From: j.procter@dundee.ac.uk Date: Fri, 4 Jul 2014 03:09:00 +0000 (-0700) Subject: JAL-1333 more abstraction and refactoring and working demo of Jalview talking to... X-Git-Tag: Jalview_2_9~179^2~13 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;ds=sidebyside;h=ae216fceddd8539d20fa5425cdaef3da73aba8f0;p=jalview.git JAL-1333 more abstraction and refactoring and working demo of Jalview talking to Chimera --- diff --git a/.classpath b/.classpath index 36a4c97..fae5ca0 100644 --- a/.classpath +++ b/.classpath @@ -9,7 +9,6 @@ - @@ -48,7 +47,10 @@ - + + + + diff --git a/lib/log4j-1.2.8.jar b/lib/log4j-1.2.8.jar deleted file mode 100755 index 05f8702..0000000 Binary files a/lib/log4j-1.2.8.jar and /dev/null differ diff --git a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java index d0bb84e..a82a6fb 100644 --- a/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java +++ b/src/ext/edu/ucsf/rbvi/strucviz2/ChimeraManager.java @@ -670,4 +670,9 @@ public class ChimeraManager return chimeraListenerThreads.getResponse(command); } + public StructureManager getStructureManager() + { + return structureManager; + } + } diff --git a/src/jalview/api/structures/JalviewStructureDisplayI.java b/src/jalview/api/structures/JalviewStructureDisplayI.java index 0b3820b..efb60dd 100644 --- a/src/jalview/api/structures/JalviewStructureDisplayI.java +++ b/src/jalview/api/structures/JalviewStructureDisplayI.java @@ -26,6 +26,8 @@ import jalview.api.SequenceStructureBinding; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.ext.jmol.JalviewJmolBinding; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.UserColourScheme; import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; @@ -57,5 +59,10 @@ public interface JalviewStructureDisplayI * shutdown any structure viewing processes started by this display */ void closeViewer(); + /** + * apply a colourscheme to the structures in the viewer + * @param colourScheme + */ + void setJalviewColourScheme(ColourSchemeI colourScheme); } diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java new file mode 100644 index 0000000..41c7abb --- /dev/null +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -0,0 +1,162 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.ext.rbvi.chimera; + +import jalview.api.FeatureRenderer; +import jalview.api.SequenceRenderer; +import jalview.api.structures.JalviewStructureDisplayI; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; +import jalview.structure.StructureMapping; +import jalview.structure.StructureMappingcommandSet; +import jalview.structure.StructureSelectionManager; +import jalview.util.Format; + +import java.awt.Color; +import java.util.ArrayList; + +/** + * Routines for generating Chimera commands for Jalview/Chimera binding + * + * @author JimP + * + */ +public class ChimeraCommands +{ + + /** + * utility to construct the commands to colour chains by the given alignment + * for passing to Chimera + * + * @returns Object[] { Object[] { , + * + */ + public static StructureMappingcommandSet[] getColourBySequenceCommand( + StructureSelectionManager ssm, String[] files, + SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, + AlignmentI alignment) + { + + ArrayList cset = new ArrayList(); + + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + float cols[] = new float[4]; + StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + StringBuffer command = new StringBuffer(); + StructureMappingcommandSet smc; + ArrayList str = new ArrayList(); + + if (mapping == null || mapping.length < 1) + continue; + + int startPos = -1, lastPos = -1, startModel = -1, lastModel = -1; + String startChain = "", lastChain = ""; + Color lastCol = null; + for (int s = 0; s < sequence[pdbfnum].length; s++) + { + for (int sp, m = 0; m < mapping.length; m++) + { + if (mapping[m].getSequence() == sequence[pdbfnum][s] + && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) + { + SequenceI asp = alignment.getSequenceAt(sp); + for (int r = 0; r < asp.getLength(); r++) + { + // no mapping to gaps in sequence + if (jalview.util.Comparison.isGap(asp.getCharAt(r))) + { + continue; + } + int pos = mapping[m].getPDBResNum(asp.findPosition(r)); + + if (pos < 1 || pos == lastPos) + continue; + + Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r); + + if (fr != null) + col = fr.findFeatureColour(col, sequence[pdbfnum][s], r); + if (lastCol != col || lastPos + 1 != pos + || pdbfnum != lastModel + || !mapping[m].getChain().equals(lastChain)) + { + if (lastCol != null) + { + + lastCol.getRGBComponents(cols); + String newSelcom = "color " + cols[0] + "," + cols[1] + + "," + cols[2] + " #" + startModel + ":" + + startPos + "-" + lastPos + "." + lastChain; + if (str.size() > 0 + && (str.get(str.size() - 1).length() + newSelcom + .length()) < 4096) + { + str.set(str.size() - 1, str.get(str.size() - 1) + ";" + + newSelcom); + } + else + { + str.add(newSelcom); + } + } + lastCol = null; + startPos = pos; + startModel = pdbfnum; + startChain = mapping[m].getChain(); + } + lastCol = col; + lastPos = pos; + lastModel = pdbfnum; + lastChain = mapping[m].getChain(); + } + // final colour range + if (lastCol != null) + { + + lastCol.getRGBComponents(cols); + String newSelcom = "color " + cols[0] + "," + cols[1] + "," + + cols[2] + " #" + startModel + ":" + startPos + "-" + + lastPos + "." + lastChain; + if (str.size() > 0 + && (str.get(str.size() - 1).length() + newSelcom + .length()) < 4096) + { + str.set(str.size() - 1, str.get(str.size() - 1) + ";" + + newSelcom); + } + else + { + str.add(newSelcom); + } + } + break; + } + } + } + // Finally, add the command set ready to be returned. + cset.add(new StructureMappingcommandSet(ChimeraCommands.class, + files[pdbfnum], str.toArray(new String[str.size()]))); + } + return cset.toArray(new StructureMappingcommandSet[cset.size()]); + } + +} diff --git a/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java new file mode 100644 index 0000000..7e72d8f --- /dev/null +++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java @@ -0,0 +1,1446 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.ext.rbvi.chimera; + +import static org.junit.Assert.assertTrue; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; +import jalview.api.SequenceRenderer; +import jalview.api.SequenceStructureBinding; +import jalview.api.StructureSelectionManagerProvider; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.io.AppletFormatAdapter; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; +import jalview.structures.models.SequenceStructureBindingModel; + +import java.awt.Color; +import java.awt.Container; +import java.awt.event.ComponentEvent; +import java.awt.event.ComponentListener; +import java.io.File; +import java.net.URL; +import java.security.AccessControlException; +import java.util.ArrayList; +import java.util.Collection; +import java.util.Enumeration; +import java.util.HashMap; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.Vector; + +import org.jmol.adapter.smarter.SmarterJmolAdapter; +import