X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=681fc7d954cce827d451bcbb89161036f9f2f505;hb=a5e22141bc3185284588761a69f023d527e7f18e;hp=f29ae773616d75fbf0e57f647f65008e09c556e4;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index f29ae77..681fc7d 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 2.9.0b1) - * Copyright (C) 2015 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. * @@ -20,12 +20,15 @@ */ package jalview.appletgui; +import jalview.bin.JalviewLite; import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; import jalview.io.FileParse; +import jalview.io.StructureFile; import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ColourSchemeI; import jalview.schemes.HelixColourScheme; import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; @@ -35,6 +38,7 @@ import jalview.schemes.TurnColourScheme; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; import jalview.structure.StructureSelectionManager; +import jalview.structures.models.AAStructureBindingModel.ColourBy; import jalview.util.MessageManager; import java.awt.BorderLayout; @@ -59,12 +63,11 @@ 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, + // StructureListener, KeyListener, ActionListener, ItemListener { @@ -87,32 +90,35 @@ 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_helix_propensity")); MenuItem strand = new MenuItem( - MessageManager.getString("label.strand_propensity")); + MessageManager.getString("label.colourScheme_strand_propensity")); MenuItem turn = new MenuItem( - MessageManager.getString("label.turn_propensity")); + MessageManager.getString("label.colourScheme_turn_propensity")); MenuItem buried = new MenuItem( - MessageManager.getString("label.buried_index")); + MessageManager.getString("label.colourScheme_buried_index")); 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")); @@ -130,7 +136,7 @@ public class AppletJmol extends EmbmenuFrame implements AlignmentPanel ap; - List _aps = new ArrayList(); // remove? never + List _aps = new ArrayList<>(); // remove? never // added to String fileLoadingError; @@ -175,19 +181,19 @@ public class AppletJmol extends EmbmenuFrame implements } 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); - jmb.setColourBySequence(true); + new PDBEntry[] + { pdbentry }, new SequenceI[][] { seq }, protocol); + jmb.setColourBy(ColourBy.Sequence); 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 { @@ -195,7 +201,7 @@ public class AppletJmol extends EmbmenuFrame implements } } - if (jalview.bin.JalviewLite.debug) + if (JalviewLite.debug) { System.err .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'"); @@ -204,12 +210,12 @@ 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 } @@ -265,15 +271,15 @@ 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(); @@ -283,27 +289,25 @@ public class AppletJmol extends EmbmenuFrame implements 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()); } @@ -318,8 +322,8 @@ 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(); @@ -328,8 +332,8 @@ 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(); @@ -345,9 +349,8 @@ public class AppletJmol extends EmbmenuFrame implements } if (freader == null) { - throw new Exception( - MessageManager - .getString("exception.invalid_datasource_couldnt_obtain_reader")); + throw new Exception(MessageManager.getString( + "exception.invalid_datasource_couldnt_obtain_reader")); } jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(), freader); @@ -371,7 +374,7 @@ public class AppletJmol extends EmbmenuFrame implements jmb.loadInline(string); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(List chains) { chainMenu.removeAll(); @@ -393,7 +396,7 @@ public class AppletJmol extends EmbmenuFrame implements void centerViewer() { - Vector toshow = new Vector(); + Vector toshow = new Vector<>(); for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof CheckboxMenuItem) @@ -415,6 +418,7 @@ public class AppletJmol extends EmbmenuFrame implements this.setVisible(false); } + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == mappingMenuItem) @@ -431,8 +435,8 @@ public class AppletJmol extends EmbmenuFrame implements } 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, @@ -453,41 +457,41 @@ public class AppletJmol extends EmbmenuFrame implements else if (evt.getSource() == zappo) { setEnabled(zappo); - jmb.setJalviewColourScheme(new ZappoColourScheme()); + setColourScheme(new ZappoColourScheme()); } else if (evt.getSource() == taylor) { setEnabled(taylor); - jmb.setJalviewColourScheme(new TaylorColourScheme()); + setColourScheme(new TaylorColourScheme()); } else if (evt.getSource() == hydro) { setEnabled(hydro); - jmb.setJalviewColourScheme(new HydrophobicColourScheme()); + setColourScheme(new HydrophobicColourScheme()); } else if (evt.getSource() == helix) { setEnabled(helix); - jmb.setJalviewColourScheme(new HelixColourScheme()); + setColourScheme(new HelixColourScheme()); } else if (evt.getSource() == strand) { setEnabled(strand); - jmb.setJalviewColourScheme(new StrandColourScheme()); + setColourScheme(new StrandColourScheme()); } else if (evt.getSource() == turn) { setEnabled(turn); - jmb.setJalviewColourScheme(new TurnColourScheme()); + setColourScheme(new TurnColourScheme()); } else if (evt.getSource() == buried) { setEnabled(buried); - jmb.setJalviewColourScheme(new BuriedColourScheme()); + setColourScheme(new BuriedColourScheme()); } else if (evt.getSource() == purinepyrimidine) { - jmb.setJalviewColourScheme(new PurinePyrimidineColourScheme()); + setColourScheme(new PurinePyrimidineColourScheme()); } else if (evt.getSource() == user) { @@ -498,10 +502,10 @@ 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) { } @@ -522,7 +526,12 @@ public class AppletJmol extends EmbmenuFrame implements } } - /** + private void setColourScheme(ColourSchemeI cs) + { + jmb.setJalviewColourScheme(cs, ap, ap.av.isShowSequenceFeatures()); + } + +/** * tick or untick the seqColour menu entry or jmoColour entry depending upon * if it was selected or not. * @@ -532,20 +541,21 @@ public class AppletJmol extends EmbmenuFrame implements { jmolColour.setState(itm == jmolColour); seqColour.setState(itm == seqColour); - jmb.setColourBySequence(itm == seqColour); + jmb.setColourBy(itm == seqColour ? ColourBy.Sequence : ColourBy.Viewer); } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == jmolColour) { setEnabled(jmolColour); - jmb.setColourBySequence(false); + jmb.setColourBy(ColourBy.Viewer); } else if (evt.getSource() == seqColour) { setEnabled(seqColour); - jmb.colourBySequence(ap); + jmb.colourBySequence(ap, ap.av.isShowSequenceFeatures()); } else if (!allChainsSelected) { @@ -553,6 +563,7 @@ public class AppletJmol extends EmbmenuFrame implements } } + @Override public void keyPressed(KeyEvent evt) { if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible()) @@ -564,10 +575,12 @@ public class AppletJmol extends EmbmenuFrame implements } + @Override public void keyTyped(KeyEvent evt) { } + @Override public void keyReleased(KeyEvent evt) { } @@ -575,18 +588,18 @@ public class AppletJmol extends EmbmenuFrame implements public void updateColours(Object source) { AlignmentPanel panel = (AlignmentPanel) source; - jmb.colourBySequence(panel); + jmb.colourBySequence(panel, ap.av.isShowSequenceFeatures()); } public void updateTitleAndMenus() { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) + if (jmb.hasFileLoadingError()) { repaint(); return; } - setChainMenuItems(jmb.chainNames); - jmb.colourBySequence(ap); + setChainMenuItems(jmb.getChainNames()); + jmb.colourBySequence(ap, ap.av.isShowSequenceFeatures()); setTitle(jmb.getViewerTitle()); } @@ -641,11 +654,13 @@ public class AppletJmol extends EmbmenuFrame implements { Dimension currentSize = new Dimension(); + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { currentSize = this.getSize(); @@ -687,7 +702,7 @@ public class AppletJmol extends EmbmenuFrame implements */ public void setJalviewColourScheme(UserColourScheme ucs) { - jmb.setJalviewColourScheme(ucs); + setColourScheme(ucs); } public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment)