X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=7bf21a8d91abffd2e7128ef5da500b05f5f2a05c;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=f64014b7fb09d21e5c1a9818219fb9aec03fe669;hpb=bc602371e44210748b5cb75e24afc14818f3e726;p=jalview.git diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java index f64014b..7bf21a8 100644 --- a/src/jalview/appletgui/AppletJmol.java +++ b/src/jalview/appletgui/AppletJmol.java @@ -1,127 +1,172 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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. + * + * 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 . */ - 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.adapter.smarter.SmarterJmolAdapter; import org.jmol.popup.*; -import jalview.schemes.*; +import org.jmol.viewer.JmolConstants; +import jalview.schemes.*; -public class AppletJmol extends Frame - implements StructureListener, JmolStatusListener, - KeyListener, ActionListener, ItemListener +public class AppletJmol extends EmbmenuFrame implements +// StructureListener, + KeyListener, ActionListener, ItemListener, SequenceStructureBinding { Menu fileMenu = new Menu("File"); + Menu viewMenu = new Menu("View"); + Menu coloursMenu = new Menu("Colours"); + Menu chainMenu = new Menu("Show Chain"); + Menu helpMenu = new Menu("Help"); + MenuItem mappingMenuItem = new MenuItem("View Mapping"); CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true); + + CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false); + MenuItem chain = new MenuItem("By Chain"); + MenuItem charge = new MenuItem("Charge & Cysteine"); + MenuItem zappo = new MenuItem("Zappo"); + MenuItem taylor = new MenuItem("Taylor"); + MenuItem hydro = new MenuItem("Hydrophobicity"); + MenuItem helix = new MenuItem("Helix Propensity"); + MenuItem strand = new MenuItem("Strand Propensity"); + MenuItem turn = new MenuItem("Turn Propensity"); + MenuItem buried = new MenuItem("Buried Index"); + MenuItem user = new MenuItem("User Defined Colours"); MenuItem jmolHelp = new MenuItem("Jmol Help"); - JmolViewer viewer; - JmolPopup jmolpopup; - Panel scriptWindow; + TextField inputLine; + TextArea history; - SequenceI[] sequence; - String [] chains; - StructureSelectionManager ssm; + RenderPanel renderPanel; + AlignmentPanel ap; + ArrayList _aps = new ArrayList(); + String fileLoadingError; + boolean loadedInline; - PDBEntry pdbentry; - boolean colourBySequence = true; - Vector atomsPicked = new Vector(); - - public AppletJmol(PDBEntry pdbentry, - SequenceI[] seq, - String[] chains, - AlignmentPanel ap, - String protocol) + + // boolean colourBySequence = true; + + FeatureRenderer fr = null; + + AppletJmolBinding jmb; + + /** + * datasource protocol for access to PDBEntry + */ + 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("Not yet implemented."); + } + + public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, + AlignmentPanel ap, String protocol) { this.ap = ap; - this.sequence = seq; - this.chains = chains; - this.pdbentry = pdbentry; + 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) + { + if (protocol.equals(AppletFormatAdapter.PASTE)) + { + pdbentry.setId("PASTED PDB" + + (chains == null ? "_" : chains.toString())); + } + else + { + pdbentry.setId(pdbentry.getFile()); + } + } - String alreadyMapped = StructureSelectionManager - .getStructureSelectionManager() - .alreadyMappedToFile(pdbentry.getId()); + if (jalview.bin.JalviewLite.debug) + { + System.err + .println("AppletJmol: PDB ID is '" + pdbentry.getId() + "'"); + } + String alreadyMapped = StructureSelectionManager + .getStructureSelectionManager(ap.av.applet).alreadyMappedToFile( + pdbentry.getId()); + MCview.PDBfile reader = null; if (alreadyMapped != null) { - StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, chains, pdbentry.getFile(), protocol); - //PROMPT USER HERE TO ADD TO NEW OR EXISTING VIEW? - //FOR NOW, LETS JUST OPEN A NEW WINDOW + 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 } - - renderPanel = new RenderPanel(); - - this.add(renderPanel, BorderLayout.CENTER); - viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter()); - - viewer.setAppletContext("jalview", - ap.av.applet.getDocumentBase(), - ap.av.applet.getCodeBase(), - null); - - viewer.setJmolStatusListener(this); - - jmolpopup = JmolPopup.newJmolPopup(viewer); - - this.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent evt) - { - closeViewer(); - } - }); - MenuBar menuBar = new MenuBar(); menuBar.add(fileMenu); fileMenu.add(mappingMenuItem); @@ -135,6 +180,7 @@ public class AppletJmol extends Frame hydro.addActionListener(this); chain.addActionListener(this); seqColour.addItemListener(this); + jmolColour.addItemListener(this); zappo.addActionListener(this); taylor.addActionListener(this); helix.addActionListener(this); @@ -142,7 +188,7 @@ public class AppletJmol extends Frame turn.addActionListener(this); buried.addActionListener(this); user.addActionListener(this); - + jmolHelp.addActionListener(this); coloursMenu.add(seqColour); @@ -156,29 +202,126 @@ public class AppletJmol extends Frame coloursMenu.add(turn); coloursMenu.add(buried); coloursMenu.add(user); - + coloursMenu.add(jmolColour); helpMenu.add(jmolHelp); + this.setLayout(new BorderLayout()); - this.setMenuBar(menuBar); + setMenuBar(menuBar); - if(pdbentry.getFile()!=null) + 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, 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=" + + ap.av.applet.getCodeBase()); + e.printStackTrace(); + dispose(); + return; + } + jmb.newJmolPopup(true, "Jmol", true); + + this.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent evt) + { + 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) + || protocol.equals(AppletFormatAdapter.URL)) + { + jmb.viewer.openFile(pdbentry.getFile()); + } else - viewer.openFile(pdbentry.getFile()); + { + // probably CLASSLOADER based datasource.. + // Try and get a reader on the datasource, and pass that to Jmol + try + { + java.io.Reader freader = null; + if (reader != null) + { + if (jalview.bin.JalviewLite.debug) + { + System.err + .println("AppletJmol:Trying to reuse existing PDBfile IO parser."); + } + // re-use the one we opened earlier + freader = reader.getReader(); + } + if (freader == null) + { + if (jalview.bin.JalviewLite.debug) + { + System.err + .println("AppletJmol:Creating new PDBfile IO parser."); + } + FileParse fp = new FileParse(pdbentry.getFile(), protocol); + fp.mark(); + // reader = new MCview.PDBfile(fp); + // could set ID, etc. + // if (!reader.isValid()) + // { + // throw new Exception("Invalid datasource. + // "+reader.getWarningMessage()); + // } + // fp.reset(); + freader = fp.getReader(); + } + if (freader == null) + { + throw new Exception( + "Invalid datasource. Could not obtain Reader."); + } + jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(), + freader); + } catch (Exception e) + { + // give up! + System.err.println("Couldn't access pdbentry id=" + + pdbentry.getId() + " and file=" + pdbentry.getFile() + + " using protocol=" + protocol); + e.printStackTrace(); + } + } } - jalview.bin.JalviewLite.addFrame(this, "Jmol", 400,400); + jalview.bin.JalviewLite.addFrame(this, jmb.getViewerTitle(), 400, 400); } public void loadInline(String string) { loadedInline = true; - viewer.openStringInline(string); + jmb.loadInline(string); } - void setChainMenuItems(Vector chains) { chainMenu.removeAll(); @@ -191,119 +334,132 @@ public class AppletJmol extends Frame CheckboxMenuItem menuItemCB; for (int c = 0; c < chains.size(); c++) { - menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(), true); + menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(), + true); menuItemCB.addItemListener(this); chainMenu.add(menuItemCB); } } boolean allChainsSelected = false; + void centerViewer() { - StringBuffer cmd = new StringBuffer(); + Vector toshow = new Vector(); + String lbl; + int mlength, p, mnum; for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof CheckboxMenuItem) { CheckboxMenuItem item = (CheckboxMenuItem) chainMenu.getItem(i); if (item.getState()) - cmd.append(":" + item.getLabel() + " or "); + { + toshow.addElement(item.getLabel()); + } } } - - if (cmd.length() > 0) - cmd.setLength(cmd.length() - 4); - - viewer.evalString("select *;restrict " - + cmd + ";cartoon;center " + cmd); + jmb.centerViewer(toshow); } - void closeViewer() { - viewer.setModeMouse(org.jmol.viewer.JmolConstants.MOUSE_NONE); - viewer.evalStringQuiet("zap"); - viewer.setJmolStatusListener(null); - viewer = null; - - //We'll need to find out what other - // listeners need to be shut down in Jmol - StructureSelectionManager - .getStructureSelectionManager() - .removeStructureViewerListener(this, pdbentry.getId()); - + jmb.closeViewer(); + jmb = null; this.setVisible(false); } public void actionPerformed(ActionEvent evt) { - if(evt.getSource()==mappingMenuItem) + if (evt.getSource() == mappingMenuItem) { - jalview.appletgui.CutAndPasteTransfer cap - = new jalview.appletgui.CutAndPasteTransfer(false, null); + jalview.appletgui.CutAndPasteTransfer cap = new jalview.appletgui.CutAndPasteTransfer( + false, null); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping", 550, - 600); - cap.setText( - StructureSelectionManager.getStructureSelectionManager().printMapping( - pdbentry.getFile()) - ); + 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()); + } catch (OutOfMemoryError ex) + { + frame.dispose(); + 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); } else if (evt.getSource() == charge) { - colourBySequence = false; - seqColour.setState(false); - viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;" - +"select LYS,ARG;color blue;select CYS;color yellow"); + setEnabled(charge); + jmb.colourByCharge(); } else if (evt.getSource() == chain) { - colourBySequence = false; - seqColour.setState(false); - viewer.evalStringQuiet("select *;color chain"); + setEnabled(chain); + jmb.colourByChain(); } else if (evt.getSource() == zappo) { - setJalviewColourScheme(new ZappoColourScheme()); + setEnabled(zappo); + jmb.setJalviewColourScheme(new ZappoColourScheme()); } else if (evt.getSource() == taylor) { - setJalviewColourScheme(new TaylorColourScheme()); + setEnabled(taylor); + jmb.setJalviewColourScheme(new TaylorColourScheme()); } else if (evt.getSource() == hydro) { - setJalviewColourScheme(new HydrophobicColourScheme()); + setEnabled(hydro); + jmb.setJalviewColourScheme(new HydrophobicColourScheme()); } else if (evt.getSource() == helix) { - setJalviewColourScheme(new HelixColourScheme()); + setEnabled(helix); + jmb.setJalviewColourScheme(new HelixColourScheme()); } else if (evt.getSource() == strand) { - setJalviewColourScheme(new StrandColourScheme()); + setEnabled(strand); + jmb.setJalviewColourScheme(new StrandColourScheme()); } else if (evt.getSource() == turn) { - setJalviewColourScheme(new TurnColourScheme()); + setEnabled(turn); + jmb.setJalviewColourScheme(new TurnColourScheme()); } else if (evt.getSource() == buried) { - setJalviewColourScheme(new BuriedColourScheme()); + setEnabled(buried); + jmb.setJalviewColourScheme(new BuriedColourScheme()); } else if (evt.getSource() == user) { + setEnabled(user); new UserDefinedColours(this); } - else if(evt.getSource() == jmolHelp) + else if (evt.getSource() == jmolHelp) { - try{ + try + { ap.av.applet.getAppletContext().showDocument( - new java.net.URL("http://jmol.sourceforge.net/docs/JmolUserGuide/"), - "jmolHelp"); - }catch(java.net.MalformedURLException ex){} + new java.net.URL( + "http://jmol.sourceforge.net/docs/JmolUserGuide/"), + "jmolHelp"); + } catch (java.net.MalformedURLException ex) + { + } } else { @@ -311,52 +467,38 @@ public class AppletJmol extends Frame for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof CheckboxMenuItem) - ( (CheckboxMenuItem) chainMenu.getItem(i)).setState(true); + ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true); } + centerViewer(); allChainsSelected = false; } } - public void setJalviewColourScheme(ColourSchemeI cs) + /** + * 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) { - colourBySequence = false; - seqColour.setState(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()); + jmolColour.setState(itm == jmolColour); + seqColour.setState(itm == seqColour); + jmb.setColourBySequence(itm == seqColour); } public void itemStateChanged(ItemEvent evt) { + if (evt.getSource() == jmolColour) + { + setEnabled(jmolColour); + jmb.setColourBySequence(false); + } else if (evt.getSource() == seqColour) { - lastCommand = null; - colourBySequence = seqColour.getState(); - colourBySequence(ap); + setEnabled(seqColour); + jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap); } else if (!allChainsSelected) centerViewer(); @@ -364,444 +506,105 @@ public class AppletJmol extends Frame public void keyPressed(KeyEvent evt) { - if (evt.getKeyCode() == KeyEvent.VK_ENTER - && scriptWindow.isVisible()) + if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible()) { - viewer.evalString(inputLine.getText()); - history.append("\n$ "+inputLine.getText()); + jmb.eval(inputLine.getText()); + history.append("\n$ " + inputLine.getText()); inputLine.setText(""); } } public void keyTyped(KeyEvent evt) - { } - - public void keyReleased(KeyEvent evt){} - - ////////////////////////////////// - ///StructureListener - public String getPdbFile() { - return "???"; } - - - String lastMessage; - public void mouseOverStructure(int atomIndex, String strInfo) + public void keyReleased(KeyEvent evt) { - int pdbResNum; - - int chainSeparator = strInfo.indexOf(":"); - - if(chainSeparator==-1) - chainSeparator = strInfo.indexOf("."); - - 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 = " "; - } - - if (lastMessage == null || !lastMessage.equals(strInfo)) - ssm.mouseOverStructure(pdbResNum, chainId, pdbentry.getFile()); - - lastMessage = strInfo; - } - - StringBuffer resetLastRes = new StringBuffer(); - StringBuffer eval = new StringBuffer(); - - public void highlightAtom(int atomIndex, int pdbResNum, String chain, String pdbfile) - { - if (!pdbfile.equals(pdbentry.getFile())) - return; - - if (resetLastRes.length() > 0) - { - viewer.evalStringQuiet(resetLastRes.toString()); - } - - eval.setLength(0); - eval.append("select " + pdbResNum); - - resetLastRes.setLength(0); - resetLastRes.append("select " + pdbResNum); - - if (!chain.equals(" ")) - { - eval.append(":" + chain); - resetLastRes.append(":" + chain); - } - - eval.append(";wireframe 100;"+eval.toString()+".CA;"); - - resetLastRes.append(";wireframe 0;"+resetLastRes.toString()+".CA;spacefill 0;"); - - eval.append("spacefill 200;select none"); - - viewer.evalStringQuiet(eval.toString()); - } public void updateColours(Object source) { - colourBySequence( (AlignmentPanel) source); - } - -//End StructureListener -//////////////////////////// - - public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile) - { - if (!pdbfile.equals(pdbentry.getFile())) - return null; - - return new Color(viewer.getAtomArgb(atomIndex)); - } - - String lastCommand; - FeatureRenderer fr=null; - public void colourBySequence(AlignmentPanel sourceap) - { - this.ap = sourceap; - - if (!colourBySequence) - return; - - StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile()); - - if (mapping.length < 1) - return; - - SequenceRenderer sr = new SequenceRenderer(ap.av); - - boolean showFeatures = false; - - if (ap.av.showSequenceFeatures) - { - showFeatures = true; - if (fr == null) - { - fr = new jalview.appletgui.FeatureRenderer(ap.av); - } - - fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer()); - } - - StringBuffer command = new StringBuffer(); - - int lastPos = -1; - for (int s = 0; s < sequence.length; s++) - { - for (int m = 0; m < mapping.length; m++) - { - if (mapping[m].getSequence() == sequence[s] - && ap.av.alignment.findIndex(sequence[s]) > -1) - { - for (int r = 0; r < sequence[s].getLength(); r++) - { - int pos = mapping[m].getPDBResNum( - sequence[s].findPosition(r)); - - if (pos < 1 || pos == lastPos) - continue; - - lastPos = pos; - - Color col = sr.getResidueBoxColour(sequence[s], r); - - if (showFeatures) - col = fr.findFeatureColour(col, sequence[s], r); - - if (command.toString().endsWith(":" + mapping[m].getChain() + - ";color[" - + col.getRed() + "," - + col.getGreen() + "," - + col.getBlue() + "]")) - { - command = condenseCommand(command.toString(), pos); - continue; - } - - command.append(";select " + pos); - - if (!mapping[m].getChain().equals(" ")) - { - command.append(":" + mapping[m].getChain()); - } - - command.append(";color[" - + col.getRed() + "," - + col.getGreen() + "," - + col.getBlue() + "]"); - } - break; - } - } - } - - if (lastCommand == null || !lastCommand.equals(command.toString())) - { - viewer.evalStringQuiet(command.toString()); - } - lastCommand = command.toString(); + AlignmentPanel ap = (AlignmentPanel) source; + jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap); } - - StringBuffer condenseCommand(String command, int pos) + public void updateTitleAndMenus() { - - StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7)); - - command = command.substring(sb.length()); - - String start; - - if (command.indexOf("-") > -1) + if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) { - 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) - {} - - public void setCallbackFunction(String callbackType, - String callbackFunction) - {} - - public void notifyFileLoaded(String fullPathName, String fileName, - String modelName, Object clientFile, - String errorMsg) - { - if(errorMsg!=null) - { - fileLoadingError = errorMsg; repaint(); return; } + setChainMenuItems(jmb.chainNames); + jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap); - fileLoadingError = null; - - if (fileName != null) - { - //FILE LOADED OK - jmolpopup.updateComputedMenus(); - viewer.evalStringQuiet( - "select backbone;restrict;cartoon;wireframe off;spacefill off"); - - ssm = StructureSelectionManager.getStructureSelectionManager(); - - MCview.PDBfile pdb; - if (loadedInline) - { - pdb = ssm.setMapping(sequence,chains, - pdbentry.getFile(), - AppletFormatAdapter.PASTE); - pdbentry.setFile("INLINE"+pdb.id); - } - else - { - pdb = ssm.setMapping(sequence,chains, - pdbentry.getFile(), - AppletFormatAdapter.URL); - } - - pdbentry.setId(pdb.id); - - ssm.addStructureViewerListener(this); - - Vector chains = new Vector(); - for (int i = 0; i < pdb.chains.size(); i++) - { - chains.addElement( ( (MCview.PDBChain) pdb.chains.elementAt(i)).id); - } - setChainMenuItems(chains); - - colourBySequence(ap); - - StringBuffer title = new StringBuffer(sequence[0].getName() + ":" + - pdbentry.getId()); - - if (pdbentry.getProperty() != null) - { - if (pdbentry.getProperty().get("method") != null) - { - title.append(" Method: "); - title.append(pdbentry.getProperty().get("method")); - } - if (pdbentry.getProperty().get("chains") != null) - { - title.append(" Chain:"); - title.append(pdbentry.getProperty().get("chains")); - } - } - - this.setTitle(title.toString()); - - } - else - return; - } - - public void notifyFrameChanged(int frameNo) - { - boolean isAnimationRunning = (frameNo <= -2); + setTitle(jmb.getViewerTitle()); } - public void notifyScriptStart(String statusMessage, String additionalInfo) - {} - - public void sendConsoleEcho(String strEcho) - { - if (scriptWindow == null) - showConsole(true); - - history.append("\n"+strEcho); - } - - public void sendConsoleMessage(String strStatus) + public void showUrl(String url) { - if(history!=null && strStatus!=null - && !strStatus.equals("Script completed")) + try + { + ap.av.applet.getAppletContext().showDocument(new java.net.URL(url), + "jmolOutput"); + } catch (java.net.MalformedURLException ex) { - history.append("\n"+strStatus); } } - public void notifyScriptTermination(String strStatus, int msWalltime) - { } + Panel splitPane = null; - public void handlePopupMenu(int x, int y) - { - jmolpopup.show(x, y); - } - - public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) - { - notifyAtomPicked(iatom, strMeasure); - } - - public void notifyNewDefaultModeMeasurement(int count, String strInfo) - {} - - public void notifyAtomPicked(int atomIndex, String strInfo) + public void showConsole(boolean showConsole) { - - int chainSeparator = strInfo.indexOf(":"); - - if(chainSeparator==-1) - chainSeparator = strInfo.indexOf("."); - - String picked = - strInfo.substring(strInfo.indexOf("]")+ 1, chainSeparator); - - - if (strInfo.indexOf(":") > -1) - picked+=strInfo.substring(strInfo.indexOf(":")+1, - strInfo.indexOf(".")); - - picked+=".CA"; - - if (!atomsPicked.contains(picked)) + if (showConsole) { - viewer.evalString("select "+picked+";label %n %r:%c"); - atomsPicked.addElement(picked); + 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 { - viewer.evalString("select "+picked+";label off"); - atomsPicked.removeElement(picked); - } - } - - public void notifyAtomHovered(int atomIndex, String strInfo) - { - mouseOverStructure(atomIndex, strInfo); - } - - public void sendSyncScript(String script, String appletName) - {} - - public void showUrl(String url) - { - try{ - ap.av.applet.getAppletContext().showDocument(new java.net.URL(url), - "jmolOutput"); - }catch(java.net.MalformedURLException ex) - {} - } - - 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); scriptWindow.setVisible(false); - history.setEditable(false); - inputLine.addKeyListener(this); + remove(splitPane); + add(renderPanel, BorderLayout.CENTER); + splitPane = null; } - - scriptWindow.setVisible(!scriptWindow.isVisible()); validate(); } - public float functionXY(String functionName, int x, int y) + public float[][] functionXY(String functionName, int x, int y) { - return 0; + return null; } - ///End JmolStatusListener - /////////////////////////////// + // /End JmolStatusListener + // ///////////////////////////// - - class RenderPanel - extends Panel + class RenderPanel extends Panel { Dimension currentSize = new Dimension(); + Rectangle rectClip = new Rectangle(); - public void update(Graphics g) { + public void update(Graphics g) + { paint(g); } + public void paint(Graphics g) { currentSize = this.getSize(); rectClip = g.getClipBounds(); - if (viewer == null) + if (jmb.viewer == null) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -811,9 +614,43 @@ public class AppletJmol extends Frame } else { - viewer.renderScreenImage(g, currentSize, rectClip); + jmb.viewer.renderScreenImage(g, currentSize, rectClip); } } } + /* + * @Override public Color getColour(int atomIndex, int pdbResNum, String + * chain, String pdbId) { return jmb.getColour(atomIndex, pdbResNum, chain, + * pdbId); } + * + * @Override public String[] getPdbFile() { return jmb.getPdbFile(); } + * + * @Override public void highlightAtom(int atomIndex, int pdbResNum, String + * chain, String pdbId) { jmb.highlightAtom(atomIndex, pdbResNum, chain, + * pdbId); + * + * } + * + * @Override public void mouseOverStructure(int atomIndex, String strInfo) { + * jmb.mouseOverStructure(atomIndex, strInfo); + * + * } + */ + public void setJalviewColourScheme(UserColourScheme ucs) + { + jmb.setJalviewColourScheme(ucs); + } + + public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) + { + for (int i=0;i<_aps.size();i++) + { + if (((AlignmentPanel)_aps.get(i)).av.getAlignment()==alignment) + { + return ((AlignmentPanel)_aps.get(i)); + } + } + return ap; + } }