org.jmol.api.JmolAppConsoleInterface; +import org.jmol.api.JmolSelectionListener; +import org.jmol.api.JmolStatusListener; +import org.jmol.api.JmolViewer; +import org.jmol.constant.EnumCallback; +import org.jmol.popup.JmolPopup; + +import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager; +import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel; +import ext.edu.ucsf.rbvi.strucviz2.StructureManager; +import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType; +import sun.rmi.runtime.Log; + +public abstract class JalviewChimeraBinding extends + SequenceStructureBindingModel implements StructureListener, + SequenceStructureBinding, StructureSelectionManagerProvider + +{ + private StructureManager csm; + + private ChimeraManager viewer; + + /** + * set if chimera state is being restored from some source - instructs binding + * not to apply default display style when structure set is updated for first + * time. + */ + private boolean loadingFromArchive = false; + + /** + * second flag to indicate if the jmol viewer should ignore sequence colouring + * events from the structure manager because the GUI is still setting up + */ + private boolean loadingFinished = true; + + /** + * state flag used to check if the Jmol viewer's paint method can be called + */ + private boolean finishedInit = false; + + public boolean isFinishedInit() + { + return finishedInit; + } + + public void setFinishedInit(boolean finishedInit) + { + this.finishedInit = finishedInit; + } + + boolean allChainsSelected = false; + + /** + * when true, try to search the associated datamodel for sequences that are + * associated with any unknown structures in the Jmol view. + */ + private boolean associateNewStructs = false; + + Vector atomsPicked = new Vector(); + + public Vector chainNames; + + Hashtable chainFile; + + /** + * array of target chains for seuqences - tied to pdbentry and sequence[] + */ + protected String[][] chains; + + boolean colourBySequence = true; + + StringBuffer eval = new StringBuffer(); + + public String fileLoadingError; + + private Map> chimmaps = new HashMap>(); + + private List mdlToFile = new ArrayList(); + + /** + * the default or current model displayed if the model cannot be identified + * from the selection message + */ + int frameNo = 0; + + String lastCommand; + + String lastMessage; + + boolean loadedInline; + + public boolean openFile(PDBEntry pe) + { + String file = pe.getFile(); + try + { + List oldList = viewer.getModelList(); + viewer.openModel(file, ModelType.PDB_MODEL); + List newList = viewer.getModelList(); + if (oldList.size() < newList.size()) + { + while (oldList.size() > 0) + { + oldList.remove(0); + newList.remove(0); + } + chimmaps.put(file, newList); + for (ChimeraModel cm : newList) + { + while (mdlToFile.size()<1+cm.getModelNumber()) + { + mdlToFile.add(new String("")); + } + mdlToFile.set(cm.getModelNumber(), file); + } + + File fl = new File(file); + String protocol = AppletFormatAdapter.URL; + try + { + if (fl.exists()) + { + protocol = AppletFormatAdapter.FILE; + } + } catch (Exception e) + { + } catch (Error e) + { + } + // Explicitly map to the filename used by Jmol ; + // pdbentry[pe].getFile(), protocol); + + if (ssm != null) + { + ssm.addStructureViewerListener(this); + // ssm.addSelectionListener(this); + FeatureRenderer fr = getFeatureRenderer(null); + if (fr != null) + { + fr.featuresAdded(); + } + refreshGUI(); + } + return true; + } + } catch (Exception q) + { + log("Exception when trying to open model " + file + "\n" + + q.toString()); + q.printStackTrace(); + } + return false; + } + + /** + * current set of model filenames loaded + */ + String[] modelFileNames = null; + + public PDBEntry[] pdbentry; + + /** + * datasource protocol for access to PDBEntrylatest + */ + String protocol = null; + + StringBuffer resetLastRes = new StringBuffer(); + + /** + * sequences mapped to each pdbentry + */ + public SequenceI[][] sequence; + + public StructureSelectionManager ssm; + + private List lastReply; + + public JalviewChimeraBinding(StructureSelectionManager ssm, + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, + String protocol) + { + this.ssm = ssm; + this.sequence = sequenceIs; + this.chains = chains; + this.pdbentry = pdbentry; + this.protocol = protocol; + if (chains == null) + { + this.chains = new String[pdbentry.length][]; + } + viewer = new ChimeraManager( + csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); + /* + * viewer = JmolViewer.allocateViewer(renderPanel, new SmarterJmolAdapter(), + * "jalviewJmol", ap.av.applet .getDocumentBase(), + * ap.av.applet.getCodeBase(), "", this); + * + * jmolpopup = JmolPopup.newJmolPopup(viewer, true, "Jmol", true); + */ + } + + public JalviewChimeraBinding(StructureSelectionManager ssm, + ChimeraManager viewer2) + { + this.ssm = ssm; + viewer = viewer2; + csm = viewer.getStructureManager(); + } + + /** + * construct a title string for the viewer window based on the data jalview + * knows about + * + * @return + */ + public String getViewerTitle() + { + if (sequence == null || pdbentry == null || sequence.length < 1 + || pdbentry.length < 1 || sequence[0].length < 1) + { + return ("Jalview Chimera Window"); + } + // TODO: give a more informative title when multiple structures are + // displayed. + StringBuffer title = new StringBuffer("Chimera view for " + + sequence[0][0].getName() + ":" + pdbentry[0].getId()); + + if (pdbentry[0].getProperty() != null) + { + if (pdbentry[0].getProperty().get("method") != null) + { + title.append(" Method: "); + title.append(pdbentry[0].getProperty().get("method")); + } + if (pdbentry[0].getProperty().get("chains") != null) + { + title.append(" Chain:"); + title.append(pdbentry[0].getProperty().get("chains")); + } + } + return title.toString(); + } + + /** + * prepare the view for a given set of models/chains. chainList contains + * strings of the form 'pdbfilename:Chaincode' + * + * @param chainList + * list of chains to make visible + */ + public void centerViewer(Vector chainList) + { + StringBuffer cmd = new StringBuffer(); + String lbl; + int mlength, p; + for (int i = 0, iSize = chainList.size(); i < iSize; i++) + { + mlength = 0; + lbl = (String) chainList.elementAt(i); + do + { + p = mlength; + mlength = lbl.indexOf(":", p); + } while (p < mlength && mlength < (lbl.length() - 2)); + // TODO: lookup each pdb id and recover proper model number for it. + cmd.append("#" + getModelNum((String) chainFile.get(lbl)) + "." + + lbl.substring(mlength + 1) + " or "); + } + if (cmd.length() > 0) + cmd.setLength(cmd.length() - 4); + evalStateCommand("~display #*; ~ribbon #*; ribbon " + cmd + ";focus " + + cmd); + } + + public void closeViewer() + { + ssm.removeStructureViewerListener(this, this.getPdbFile()); + // and shut down Chimera + viewer.exitChimera(); + // viewer.evalStringQuiet("zap"); + // viewer.setJmolStatusListener(null); + lastCommand = null; + viewer = null; + releaseUIResources(); + } + + /** + * called by JalviewJmolbinding after closeViewer is called - release any + * resources and references so they can be garbage collected. + */ + protected abstract void releaseUIResources(); + + public void colourByChain() + { + colourBySequence = false; + // TODO: colour by chain should colour each chain distinctly across all + // visible models + // TODO: http://issues.jalview.org/browse/JAL-628 + evalStateCommand("select *;color chain"); + } + + public void colourByCharge() + { + colourBySequence = false; + evalStateCommand("colour *;color white;select ASP,GLU;color red;" + + "select LYS,ARG;color blue;select CYS;color yellow"); + } + + /** + * superpose the structures associated with sequences in the alignment + * according to their corresponding positions. + */ + public void superposeStructures(AlignmentI alignment) + { + superposeStructures(alignment, -1, null); + } + + /** + * superpose the structures associated with sequences in the alignment + * according to their corresponding positions. ded) + * + * @param refStructure + * - select which pdb file to use as reference (default is -1 - the + * first structure in the alignment) + */ + public void superposeStructures(AlignmentI alignment, int refStructure) + { + superposeStructures(alignment, refStructure, null); + } + + /** + * superpose the structures associated with sequences in the alignment + * according to their corresponding positions. ded) + * + * @param refStructure + * - select which pdb file to use as reference (default is -1 - the + * first structure in the alignment) + * @param hiddenCols + * TODO + */ + public void superposeStructures(AlignmentI alignment, int refStructure, + ColumnSelection hiddenCols) + { + superposeStructures(new AlignmentI[] + { alignment }, new int[] + { refStructure }, new ColumnSelection[] + { hiddenCols }); + } + + public void superposeStructures(AlignmentI[] _alignment, + int[] _refStructure, ColumnSelection[] _hiddenCols) + { + assert (_alignment.length == _refStructure.length && _alignment.length != _hiddenCols.length); + + String[] files = getPdbFile(); + // check to see if we are still waiting for Jmol files + long starttime = System.currentTimeMillis(); + boolean waiting = true; + do + { + waiting = false; + for (String file : files) + { + try + { + // HACK - in Jalview 2.8 this call may not be threadsafe so we catch + // every possible exception + StructureMapping[] sm = ssm.getMapping(file); + if (sm == null || sm.length == 0) + { + waiting = true; + } + } catch (Exception x) + { + waiting = true; + } catch (Error q) + { + waiting = true; + } + } + // we wait around for a reasonable time before we give up + } while (waiting + && System.currentTimeMillis() < (10000 + 1000 * files.length + starttime)); + if (waiting) + { + System.err + .println("RUNTIME PROBLEM: Jmol seems to be taking a long time to process all the structures."); + return; + } + StringBuffer selectioncom = new StringBuffer(); + // In principle - nSeconds specifies the speed of animation for each + // superposition - but is seems to behave weirdly, so we don't specify it. + String nSeconds = " "; + if (files.length > 10) + { + nSeconds = " 0.00001 "; + } + else + { + nSeconds = " " + (2.0 / files.length) + " "; + // if (nSeconds).substring(0,5)+" "; + } + // see JAL-1345 - should really automatically turn off the animation for + // large numbers of structures, but Jmol doesn't seem to allow that. + nSeconds = " "; + // union of all aligned positions are collected together. + for (int a = 0; a < _alignment.length; a++) + { + int refStructure = _refStructure[a]; + AlignmentI alignment = _alignment[a]; + ColumnSelection hiddenCols = _hiddenCols[a]; + if (a > 0 + && selectioncom.length() > 0 + && !selectioncom.substring(selectioncom.length() - 1).equals( + "|")) + { + selectioncom.append("|"); + } + // process this alignment + if (refStructure >= files.length) + { + System.err.println("Invalid reference structure value " + + refStructure); + refStructure = -1; + } + if (refStructure < -1) + { + refStructure = -1; + } + StringBuffer command = new StringBuffer(); + + boolean matched[] = new boolean[alignment.getWidth()]; + for (int m = 0; m < matched.length; m++) + { + + matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true; + } + + int commonrpositions[][] = new int[files.length][alignment.getWidth()]; + String isel[] = new String[files.length]; + // reference structure - all others are superposed in it + String[] targetC = new String[files.length]; + String[] chainNames = new String[files.length]; + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + // RACE CONDITION - getMapping only returns Jmol loaded filenames once + // Jmol callback has completed. + if (mapping == null || mapping.length < 1) + { + throw new Error( + "Implementation error - Jmol seems to be still working on getting its data - report at http://issues.jalview.org/browse/JAL-1016"); + } + int lastPos = -1; + for (int s = 0; s < sequence[pdbfnum].length; s++) + { + for (int sp, m = 0; m < mapping.length; m++) + { + if (mapping[m].getSequence() == sequence[pdbfnum][s] + && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1) + { + if (refStructure == -1) + { + refStructure = pdbfnum; + } + SequenceI asp = alignment.getSequenceAt(sp); + for (int r = 0; r < matched.length; r++) + { + if (!matched[r]) + { + continue; + } + matched[r] = false; // assume this is not a good site + if (r >= asp.getLength()) + { + continue; + } + + if (jalview.util.Comparison.isGap(asp.getCharAt(r))) + { + // no mapping to gaps in sequence + continue; + } + int t = asp.findPosition(r); // sequence position + int apos = mapping[m].getAtomNum(t); + int pos = mapping[m].getPDBResNum(t); + + if (pos < 1 || pos == lastPos) + { + // can't align unmapped sequence + continue; + } + matched[r] = true; // this is a good ite + lastPos = pos; + // just record this residue position + commonrpositions[pdbfnum][r] = pos; + } + // create model selection suffix + isel[pdbfnum] = "/" + (pdbfnum + 1) + ".1"; + if (mapping[m].getChain() == null + || mapping[m].getChain().trim().length() == 0) + { + targetC[pdbfnum] = ""; + } + else + { + targetC[pdbfnum] = ":" + mapping[m].getChain(); + } + chainNames[pdbfnum] = mapping[m].getPdbId() + + targetC[pdbfnum]; + // move on to next pdb file + s = sequence[pdbfnum].length; + break; + } + } + } + } + + // TODO: consider bailing if nmatched less than 4 because superposition + // not + // well defined. + // TODO: refactor superposable position search (above) from jmol selection + // construction (below) + + String[] selcom = new String[files.length]; + int nmatched = 0; + // generate select statements to select regions to superimpose structures + { + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + String chainCd = targetC[pdbfnum]; + int lpos = -1; + boolean run = false; + StringBuffer molsel = new StringBuffer(); + molsel.append("{"); + for (int r = 0; r < matched.length; r++) + { + if (matched[r]) + { + if (pdbfnum == 0) + { + nmatched++; + } + if (lpos != commonrpositions[pdbfnum][r] - 1) + { + // discontinuity + if (lpos != -1) + { + molsel.append(lpos); + molsel.append(chainCd); + // molsel.append("} {"); + molsel.append("|"); + } + } + else + { + // continuous run - and lpos >-1 + if (!run) + { + // at the beginning, so add dash + molsel.append(lpos); + molsel.append("-"); + } + run = true; + } + lpos = commonrpositions[pdbfnum][r]; + // molsel.append(lpos); + } + } + // add final selection phrase + if (lpos != -1) + { + molsel.append(lpos); + molsel.append(chainCd); + molsel.append("}"); + } + if (molsel.length() > 1) + { + selcom[pdbfnum] = molsel.toString(); + selectioncom.append("(("); + selectioncom.append(selcom[pdbfnum].substring(1, + selcom[pdbfnum].length() - 1)); + selectioncom.append(" )& "); + selectioncom.append(pdbfnum + 1); + selectioncom.append(".1)"); + if (pdbfnum < files.length - 1) + { + selectioncom.append("|"); + } + } + else + { + selcom[pdbfnum] = null; + } + } + } + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + if (pdbfnum == refStructure || selcom[pdbfnum] == null + || selcom[refStructure] == null) + { + continue; + } + command.append("echo "); + command.append("\"Superposing ("); + command.append(chainNames[pdbfnum]); + command.append(") against reference ("); + command.append(chainNames[refStructure]); + command.append(")\";\ncompare " + nSeconds); + command.append("{"); + command.append(1 + pdbfnum); + command.append(".1} {"); + command.append(1 + refStructure); + command.append(".1} SUBSET {*.CA | *.P} ATOMS "); + + // form the matched pair strings + String sep = ""; + for (int s = 0; s < 2; s++) + { + command.append(selcom[(s == 0 ? pdbfnum : refStructure)]); + } + command.append(" ROTATE TRANSLATE;\n"); + } + if (selectioncom.length() > 0) + { + System.out.println("Select regions:\n" + selectioncom.toString()); + evalStateCommand("select *; cartoons off; backbone; select (" + + selectioncom.toString() + "); cartoons; "); + // selcom.append("; ribbons; "); + System.out + .println("Superimpose command(s):\n" + command.toString()); + + evalStateCommand(command.toString()); + } + } + if (selectioncom.length() > 0) + {// finally, mark all regions that were superposed. + if (selectioncom.substring(selectioncom.length() - 1).equals("|")) + { + selectioncom.setLength(selectioncom.length() - 1); + } + System.out.println("Select regions:\n" + selectioncom.toString()); + evalStateCommand("select *; cartoons off; backbone; select (" + + selectioncom.toString() + "); cartoons; "); + // evalStateCommand("select *; backbone; select "+selcom.toString()+"; cartoons; center "+selcom.toString()); + } + } + + private void checkLaunched() + { + if (!viewer.isChimeraLaunched()) + { + viewer.launchChimera(csm.getChimeraPaths()); + } + if (!viewer.isChimeraLaunched()) + { + log("Failed to launch Chimera!"); + } + } + + public void evalStateCommand(String command) + { + viewerCommandHistory(false); + checkLaunched(); + if (lastCommand == null || !lastCommand.equals(command)) + { + + lastReply = viewer.sendChimeraCommand(command, true); + if (debug) + { + log("Response from command ('" + command + "') was:\n" + lastReply); + } + } + viewerCommandHistory(true); + lastCommand = command; + } + + /** + * colour any structures associated with sequences in the given alignment + * using the getFeatureRenderer() and getSequenceRenderer() renderers but only + * if colourBySequence is enabled. + */ + public void colourBySequence(boolean showFeatures, + jalview.api.AlignmentViewPanel alignmentv) + { + if (!colourBySequence || !loadingFinished) + return; + if (ssm == null) + { + return; + } + String[] files = getPdbFile(); + + SequenceRenderer sr = getSequenceRenderer(alignmentv); + + FeatureRenderer fr = null; + if (showFeatures) + { + fr = getFeatureRenderer(alignmentv); + } + AlignmentI alignment = alignmentv.getAlignment(); + + for (jalview.structure.StructureMappingcommandSet cpdbbyseq : ChimeraCommands + .getColourBySequenceCommand(ssm, files, sequence, sr, fr, + alignment)) + for (String cbyseq : cpdbbyseq.commands) + { + evalStateCommand(cbyseq); + } + } + + public boolean isColourBySequence() + { + return colourBySequence; + } + + public void setColourBySequence(boolean colourBySequence) + { + this.colourBySequence = colourBySequence; + } + + public void createImage(String file, String type, int quality) + { + System.out.println("JMOL CREATE IMAGE"); + } + + public String createImage(String fileName, String type, + Object textOrBytes, int quality) + { + System.out.println("JMOL CREATE IMAGE"); + return null; + } + + public String eval(String strEval) + { + // System.out.println(strEval); + // "# 'eval' is implemented only for the applet."; + return null; + } + + // End StructureListener + // ////////////////////////// + + public float[][] functionXY(String functionName, int x, int y) + { + return null; + } + + public float[][][] functionXYZ(String functionName, int nx, int ny, int nz) + { + // TODO Auto-generated method stub + return null; + } + + public Color getColour(int atomIndex, int pdbResNum, String chain, + String pdbfile) + { + if (getModelNum(pdbfile) < 0) + return null; + log("get model / residue colour attribute unimplemented"); + return null; + } + + /** + * returns the current featureRenderer that should be used to colour the + * structures + * + * @param alignment + * + * @return + */ + public abstract FeatureRenderer getFeatureRenderer( + AlignmentViewPanel alignment); + + /** + * instruct the Jalview binding to update the pdbentries vector if necessary + * prior to matching the jmol view's contents to the list of structure files + * Jalview knows about. + */ + public abstract void refreshPdbEntries(); + + private int getModelNum(String modelFileName) + { + String[] mfn = getPdbFile(); + if (mfn == null) + { + return -1; + } + for (int i = 0; i < mfn.length; i++) + { + if (mfn[i].equalsIgnoreCase(modelFileName)) + return i; + } + return -1; + } + + /** + * map between index of model filename returned from getPdbFile and the first + * index of models from this file in the viewer. Note - this is not trimmed - + * use getPdbFile to get number of unique models. + */ + private int _modelFileNameMap[]; + + // //////////////////////////////// + // /StructureListener + public synchronized String[] getPdbFile() + { + if (viewer == null) + { + return new String[0]; + } +// if (modelFileNames == null) +// { +// Collection chimodels = viewer.getChimeraModels(); +// _modelFileNameMap = new int[chimodels.size()]; +// int j = 0; +// for (ChimeraModel chimodel : chimodels) +// { +// String mdlName = chimodel.getModelName(); +// } +// modelFileNames = new String[j]; +// // System.arraycopy(mset, 0, modelFileNames, 0, j); +// } + + return chimmaps.keySet().toArray( + modelFileNames = new String[chimmaps.size()]); + } + + /** + * map from string to applet + */ + public Map getRegistryInfo() + { + // TODO Auto-generated method stub + return null; + } + + /** + * returns the current sequenceRenderer that should be used to colour the + * structures + * + * @param alignment + * + * @return + */ + public abstract SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment); + + // jmol/ssm only + public void highlightAtom(int atomIndex, int pdbResNum, String chain, + String pdbfile) + { + List cms = chimmaps.get(pdbfile); + if (cms != null) + { + int mdlNum = cms.get(0).getModelNumber(); + + viewerCommandHistory(false); + viewer.stopListening(); + if (resetLastRes.length() > 0) + { + viewer.sendChimeraCommand(resetLastRes.toString(), false); + } + + eval.setLength(0); + eval.append("display "); // +modelNum + + resetLastRes.setLength(0); + resetLastRes.append("~display "); + { + eval.append(" #" + (mdlNum)); + resetLastRes.append("#" + (mdlNum)); + } + // complete select string + + eval.append(":" + pdbResNum); + resetLastRes.append(":" + pdbResNum); + if (!chain.equals(" ")) + { + eval.append("." + chain); + resetLastRes.append("." + chain); + } + eval.append(eval.toString()); + + resetLastRes.append(resetLastRes.toString() + ); + + viewer.sendChimeraCommand(eval.toString(), false); + viewerCommandHistory(true); + viewer.startListening(); + } + } + + boolean debug = true; + + private void log(String message) + { + System.err.println("## Chimera log: " + message); + } + + private void viewerCommandHistory(boolean enable) + { + log("(Not yet implemented) History " + + ((debug || enable) ? "on" : "off")); + } + + public void loadInline(String string) + { + loadedInline = true; + // TODO: re JAL-623 + // viewer.loadInline(strModel, isAppend); + // could do this: + // construct fake fullPathName and fileName so we can identify the file + // later. + // Then, construct pass a reader for the string to Jmol. + // ((org.jmol.Viewer.Viewer) viewer).loadModelFromFile(fullPathName, + // fileName, null, reader, false, null, null, 0); + // viewer.openStringInline(string); + log("cannot load inline in Chimera, yet"); + } + + public void mouseOverStructure(int atomIndex, String strInfo) + { + // function to parse a mouseOver event from Chimera + // + int pdbResNum; + int alocsep = strInfo.indexOf("^"); + int mdlSep = strInfo.indexOf("/"); + int chainSeparator = strInfo.indexOf(":"), chainSeparator1 = -1; + + if (chainSeparator == -1) + { + chainSeparator = strInfo.indexOf("."); + if (mdlSep > -1 && mdlSep < chainSeparator) + { + chainSeparator1 = chainSeparator; + chainSeparator = mdlSep; + } + } + // handle insertion codes + if (alocsep != -1) + { + pdbResNum = Integer.parseInt(strInfo.substring( + strInfo.indexOf("]") + 1, alocsep)); + + } + else + { + 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 = " "; + } + + String pdbfilename = modelFileNames[frameNo]; // default is first or current + // model + if (mdlSep > -1) + { + if (chainSeparator1 == -1) + { + chainSeparator1 = strInfo.indexOf(".", mdlSep); + } + String mdlId = (chainSeparator1 > -1) ? strInfo.substring(mdlSep + 1, + chainSeparator1) : strInfo.substring(mdlSep + 1); + try + { + // recover PDB filename for the model hovered over. + int _mp = _modelFileNameMap.length - 1, mnumber = new Integer(mdlId) + .intValue() - 1; + while (mnumber < _modelFileNameMap[_mp]) + { + _mp--; + } + pdbfilename = modelFileNames[_mp]; + if (pdbfilename == null) + { + // pdbfilename = new File(viewer.getModelFileName(mnumber)) + // .getAbsolutePath(); + } + + } catch (Exception e) + { + } + ; + } + if (lastMessage == null || !lastMessage.equals(strInfo)) + ssm.mouseOverStructure(pdbResNum, chainId, pdbfilename); + + lastMessage = strInfo; + } + + public void notifyAtomPicked(int atomIndex, String strInfo, String strData) + { + /** + * this implements the toggle label behaviour copied from the original + * structure viewer, MCView + */ + if (strData != null) + { + System.err.println("Ignoring additional pick data string " + strData); + } + // rewrite these selections for chimera (DNA, RNA and protein) + int chainSeparator = strInfo.indexOf(":"); + int p = 0; + if (chainSeparator == -1) + chainSeparator = strInfo.indexOf("."); + + String picked = strInfo.substring(strInfo.indexOf("]") + 1, + chainSeparator); + String mdlString = ""; + if ((p = strInfo.indexOf(":")) > -1) + picked += strInfo.substring(p + 1, strInfo.indexOf(".")); + + if ((p = strInfo.indexOf("/")) > -1) + { + mdlString += strInfo.substring(p, strInfo.indexOf(" #")); + } + picked = "((" + picked + ".CA" + mdlString + ")|(" + picked + ".P" + + mdlString + "))"; + viewerCommandHistory(false); + + if (!atomsPicked.contains(picked)) + { + viewer.select(picked); + atomsPicked.addElement(picked); + } + else + { + viewer.select("not " + picked); + atomsPicked.removeElement(picked); + } + viewerCommandHistory(true); + // TODO: in application this happens + // + // if (scriptWindow != null) + // { + // scriptWindow.sendConsoleMessage(strInfo); + // scriptWindow.sendConsoleMessage("\n"); + // } + + } + + // incremented every time a load notification is successfully handled - + // lightweight mechanism for other threads to detect when they can start + // referrring to new structures. + private long loadNotifiesHandled = 0; + + public long getLoadNotifiesHandled() + { + return loadNotifiesHandled; + } + + public void notifyFileLoaded(String fullPathName, String fileName2, + String modelName, String errorMsg, int modelParts) + { + if (errorMsg != null) + { + fileLoadingError = errorMsg; + refreshGUI(); + return; + } + // TODO: deal sensibly with models loaded inLine: + // modelName will be null, as will fullPathName. + + // the rest of this routine ignores the arguments, and simply interrogates + // the Jmol view to find out what structures it contains, and adds them to + // the structure selection manager. + fileLoadingError = null; + String[] oldmodels = modelFileNames; + modelFileNames = null; + chainNames = new Vector(); + chainFile = new Hashtable(); + boolean notifyLoaded = false; + String[] modelfilenames = getPdbFile(); + // first check if we've lost any structures + if (oldmodels != null && oldmodels.length > 0) + { + int oldm = 0; + for (int i = 0; i < oldmodels.length; i++) + { + for (int n = 0; n < modelfilenames.length; n++) + { + if (modelfilenames[n] == oldmodels[i]) + { + oldmodels[i] = null; + break; + } + } + if (oldmodels[i] != null) + { + oldm++; + } + } + if (oldm > 0) + { + String[] oldmfn = new String[oldm]; + oldm = 0; + for (int i = 0; i < oldmodels.length; i++) + { + if (oldmodels[i] != null) + { + oldmfn[oldm++] = oldmodels[i]; + } + } + // deregister the Jmol instance for these structures - we'll add + // ourselves again at the end for the current structure set. + ssm.removeStructureViewerListener(this, oldmfn); + } + } + + // register ourselves as a listener and notify the gui that it needs to + // update itself. + ssm.addStructureViewerListener(this); + + if (notifyLoaded) + { + FeatureRenderer fr = getFeatureRenderer(null); + if (fr != null) + { + fr.featuresAdded(); + } + refreshGUI(); + loadNotifiesHandled++; + } + setLoadingFromArchive(false); + } + + public void setJalviewColourScheme(ColourSchemeI cs) + { + colourBySequence = false; + + if (cs == null) + return; + + String res; + int index; + Color col; + viewerCommandHistory(false); + // TODO: Switch between nucleotide or aa selection expressions + 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)); + // TODO: need colour string function and res selection here + command.append("select " + res + ";color[" + col.getRed() + "," + + col.getGreen() + "," + col.getBlue() + "];"); + } + + evalStateCommand(command.toString()); + viewerCommandHistory(true); + } + + public void showHelp() + { + // chimera help + showUrl("http://jmol.sourceforge.net/docs/JmolUserGuide/", "jmolHelp"); + } + + /** + * open the URL somehow + * + * @param target + */ + public abstract void showUrl(String url, String target); + + /** + * called when the binding thinks the UI needs to be refreshed after a Jmol + * state change. this could be because structures were loaded, or because an + * error has occured. + */ + public abstract void refreshGUI(); + + public void componentResized(ComponentEvent e) + { + + } + + public void componentMoved(ComponentEvent e) + { + + } + + public void componentShown(ComponentEvent e) + { + } + + public void componentHidden(ComponentEvent e) + { + } + + public void setLoadingFromArchive(boolean loadingFromArchive) + { + this.loadingFromArchive = loadingFromArchive; + } + + /** + * + * @return true if Jmol is still restoring state or loading is still going on + * (see setFinsihedLoadingFromArchive) + */ + public boolean isLoadingFromArchive() + { + return loadingFromArchive && !loadingFinished; + } + + /** + * modify flag which controls if sequence colouring events are honoured by the + * binding. Should be true for normal operation + * + * @param finishedLoading + */ + public void setFinishedLoadingFromArchive(boolean finishedLoading) + { + loadingFinished = finishedLoading; + } + + public void setBackgroundColour(java.awt.Color col) + { + viewerCommandHistory(false); + // todo set background colour + viewer.sendChimeraCommand( + "background [" + col.getRed() + "," + col.getGreen() + "," + + col.getBlue() + "];", false); + viewerCommandHistory(true); + } + + /** + * add structures and any known sequence associations + * + * @returns the pdb entries added to the current set. + */ + public synchronized PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe, + SequenceI[][] seq, String[][] chns) + { + int pe = -1; + Vector v = new Vector(); + Vector rtn = new Vector(); + for (int i = 0; i < pdbentry.length; i++) + { + v.addElement(pdbentry[i]); + } + for (int i = 0; i < pdbe.length; i++) + { + int r = v.indexOf(pdbe[i]); + if (r == -1 || r >= pdbentry.length) + { + rtn.addElement(new int[] + { v.size(), i }); + v.addElement(pdbe[i]); + } + else + { + // just make sure the sequence/chain entries are all up to date + addSequenceAndChain(r, seq[i], chns[i]); + } + } + pdbe = new PDBEntry[v.size()]; + v.copyInto(pdbe); + pdbentry = pdbe; + if (rtn.size() > 0) + { + // expand the tied seuqence[] and string[] arrays + SequenceI[][] sqs = new SequenceI[pdbentry.length][]; + String[][] sch = new String[pdbentry.length][]; + System.arraycopy(sequence, 0, sqs, 0, sequence.length); + System.arraycopy(chains, 0, sch, 0, this.chains.length); + sequence = sqs; + chains = sch; + pdbe = new PDBEntry[rtn.size()]; + for (int r = 0; r < pdbe.length; r++) + { + int[] stri = ((int[]) rtn.elementAt(r)); + // record the pdb file as a new addition + pdbe[r] = pdbentry[stri[0]]; + // and add the new sequence/chain entries + addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]); + } + } + else + { + pdbe = null; + } + return pdbe; + } + + public void addSequence(int pe, SequenceI[] seq) + { + // add sequences to the pe'th pdbentry's seuqence set. + addSequenceAndChain(pe, seq, null); + } + + private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain) + { + if (pe < 0 || pe >= pdbentry.length) + { + throw new Error( + "Implementation error - no corresponding pdbentry (for index " + + pe + ") to add sequences mappings to"); + } + final String nullChain = "TheNullChain"; + Vector s = new Vector(); + Vector c = new Vector(); + if (chains == null) + { + chains = new String[pdbentry.length][]; + } + if (sequence[pe] != null) + { + for (int i = 0; i < sequence[pe].length; i++) + { + s.addElement(sequence[pe][i]); + if (chains[pe] != null) + { + if (i < chains[pe].length) + { + c.addElement(chains[pe][i]); + } + else + { + c.addElement(nullChain); + } + } + else + { + if (tchain != null && tchain.length > 0) + { + c.addElement(nullChain); + } + } + } + } + for (int i = 0; i < seq.length; i++) + { + if (!s.contains(seq[i])) + { + s.addElement(seq[i]); + if (tchain != null && i < tchain.length) + { + c.addElement(tchain[i] == null ? nullChain : tchain[i]); + } + } + } + SequenceI[] tmp = new SequenceI[s.size()]; + s.copyInto(tmp); + sequence[pe] = tmp; + if (c.size() > 0) + { + String[] tch = new String[c.size()]; + c.copyInto(tch); + for (int i = 0; i < tch.length; i++) + { + if (tch[i] == nullChain) + { + tch[i] = null; + } + } + chains[pe] = tch; + } + else + { + chains[pe] = null; + } + } + + /** + * + * @param pdbfile + * @return text report of alignment between pdbfile and any associated + * alignment sequences + */ + public String printMapping(String pdbfile) + { + return ssm.printMapping(pdbfile); + } + +} diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java new file mode 100644 index 0000000..a3ff00b --- /dev/null +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -0,0 +1,1228 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * Copyright (C) 2014 The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.gui; + +import jalview.api.SequenceStructureBinding; +import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Cache; +import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.io.AppletFormatAdapter; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.jbgui.GStructureViewer; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ColourSchemeI; +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.ZappoColourScheme; +import jalview.util.MessageManager; +import jalview.util.Platform; + +import java.awt.Component; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.io.BufferedReader; +import java.io.File; +import java.io.FileOutputStream; +import java.io.FileReader; +import java.io.PrintWriter; +import java.util.ArrayList; +import java.util.Enumeration; +import java.util.List; +import java.util.Vector; + +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JColorChooser; +import javax.swing.JInternalFrame; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JOptionPane; +import javax.swing.event.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; +import javax.swing.event.MenuEvent; +import javax.swing.event.MenuListener; + +/** + * GUI elements for handlnig an external chimera display + * + * @author jprocter + * + */ +public class ChimeraViewFrame extends GStructureViewer implements Runnable, + ViewSetProvider, JalviewStructureDisplayI + +{ + JalviewChimeraBindingModel jmb; + + AlignmentPanel ap; + + Vector atomsPicked = new Vector(); + + private boolean addingStructures = false; + + ViewSelectionMenu seqColourBy; + + /** + * + * @param files + * @param ids + * @param seqs + * @param ap + * @param usetoColour + * - add the alignment panel to the list used for colouring these + * structures + * @param useToAlign + * - add the alignment panel to the list used for aligning these + * structures + * @param leaveColouringToJmol + * - do not update the colours from any other source. Jmol is + * handling them + * @param loadStatus + * @param bounds + * @param viewid + * + * public ChimeraViewFrame(String[] files, String[] ids, + * SequenceI[][] seqs, AlignmentPanel ap, boolean usetoColour, + * boolean useToAlign, boolean leaveColouringToJmol, String + * loadStatus, Rectangle bounds, String viewid) { PDBEntry[] + * pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < + * pdbentrys.length; i++) { PDBEntry pdbentry = new PDBEntry(); + * pdbentry.setFile(files[i]); pdbentry.setId(ids[i]); pdbentrys[i] = + * pdbentry; } // / TODO: check if protocol is needed to be set, and + * if chains are // autodiscovered. jmb = new + * JalviewChimeraBindingModel(this, + * ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); + * + * jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); if + * (useToAlign) { useAlignmentPanelForSuperposition(ap); } if + * (leaveColouringToJmol || !usetoColour) { + * jmb.setColourBySequence(false); seqColour.setSelected(false); + * jmolColour.setSelected(true); } if (usetoColour) { + * useAlignmentPanelForColourbyseq(ap); + * jmb.setColourBySequence(true); seqColour.setSelected(true); + * jmolColour.setSelected(false); } this.setBounds(bounds); + * initMenus(); viewId = viewid; // + * jalview.gui.Desktop.addInternalFrame(this, "Loading File", // + * bounds.width,bounds.height); + * + * this.addInternalFrameListener(new InternalFrameAdapter() { public + * void internalFrameClosing(InternalFrameEvent internalFrameEvent) { + * closeViewer(); } }); initJmol(loadStatus); // pdbentry, seq, + * JBPCHECK! + * + * } + */ + private void initMenus() + { + seqColour.setSelected(jmb.isColourBySequence()); + jmolColour.setSelected(!jmb.isColourBySequence()); + if (_colourwith == null) + { + _colourwith = new Vector(); + } + if (_alignwith == null) + { + _alignwith = new Vector(); + } + + seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith, + new ItemListener() + { + + @Override + public void itemStateChanged(ItemEvent e) + { + if (!seqColour.isSelected()) + { + seqColour.doClick(); + } + else + { + // update the jmol display now. + seqColour_actionPerformed(null); + } + } + }); + viewMenu.add(seqColourBy); + final ItemListener handler; + JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this, + _alignwith, handler = new ItemListener() + { + + @Override + public void itemStateChanged(ItemEvent e) + { + alignStructs.setEnabled(_alignwith.size() > 0); + alignStructs.setToolTipText(MessageManager + .formatMessage( + "label.align_structures_using_linked_alignment_views", + new String[] + { new Integer(_alignwith.size()).toString() })); + } + }); + handler.itemStateChanged(null); + jmolActionMenu.add(alpanels); + jmolActionMenu.addMenuListener(new MenuListener() + { + + @Override + public void menuSelected(MenuEvent e) + { + handler.itemStateChanged(null); + } + + @Override + public void menuDeselected(MenuEvent e) + { + // TODO Auto-generated method stub + + } + + @Override + public void menuCanceled(MenuEvent e) + { + // TODO Auto-generated method stub + + } + }); + } + + IProgressIndicator progressBar = null; + + /** + * add a single PDB structure to a new or existing Jmol view + * + * @param pdbentry + * @param seq + * @param chains + * @param ap + */ + public ChimeraViewFrame(PDBEntry pdbentry, SequenceI[] seq, + String[] chains, final AlignmentPanel ap) + { + progressBar = ap.alignFrame; + // //////////////////////////////// + // Is the pdb file already loaded? + String alreadyMapped = ap.getStructureSelectionManager() + .alreadyMappedToFile(pdbentry.getId()); + + if (alreadyMapped != null) + { + int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.pdb_entry_is_already_displayed", new String[] + { pdbentry.getId() }), MessageManager.formatMessage( + "label.map_sequences_to_visible_window", new String[] + { pdbentry.getId() }), JOptionPane.YES_NO_OPTION); + + if (option == JOptionPane.YES_OPTION) + { + // TODO : Fix multiple seq to one chain issue here. + ap.getStructureSelectionManager().setMapping(seq, chains, + alreadyMapped, AppletFormatAdapter.FILE); + if (ap.seqPanel.seqCanvas.fr != null) + { + ap.seqPanel.seqCanvas.fr.featuresAdded(); + ap.paintAlignment(true); + } + + // Now this AppJmol is mapped to new sequences. We must add them to + // the exisiting array + JInternalFrame[] frames = Desktop.instance.getAllFrames(); + + for (int i = 0; i < frames.length; i++) + { + if (frames[i] instanceof ChimeraViewFrame) + { + final ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]); + // JBPNOTE: this looks like a binding routine, rather than a gui + // routine + for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++) + { + if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped)) + { + topJmol.jmb.addSequence(pe, seq); + topJmol.addAlignmentPanel(ap); + // add it to the set used for colouring + topJmol.useAlignmentPanelForColourbyseq(ap); + topJmol.buildChimeraActionMenu(); + ap.getStructureSelectionManager() + .sequenceColoursChanged(ap); + break; + } + } + } + } + + return; + } + } + // ///////////////////////////////// + // Check if there are other Jmol views involving this alignment + // and prompt user about adding this molecule to one of them + Vector existingViews = getJmolsFor(ap); + if (existingViews.size() > 0) + { + Enumeration jm = existingViews.elements(); + while (jm.hasMoreElements()) + { + ChimeraViewFrame topJmol = (ChimeraViewFrame) jm.nextElement(); + // TODO: highlight topJmol in view somehow + int option = JOptionPane + .showInternalConfirmDialog( + Desktop.desktop, + MessageManager.formatMessage( + "label.add_pdbentry_to_view", new String[] + { pdbentry.getId(), topJmol.getTitle() }), + MessageManager + .getString("label.align_to_existing_structure_view"), + JOptionPane.YES_NO_OPTION); + if (option == JOptionPane.YES_OPTION) + { + topJmol.useAlignmentPanelForSuperposition(ap); + topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); + return; + } + } + } + // ///////////////////////////////// + openNewJmol(ap, new PDBEntry[] + { pdbentry }, new SequenceI[][] + { seq }); + } + + private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, + SequenceI[][] seqs) + { + progressBar = ap.alignFrame; + jmb = new JalviewChimeraBindingModel(this, + ap.getStructureSelectionManager(), pdbentrys, seqs, null, null); + addAlignmentPanel(ap); + useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length > 1) + { + alignAddedStructures = true; + useAlignmentPanelForSuperposition(ap); + } + jmb.setColourBySequence(true); + setSize(400, 400); // probably should be a configurable/dynamic default