From 5c4ae10dd4841be26efc77548bb5b9e2a9d7ff0b Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 26 Mar 2007 14:19:52 +0000 Subject: [PATCH] PDB residue numberings transfered and alignment view refreshed to update featureRenderer. --- src/MCview/PDBChain.java | 7 +- src/jalview/gui/AppJMol.java | 1744 ++++++++++---------- src/jalview/gui/FeatureRenderer.java | 6 +- .../structure/StructureSelectionManager.java | 700 ++++---- 4 files changed, 1231 insertions(+), 1226 deletions(-) diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 6f1b31a..76a0cde 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -104,13 +104,13 @@ public class PDBChain public SequenceFeature[] transferRESNUMFeatures(SequenceI seq, String status) { SequenceI sq = seq; - while (sq != null) + while (sq!=null && sq.getDatasetSequence()!=null) { + sq = sq.getDatasetSequence(); if (sq == sequence) { return null; } - sq = sq.getDatasetSequence(); } /** * Remove any existing features for this chain if they exist ? @@ -138,7 +138,8 @@ public class PDBChain tx.setStatus(status + ( (tx.getStatus() == null || tx.getStatus().length() == 0) ? "" : ":" + tx.getStatus())); - seq.addSequenceFeature(tx); + if (tx.begin!=0 && tx.end!=0) + sq.addSequenceFeature(tx); } } return features; diff --git a/src/jalview/gui/AppJMol.java b/src/jalview/gui/AppJMol.java index 2f9fadc..50e2b96 100644 --- a/src/jalview/gui/AppJMol.java +++ b/src/jalview/gui/AppJMol.java @@ -1,871 +1,873 @@ -/* - * 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 - */ -package jalview.gui; - -import java.util.regex.*; -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.datamodel.*; -import jalview.gui.*; -import jalview.structure.*; -import jalview.datamodel.PDBEntry; -import jalview.io.*; -import jalview.schemes.*; - -import org.jmol.api.*; -import org.jmol.adapter.smarter.SmarterJmolAdapter; -import org.jmol.popup.*; - - -public class AppJMol - extends GStructureViewer - implements StructureListener, JmolStatusListener, Runnable - -{ - JmolViewer viewer; - JmolPopup jmolpopup; - ScriptWindow scriptWindow; - PDBEntry pdbentry; - SequenceI[] sequence; - StructureSelectionManager ssm; - JSplitPane splitPane; - RenderPanel renderPanel; - AlignmentPanel ap; - String fileLoadingError; - boolean colourBySequence = true; - boolean loadingFromArchive = false; - - public AppJMol(String file, String id, - SequenceI[] seq, - AlignmentPanel ap, - String loadStatus, - Rectangle bounds) - { - loadingFromArchive = true; - pdbentry = new PDBEntry(); - pdbentry.setFile(file); - pdbentry.setId(id); - this.sequence = seq; - this.ap = ap; - this.setBounds(bounds); - - colourBySequence = false; - seqColour.setSelected(false); - - jalview.gui.Desktop.addInternalFrame(this, "Loading File", - bounds.width,bounds.height); - - initJmol(loadStatus); - - this.addInternalFrameListener(new InternalFrameAdapter() - { - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) - { - closeViewer(); - } - }); - } - - public AppJMol(PDBEntry pdbentry, SequenceI[] seq, AlignmentPanel ap) - { - ////////////////////////////////// - //Is the pdb file already loaded? - String alreadyMapped = StructureSelectionManager - .getStructureSelectionManager() - .alreadyMappedToFile(pdbentry.getId()); - - if (alreadyMapped != null) - { - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - pdbentry.getId() + " is already displayed." - + "\nDo you want to map sequences to the visible structure?", - "Map Sequences to Visible Window: " + pdbentry.getId(), - JOptionPane.YES_NO_OPTION); - - if (option == JOptionPane.YES_OPTION) - { - StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, alreadyMapped, AppletFormatAdapter.FILE); - return; - } - } - /////////////////////////////////// - - this.ap = ap; - this.pdbentry = pdbentry; - this.sequence = seq; - - jalview.gui.Desktop.addInternalFrame(this, "Loading File", 400, 400); - - if (pdbentry.getFile() != null) - { - initJmol("load \""+pdbentry.getFile()+"\""); - } - else - { - Thread worker = new Thread(this); - worker.start(); - } - - this.addInternalFrameListener(new InternalFrameAdapter() - { - public