.getViewerTitle()); } @@ -614,19 +647,18 @@ public class AppletJmol extends EmbmenuFrame implements { Dimension currentSize = new Dimension(); - Rectangle rectClip = new Rectangle(); - + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { currentSize = this.getSize(); - rectClip = g.getClipBounds(); - if (jmb.viewer == null) + if (jmb.jmolViewer == null) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -637,7 +669,8 @@ public class AppletJmol extends EmbmenuFrame implements } else { - jmb.viewer.renderScreenImage(g, currentSize, rectClip); + jmb.jmolViewer.renderScreenImage(g, currentSize.width, + currentSize.height); } } } @@ -660,20 +693,34 @@ public class AppletJmol extends EmbmenuFrame implements * * } */ - public void setJalviewColourScheme(UserColourScheme ucs) + public void colourByJalviewColourScheme(UserColourScheme ucs) { - jmb.setJalviewColourScheme(ucs); + jmb.colourByJalviewColourScheme(ucs); } public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) { for (int i = 0; i < _aps.size(); i++) { - if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment) + if (_aps.get(i).av.getAlignment() == alignment) { - return ((AlignmentPanel) _aps.get(i)); + 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); + } + } }