void internalFrameClosing(InternalFrameEvent internalFrameEvent) - { - closeViewer(); - } - }); - } - - void initJmol(String command) - { - renderPanel = new RenderPanel(); - - this.getContentPane().add(renderPanel, java.awt.BorderLayout.CENTER); - - 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()); - - viewer = org.jmol.api.JmolViewer.allocateViewer(renderPanel, - new SmarterJmolAdapter()); - - - viewer.setAppletContext("", null, null, ""); - - viewer.setJmolStatusListener(this); - - jmolpopup = JmolPopup.newJmolPopup(viewer); - - viewer.evalStringQuiet(command); - } - - - void setChainMenuItems(Vector chains) - { - chainMenu.removeAll(); - - JMenuItem menuItem = new JMenuItem("All"); - menuItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent evt) - { - allChainsSelected = true; - for(int i=0; i 0) - cmd.setLength(cmd.length() - 4); - - viewer.evalStringQuiet("select *;restrict " - +cmd+";cartoon;center "+cmd); - } - - 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.getFile()); - } - - public void run() - { - try - { - EBIFetchClient ebi = new EBIFetchClient(); - String query = "pdb:" + pdbentry.getId(); - pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw") - .getAbsolutePath()); - initJmol("load "+pdbentry.getFile()); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - 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"); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - try - { - BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile())); - File outFile = chooser.getSelectedFile(); - - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; - while ( (data = in.readLine()) != null) - { - if ( - ! (data.indexOf("
") > -1 || data.indexOf("
") > -1) - ) - { - out.println(data); - } - } - out.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - } - - public void viewMapping_actionPerformed(ActionEvent actionEvent) - { - jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); - jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, - 600); - cap.setText( - StructureSelectionManager.getStructureSelectionManager().printMapping( - pdbentry.getFile()) - ); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void eps_actionPerformed(ActionEvent e) - { - makePDBImage(jalview.util.ImageMaker.EPS); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void png_actionPerformed(ActionEvent e) - { - makePDBImage(jalview.util.ImageMaker.PNG); - } - - void makePDBImage(int type) - { - int width = getWidth(); - int height = getHeight(); - - jalview.util.ImageMaker im; - - if (type == jalview.util.ImageMaker.PNG) - { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.PNG, - "Make PNG image from view", - width, height, - null, null); - } - else - { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.EPS, - "Make EPS file from view", - width, height, - null, this.getTitle()); - } - - if (im.getGraphics() != null) - { - Rectangle rect = new Rectangle(width, height); - viewer.renderScreenImage(im.getGraphics(), - rect.getSize(), rect); - im.writeImage(); - } - } - - - public void seqColour_actionPerformed(ActionEvent actionEvent) - { - colourBySequence = seqColour.isSelected(); - colourBySequence(ap); - } - - public void chainColour_actionPerformed(ActionEvent actionEvent) - { - colourBySequence = false; - seqColour.setSelected(false); - viewer.evalStringQuiet("select *;color chain"); - } - - public void chargeColour_actionPerformed(ActionEvent actionEvent) - { - colourBySequence = false; - seqColour.setSelected(false); - viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;" - +"select LYS,ARG;color blue;select CYS;color yellow"); - } - - public void zappoColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new ZappoColourScheme()); - } - - public void taylorColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new TaylorColourScheme()); - } - - public void hydroColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new HydrophobicColourScheme()); - } - - public void helixColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new HelixColourScheme()); - } - - public void strandColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new StrandColourScheme()); - } - - public void turnColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new TurnColourScheme()); - } - - public void buriedColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new BuriedColourScheme()); - } - - public void setJalviewColourScheme(ColourSchemeI cs) - { - colourBySequence = false; - seqColour.setSelected(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()); - } - - public void userColour_actionPerformed(ActionEvent actionEvent) - { - new UserDefinedColours(this, null); - } - - public void backGround_actionPerformed(ActionEvent actionEvent) - { - java.awt.Color col = JColorChooser.showDialog(this, - "Select Background Colour", - null); - - if (col != null) - { - viewer.evalStringQuiet("background [" - + col.getRed() + "," - + col.getGreen() + "," - + col.getBlue() + "];"); - } - } - - - public void jmolHelp_actionPerformed(ActionEvent actionEvent) - { - try{ - jalview.util.BrowserLauncher.openURL( - "http://jmol.sourceforge.net/docs/JmolUserGuide/"); - }catch(Exception ex){} - } - - - ////////////////////////////////// - ///StructureListener - public String getPdbFile() - { - return pdbentry.getFile(); - } - - Pattern pattern = Pattern.compile( - "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?" - ); - - String lastMessage; - public void mouseOverStructure(int atomIndex, String strInfo) - { - Matcher matcher = pattern.matcher(strInfo); - matcher.find(); - matcher.group(1); - int pdbResNum = Integer.parseInt(matcher.group(2)); - String chainId = matcher.group(3); - - if (chainId != null) - chainId = chainId.substring(1, chainId.length()); - 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(";color gold;wireframe 100"); - - Color col = new Color(viewer.getAtomArgb(atomIndex)); - - resetLastRes.append(";color[" - + col.getRed() + "," - + col.getGreen() + "," - + col.getBlue() + "];wireframe 0"); - - viewer.evalStringQuiet(eval.toString()); - - } - - public void updateColours(Object source) - { - colourBySequence( (AlignmentPanel) source); - } - - -//End StructureListener -//////////////////////////// - - FeatureRenderer fr; - public void colourBySequence(AlignmentPanel ap) - { - if(!colourBySequence) - return; - - - StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile()); - - if (mapping.length < 1) - return; - - SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer(); - - boolean showFeatures = false; - if (ap.av.showSequenceFeatures) - { - showFeatures = true; - if (fr == null) - { - fr = new jalview.gui.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]) - { - 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, 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; - } - } - } - - viewer.evalStringQuiet(command.toString()); - } - - StringBuffer condenseCommand(StringBuffer command, int pos) - { - StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7)); - - command.delete(0, sb.length()); - - String start; - - if (command.indexOf("-") > -1) - { - 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) - { - System.out.println("JMOL CREATE IMAGE"); - } - - 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; - } - - fileLoadingError = null; - - if (fileName != null) - { - - //FILE LOADED OK - ssm = StructureSelectionManager.getStructureSelectionManager(); - MCview.PDBfile pdbFile = ssm.setMapping(sequence, pdbentry.getFile(), AppletFormatAdapter.FILE); - ssm.addStructureViewerListener(this); - - Vector chains = new Vector(); - for(int i=0; i 0) + cmd.setLength(cmd.length() - 4); + + viewer.evalStringQuiet("select *;restrict " + +cmd+";cartoon;center "+cmd); + } + + 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.getFile()); + } + + public void run() + { + try + { + EBIFetchClient ebi = new EBIFetchClient(); + String query = "pdb:" + pdbentry.getId(); + pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw") + .getAbsolutePath()); + initJmol("load "+pdbentry.getFile()); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + 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"); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + try + { + BufferedReader in = new BufferedReader(new FileReader(pdbentry.getFile())); + File outFile = chooser.getSelectedFile(); + + PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); + String data; + while ( (data = in.readLine()) != null) + { + if ( + ! (data.indexOf("
") > -1 || data.indexOf("
") > -1) + ) + { + out.println(data); + } + } + out.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + public void viewMapping_actionPerformed(ActionEvent actionEvent) + { + jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); + jalview.gui.Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, + 600); + cap.setText( + StructureSelectionManager.getStructureSelectionManager().printMapping( + pdbentry.getFile()) + ); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void eps_actionPerformed(ActionEvent e) + { + makePDBImage(jalview.util.ImageMaker.EPS); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void png_actionPerformed(ActionEvent e) + { + makePDBImage(jalview.util.ImageMaker.PNG); + } + + void makePDBImage(int type) + { + int width = getWidth(); + int height = getHeight(); + + jalview.util.ImageMaker im; + + if (type == jalview.util.ImageMaker.PNG) + { + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.PNG, + "Make PNG image from view", + width, height, + null, null); + } + else + { + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.EPS, + "Make EPS file from view", + width, height, + null, this.getTitle()); + } + + if (im.getGraphics() != null) + { + Rectangle rect = new Rectangle(width, height); + viewer.renderScreenImage(im.getGraphics(), + rect.getSize(), rect); + im.writeImage(); + } + } + + + public void seqColour_actionPerformed(ActionEvent actionEvent) + { + colourBySequence = seqColour.isSelected(); + colourBySequence(ap); + } + + public void chainColour_actionPerformed(ActionEvent actionEvent) + { + colourBySequence = false; + seqColour.setSelected(false); + viewer.evalStringQuiet("select *;color chain"); + } + + public void chargeColour_actionPerformed(ActionEvent actionEvent) + { + colourBySequence = false; + seqColour.setSelected(false); + viewer.evalStringQuiet("select *;color white;select ASP,GLU;color red;" + +"select LYS,ARG;color blue;select CYS;color yellow"); + } + + public void zappoColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new ZappoColourScheme()); + } + + public void taylorColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new TaylorColourScheme()); + } + + public void hydroColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new HydrophobicColourScheme()); + } + + public void helixColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new HelixColourScheme()); + } + + public void strandColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new StrandColourScheme()); + } + + public void turnColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new TurnColourScheme()); + } + + public void buriedColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new BuriedColourScheme()); + } + + public void setJalviewColourScheme(ColourSchemeI cs) + { + colourBySequence = false; + seqColour.setSelected(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()); + } + + public void userColour_actionPerformed(ActionEvent actionEvent) + { + new UserDefinedColours(this, null); + } + + public void backGround_actionPerformed(ActionEvent actionEvent) + { + java.awt.Color col = JColorChooser.showDialog(this, + "Select Background Colour", + null); + + if (col != null) + { + viewer.evalStringQuiet("background [" + + col.getRed() + "," + + col.getGreen() + "," + + col.getBlue() + "];"); + } + } + + + public void jmolHelp_actionPerformed(ActionEvent actionEvent) + { + try{ + jalview.util.BrowserLauncher.openURL( + "http://jmol.sourceforge.net/docs/JmolUserGuide/"); + }catch(Exception ex){} + } + + + ////////////////////////////////// + ///StructureListener + public String getPdbFile() + { + return pdbentry.getFile(); + } + + Pattern pattern = Pattern.compile( + "\\[(.*)\\]([0-9]+)(:[a-zA-Z]*)?\\.([a-zA-Z]+)(/[0-9]*)?" + ); + + String lastMessage; + public void mouseOverStructure(int atomIndex, String strInfo) + { + Matcher matcher = pattern.matcher(strInfo); + matcher.find(); + matcher.group(1); + int pdbResNum = Integer.parseInt(matcher.group(2)); + String chainId = matcher.group(3); + + if (chainId != null) + chainId = chainId.substring(1, chainId.length()); + 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(";color gold;wireframe 100"); + + Color col = new Color(viewer.getAtomArgb(atomIndex)); + + resetLastRes.append(";color[" + + col.getRed() + "," + + col.getGreen() + "," + + col.getBlue() + "];wireframe 0"); + + viewer.evalStringQuiet(eval.toString()); + + } + + public void updateColours(Object source) + { + colourBySequence( (AlignmentPanel) source); + } + + +//End StructureListener +//////////////////////////// + + FeatureRenderer fr; + public void colourBySequence(AlignmentPanel ap) + { + if(!colourBySequence) + return; + + + StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile()); + + if (mapping.length < 1) + return; + + SequenceRenderer sr = ap.seqPanel.seqCanvas.getSequenceRenderer(); + + boolean showFeatures = false; + if (ap.av.showSequenceFeatures) + { + showFeatures = true; + if (fr == null) + { + fr = new jalview.gui.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]) + { + 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, 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; + } + } + } + + viewer.evalStringQuiet(command.toString()); + } + + StringBuffer condenseCommand(StringBuffer command, int pos) + { + StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7)); + + command.delete(0, sb.length()); + + String start; + + if (command.indexOf("-") > -1) + { + 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) + { + System.out.println("JMOL CREATE IMAGE"); + } + + 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; + } + + fileLoadingError = null; + + if (fileName != null) + { + + //FILE LOADED OK + ssm = StructureSelectionManager.getStructureSelectionManager(); + MCview.PDBfile pdbFile = ssm.setMapping(sequence, pdbentry.getFile(), AppletFormatAdapter.FILE); + ssm.addStructureViewerListener(this); + + Vector chains = new Vector(); + for(int i=0; i 0) diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index b4e63f4..37702af 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -1,350 +1,350 @@ -/* - * 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 - */ -package jalview.structure; - -import java.io.*; -import java.util.*; - -import MCview.*; -import jalview.analysis.*; -import jalview.datamodel.*; - -public class StructureSelectionManager -{ - static StructureSelectionManager instance; - StructureMapping[] mappings; - Hashtable mappingData = new Hashtable(); - - public static StructureSelectionManager getStructureSelectionManager() - { - if (instance == null) - { - instance = new StructureSelectionManager(); - } - - return instance; - } - - Vector listeners = new Vector(); - public void addStructureViewerListener(Object svl) - { - if (!listeners.contains(svl)) - { - listeners.addElement(svl); - } - } - - public String alreadyMappedToFile(String pdbid) - { - if (mappings != null) - { - for (int i = 0; i < mappings.length; i++) - { - if (mappings[i].getPdbId().equals(pdbid)) - { - return mappings[i].pdbfile; - } - } - } - return null; - } - - /* - There will be better ways of doing this in the future, for now we'll use - the tried and tested MCview pdb mapping - */ - public MCview.PDBfile setMapping(SequenceI[] sequence, - String pdbFile, - String protocol) - { - MCview.PDBfile pdb = null; - try - { - pdb = new MCview.PDBfile(pdbFile, protocol); - } - catch (Exception ex) - { - ex.printStackTrace(); - return null; - } - - for (int s = 0; s < sequence.length; s++) - { - String targetChain = ""; - - if (sequence[s].getName().indexOf("|") > -1) - { - targetChain = sequence[s].getName().substring( - sequence[s].getName().lastIndexOf("|") + 1); - } - - int max = -10; - AlignSeq maxAlignseq = null; - String maxChainId = " "; - PDBChain maxChain = null; - - for (int i = 0; i < pdb.chains.size(); i++) - { - AlignSeq as = new AlignSeq(sequence[s], - ( (PDBChain) pdb.chains.elementAt(i)). - sequence, - AlignSeq.PEP); - as.calcScoreMatrix(); - as.traceAlignment(); - PDBChain chain = ( (PDBChain) pdb.chains.elementAt(i)); - - if (as.maxscore > max - || (as.maxscore == max && chain.id.equals(targetChain))) - { - maxChain = chain; - max = as.maxscore; - maxAlignseq = as; - maxChainId = chain.id; - } - } - - final StringBuffer mappingDetails = new StringBuffer(); - mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + - maxChain.sequence.getSequenceAsString()); - mappingDetails.append("\nNo of residues = " + - maxChain.residues. - size() + - "\n\n"); - PrintStream ps = new PrintStream(System.out) - { - public void print(String x) - { - mappingDetails.append(x); - } - - public void println() - { - mappingDetails.append("\n"); - } - }; - - maxAlignseq.printAlignment(ps); - - mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start + " " + - maxAlignseq.seq2end); - mappingDetails.append("\nSEQ start/end " - + (maxAlignseq.seq1start + sequence[s].getStart() - 1) + - " " - + (maxAlignseq.seq1end + sequence[s].getEnd() - 1)); - - maxChain.makeExactMapping(maxAlignseq, sequence[s]); - - // maxChain.transferRESNUMFeatures(sequence[s], null); - - int[][] mapping = new int[sequence[s].getEnd() + 2][2]; - int resNum = -10000; - int index = 0; - - - do - { - Atom tmp = (Atom) maxChain.atoms.elementAt(index); - if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) - { - resNum = tmp.resNumber; - mapping[tmp.alignmentMapping+1][0] = tmp.resNumber; - mapping[tmp.alignmentMapping+1][1] = tmp.atomIndex; - } - - index++; - } - while(index < maxChain.atoms.size()); - - if (mappings == null) - { - mappings = new StructureMapping[1]; - } - else - { - StructureMapping[] tmp = new StructureMapping[mappings.length + 1]; - System.arraycopy(mappings, 0, tmp, 0, mappings.length); - mappings = tmp; - } - - if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) - pdbFile = "INLINE"+pdb.id; - - mappings[mappings.length - 1] - = new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId, - mapping, mappingDetails.toString()); - } - ///////// - - return pdb; - } - - public void removeStructureViewerListener(Object svl, String pdbfile) - { - listeners.removeElement(svl); - - boolean removeMapping = true; - - StructureListener sl; - for (int i = 0; i < listeners.size(); i++) - { - if (listeners.elementAt(i) instanceof StructureListener) - { - sl = (StructureListener) listeners.elementAt(i); - if (sl.getPdbFile().equals(pdbfile)) - { - removeMapping = false; - break; - } - } - } - - if (removeMapping && mappings!=null) - { - Vector tmp = new Vector(); - for (int i = 0; i < mappings.length; i++) - { - if (!mappings[i].pdbfile.equals(pdbfile)) - { - tmp.addElement(mappings[i]); - } - } - - mappings = new StructureMapping[tmp.size()]; - tmp.copyInto(mappings); - } - } - - public void mouseOverStructure(int pdbResNum, String chain, String pdbfile) - { - SequenceListener sl; - for (int i = 0; i < listeners.size(); i++) - { - if (listeners.elementAt(i) instanceof SequenceListener) - { - sl = (SequenceListener) listeners.elementAt(i); - - for (int j = 0; j < mappings.length; j++) - { - if (mappings[j].pdbfile.equals(pdbfile) && - mappings[j].pdbchain.equals(chain)) - { - sl.highlightSequence(mappings[j].sequence, - mappings[j].getSeqPos(pdbResNum)); - } - } - - sl.highlightSequence(null, pdbResNum); - } - } - } - - public void mouseOverSequence(SequenceI seq, int index) - { - StructureListener sl; - int atomNo = 0; - for (int i = 0; i < listeners.size(); i++) - { - if (listeners.elementAt(i) instanceof StructureListener) - { - sl = (StructureListener) listeners.elementAt(i); - - for (int j = 0; j < mappings.length; j++) - { - if (mappings[j].sequence == seq) - { - atomNo = mappings[j].getAtomNum(index); - - if (atomNo > 0) - { - sl.highlightAtom(atomNo, - mappings[j].getPDBResNum(index), - mappings[j].pdbchain, - mappings[j].pdbfile); - } - } - } - } - } - } - - public void structureSelectionChanged() - { - StructureListener svl; - for (int i = 0; i < listeners.size(); i++) - { - svl = (StructureListener) listeners.elementAt(i); - } - } - - public void sequenceSelectionChanged() - { - StructureListener svl; - for (int i = 0; i < listeners.size(); i++) - { - svl = (StructureListener) listeners.elementAt(i); - } - } - - public void sequenceColoursChanged(Object source) - { - StructureListener sl; - for (int i = 0; i < listeners.size(); i++) - { - if (listeners.elementAt(i) instanceof StructureListener) - { - sl = (StructureListener) listeners.elementAt(i); - sl.updateColours(source); - } - } - } - - public StructureMapping[] getMapping(String pdbfile) - { - Vector tmp = new Vector(); - for (int i = 0; i < mappings.length; i++) - { - if (mappings[i].pdbfile.equals(pdbfile)) - { - tmp.addElement(mappings[i]); - } - } - - StructureMapping[] ret = new StructureMapping[tmp.size()]; - for (int i = 0; i < tmp.size(); i++) - { - ret[i] = (StructureMapping) tmp.elementAt(i); - } - - return ret; - } - - public String printMapping(String pdbfile) - { - StringBuffer sb = new StringBuffer(); - for (int i = 0; i < mappings.length; i++) - { - if (mappings[i].pdbfile.equals(pdbfile)) - { - sb.append(mappings[i].mappingDetails); - } - } - - return sb.toString(); - } -} +/* + * 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 + */ +package jalview.structure; + +import java.io.*; +import java.util.*; + +import MCview.*; +import jalview.analysis.*; +import jalview.datamodel.*; + +public class StructureSelectionManager +{ + static StructureSelectionManager instance; + StructureMapping[] mappings; + Hashtable mappingData = new Hashtable(); + + public static StructureSelectionManager getStructureSelectionManager() + { + if (instance == null) + { + instance = new StructureSelectionManager(); + } + + return instance; + } + + Vector listeners = new Vector(); + public void addStructureViewerListener(Object svl) + { + if (!listeners.contains(svl)) + { + listeners.addElement(svl); + } + } + + public String alreadyMappedToFile(String pdbid) + { + if (mappings != null) + { + for (int i = 0; i < mappings.length; i++) + { + if (mappings[i].getPdbId().equals(pdbid)) + { + return mappings[i].pdbfile; + } + } + } + return null; + } + + /* + There will be better ways of doing this in the future, for now we'll use + the tried and tested MCview pdb mapping + */ + public MCview.PDBfile setMapping(SequenceI[] sequence, + String pdbFile, + String protocol) + { + MCview.PDBfile pdb = null; + try + { + pdb = new MCview.PDBfile(pdbFile, protocol); + } + catch (Exception ex) + { + ex.printStackTrace(); + return null; + } + + for (int s = 0; s < sequence.length; s++) + { + String targetChain = ""; + + if (sequence[s].getName().indexOf("|") > -1) + { + targetChain = sequence[s].getName().substring( + sequence[s].getName().lastIndexOf("|") + 1); + } + + int max = -10; + AlignSeq maxAlignseq = null; + String maxChainId = " "; + PDBChain maxChain = null; + + for (int i = 0; i < pdb.chains.size(); i++) + { + AlignSeq as = new AlignSeq(sequence[s], + ( (PDBChain) pdb.chains.elementAt(i)). + sequence, + AlignSeq.PEP); + as.calcScoreMatrix(); + as.traceAlignment(); + PDBChain chain = ( (PDBChain) pdb.chains.elementAt(i)); + + if (as.maxscore > max + || (as.maxscore == max && chain.id.equals(targetChain))) + { + maxChain = chain; + max = as.maxscore; + maxAlignseq = as; + maxChainId = chain.id; + } + } + + final StringBuffer mappingDetails = new StringBuffer(); + mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + + maxChain.sequence.getSequenceAsString()); + mappingDetails.append("\nNo of residues = " + + maxChain.residues. + size() + + "\n\n"); + PrintStream ps = new PrintStream(System.out) + { + public void print(String x) + { + mappingDetails.append(x); + } + + public void println() + { + mappingDetails.append("\n"); + } + }; + + maxAlignseq.printAlignment(ps); + + mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start + " " + + maxAlignseq.seq2end); + mappingDetails.append("\nSEQ start/end " + + (maxAlignseq.seq1start + sequence[s].getStart() - 1) + + " " + + (maxAlignseq.seq1end + sequence[s].getEnd() - 1)); + + maxChain.makeExactMapping(maxAlignseq, sequence[s]); + + maxChain.transferRESNUMFeatures(sequence[s], null); + + int[][] mapping = new int[sequence[s].getEnd() + 2][2]; + int resNum = -10000; + int index = 0; + + + do + { + Atom tmp = (Atom) maxChain.atoms.elementAt(index); + if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + { + resNum = tmp.resNumber; + mapping[tmp.alignmentMapping+1][0] = tmp.resNumber; + mapping[tmp.alignmentMapping+1][1] = tmp.atomIndex; + } + + index++; + } + while(index < maxChain.atoms.size()); + + if (mappings == null) + { + mappings = new StructureMapping[1]; + } + else + { + StructureMapping[] tmp = new StructureMapping[mappings.length + 1]; + System.arraycopy(mappings, 0, tmp, 0, mappings.length); + mappings = tmp; + } + + if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + pdbFile = "INLINE"+pdb.id; + + mappings[mappings.length - 1] + = new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId, + mapping, mappingDetails.toString()); + } + ///////// + + return pdb; + } + + public void removeStructureViewerListener(Object svl, String pdbfile) + { + listeners.removeElement(svl); + + boolean removeMapping = true; + + StructureListener sl; + for (int i = 0; i < listeners.size(); i++) + { + if (listeners.elementAt(i) instanceof StructureListener) + { + sl = (StructureListener) listeners.elementAt(i); + if (sl.getPdbFile().equals(pdbfile)) + { + removeMapping = false; + break; + } + } + } + + if (removeMapping && mappings!=null) + { + Vector tmp = new Vector(); + for (int i = 0; i < mappings.length; i++) + { + if (!mappings[i].pdbfile.equals(pdbfile)) + { + tmp.addElement(mappings[i]); + } + } + + mappings = new StructureMapping[tmp.size()]; + tmp.copyInto(mappings); + } + } + + public void mouseOverStructure(int pdbResNum, String chain, String pdbfile) + { + SequenceListener sl; + for (int i = 0; i < listeners.size(); i++) + { + if (listeners.elementAt(i) instanceof SequenceListener) + { + sl = (SequenceListener) listeners.elementAt(i); + + for (int j = 0; j < mappings.length; j++) + { + if (mappings[j].pdbfile.equals(pdbfile) && + mappings[j].pdbchain.equals(chain)) + { + sl.highlightSequence(mappings[j].sequence, + mappings[j].getSeqPos(pdbResNum)); + } + } + + sl.highlightSequence(null, pdbResNum); + } + } + } + + public void mouseOverSequence(SequenceI seq, int index) + { + StructureListener sl; + int atomNo = 0; + for (int i = 0; i < listeners.size(); i++) + { + if (listeners.elementAt(i) instanceof StructureListener) + { + sl = (StructureListener) listeners.elementAt(i); + + for (int j = 0; j < mappings.length; j++) + { + if (mappings[j].sequence == seq) + { + atomNo = mappings[j].getAtomNum(index); + + if (atomNo > 0) + { + sl.highlightAtom(atomNo, + mappings[j].getPDBResNum(index), + mappings[j].pdbchain, + mappings[j].pdbfile); + } + } + } + } + } + } + + public void structureSelectionChanged() + { + StructureListener svl; + for (int i = 0; i < listeners.size(); i++) + { + svl = (StructureListener) listeners.elementAt(i); + } + } + + public void sequenceSelectionChanged() + { + StructureListener svl; + for (int i = 0; i < listeners.size(); i++) + { + svl = (StructureListener) listeners.elementAt(i); + } + } + + public void sequenceColoursChanged(Object source) + { + StructureListener sl; + for (int i = 0; i < listeners.size(); i++) + { + if (listeners.elementAt(i) instanceof StructureListener) + { + sl = (StructureListener) listeners.elementAt(i); + sl.updateColours(source); + } + } + } + + public StructureMapping[] getMapping(String pdbfile) + { + Vector tmp = new Vector(); + for (int i = 0; i < mappings.length; i++) + { + if (mappings[i].pdbfile.equals(pdbfile)) + { + tmp.addElement(mappings[i]); + } + } + + StructureMapping[] ret = new StructureMapping[tmp.size()]; + for (int i = 0; i < tmp.size(); i++) + { + ret[i] = (StructureMapping) tmp.elementAt(i); + } + + return ret; + } + + public String printMapping(String pdbfile) + { + StringBuffer sb = new StringBuffer(); + for (int i = 0; i < mappings.length; i++) + { + if (mappings[i].pdbfile.equals(pdbfile)) + { + sb.append(mappings[i].mappingDetails); + } + } + + return sb.toString(); + } +} -- 1.7.10.2