here + initMenus(); + worker = null; + { + addingStructures = false; + worker = new Thread(this); + worker.start(); + } + this.addInternalFrameListener(new InternalFrameAdapter() + { + public void internalFrameClosing(InternalFrameEvent internalFrameEvent) + { + closeViewer(); + } + }); + + } + + /** + * create a new Jmol containing several structures superimposed using the + * given alignPanel. + * + * @param ap + * @param pe + * @param seqs + */ + public ChimeraViewFrame(AlignmentPanel ap, PDBEntry[] pe, + SequenceI[][] seqs) + { + openNewJmol(ap, pe, seqs); + } + + /** + * list of sequenceSet ids associated with the view + */ + ArrayList _aps = new ArrayList(); + + public AlignmentPanel[] getAllAlignmentPanels() + { + AlignmentPanel[] t, list = new AlignmentPanel[0]; + for (String setid : _aps) + { + AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid); + if (panels != null) + { + t = new AlignmentPanel[list.length + panels.length]; + System.arraycopy(list, 0, t, 0, list.length); + System.arraycopy(panels, 0, t, list.length, panels.length); + list = t; + } + } + + return list; + } + + /** + * list of alignment panels to use for superposition + */ + Vector _alignwith = new Vector(); + + /** + * list of alignment panels that are used for colouring structures by aligned + * sequences + */ + Vector _colourwith = new Vector(); + + /** + * set the primary alignmentPanel reference and add another alignPanel to the + * list of ones to use for colouring and aligning + * + * @param nap + */ + public void addAlignmentPanel(AlignmentPanel nap) + { + if (ap == null) + { + ap = nap; + } + if (!_aps.contains(nap.av.getSequenceSetId())) + { + _aps.add(nap.av.getSequenceSetId()); + } + } + + /** + * remove any references held to the given alignment panel + * + * @param nap + */ + public void removeAlignmentPanel(AlignmentPanel nap) + { + try + { + _alignwith.remove(nap); + _colourwith.remove(nap); + if (ap == nap) + { + ap = null; + for (AlignmentPanel aps : getAllAlignmentPanels()) + { + if (aps != nap) + { + ap = aps; + break; + } + } + } + } catch (Exception ex) + { + } + if (ap != null) + { + buildChimeraActionMenu(); + } + } + + public void useAlignmentPanelForSuperposition(AlignmentPanel nap) + { + addAlignmentPanel(nap); + if (!_alignwith.contains(nap)) + { + _alignwith.add(nap); + } + } + + public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap) + { + if (_alignwith.contains(nap)) + { + _alignwith.remove(nap); + } + } + + public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, + boolean enableColourBySeq) + { + useAlignmentPanelForColourbyseq(nap); + jmb.setColourBySequence(enableColourBySeq); + seqColour.setSelected(enableColourBySeq); + jmolColour.setSelected(!enableColourBySeq); + } + + public void useAlignmentPanelForColourbyseq(AlignmentPanel nap) + { + addAlignmentPanel(nap); + if (!_colourwith.contains(nap)) + { + _colourwith.add(nap); + } + } + + public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap) + { + if (_colourwith.contains(nap)) + { + _colourwith.remove(nap); + } + } + + /** + * pdb retrieval thread. + */ + private Thread worker = null; + + /** + * add a new structure (with associated sequences and chains) to this viewer, + * retrieving it if necessary first. + * + * @param pdbentry + * @param seq + * @param chains + * @param alignFrame + * @param align + * if true, new structure(s) will be align using associated alignment + */ + private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq, + final String[] chains, final boolean b, + final IProgressIndicator alignFrame) + { + if (pdbentry.getFile() == null) + { + if (worker != null && worker.isAlive()) + { + // a retrieval is in progress, wait around and add ourselves to the + // queue. + new Thread(new Runnable() + { + public void run() + { + while (worker != null && worker.isAlive() && _started) + { + try + { + Thread.sleep(100 + ((int) Math.random() * 100)); + + } catch (Exception e) + { + } + + } + // and call ourselves again. + addStructure(pdbentry, seq, chains, b, alignFrame); + } + }).start(); + return; + } + } + // otherwise, start adding the structure. + jmb.addSequenceAndChain(new PDBEntry[] + { pdbentry }, new SequenceI[][] + { seq }, new String[][] + { chains }); + addingStructures = true; + _started = false; + alignAddedStructures = b; + progressBar = alignFrame; // visual indication happens on caller frame. + (worker = new Thread(this)).start(); + return; + } + + private Vector getJmolsFor(AlignmentPanel ap2) + { + Vector otherJmols = new Vector(); + // Now this AppJmol is mapped to new sequences. We must add them to + // the exisiting array + JInternalFrame[] frames = Desktop.instance.getAllFrames(); + + for (int i = 0; i < frames.length; i++) + { + if (frames[i] instanceof ChimeraViewFrame) + { + ChimeraViewFrame topJmol = ((ChimeraViewFrame) frames[i]); + if (topJmol.isLinkedWith(ap2)) + { + otherJmols.addElement(topJmol); + } + } + } + return otherJmols; + } + + void initChimera(String command) + { + jmb.setFinishedInit(false); + // TODO: consider waiting until the structure/view is fully loaded before + // displaying + jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle(), + getBounds().width, getBounds().height); + if (command == null) + { + command = ""; + } + jmb.evalStateCommand(command); + jmb.setFinishedInit(true); + } + + void setChainMenuItems(Vector chains) + { + chainMenu.removeAll(); + if (chains == null) + { + return; + } + JMenuItem menuItem = new JMenuItem( + MessageManager.getString("label.all")); + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + allChainsSelected = true; + for (int i = 0; i < chainMenu.getItemCount(); i++) + { + if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) + ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); + } + centerViewer(); + allChainsSelected = false; + } + }); + + chainMenu.add(menuItem); + + for (int c = 0; c < chains.size(); c++) + { + menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true); + menuItem.addItemListener(new ItemListener() + { + public void itemStateChanged(ItemEvent evt) + { + if (!allChainsSelected) + centerViewer(); + } + }); + + chainMenu.add(menuItem); + } + } + + boolean allChainsSelected = false; + + private boolean alignAddedStructures = false; + + void centerViewer() + { + Vector toshow = new Vector(); + String lbl; + int mlength, p, mnum; + for (int i = 0; i < chainMenu.getItemCount(); i++) + { + if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) + { + JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i); + if (item.isSelected()) + { + toshow.addElement(item.getText()); + } + } + } + jmb.centerViewer(toshow); + } + + public void closeViewer() + { + jmb.closeViewer(); + ap = null; + _aps.clear(); + _alignwith.clear(); + _colourwith.clear(); + // TODO: check for memory leaks where instance isn't finalised because jmb + // holds a reference to the window + jmb = null; + } + + /** + * state flag for PDB retrieval thread + */ + private boolean _started = false; + + public void run() + { + _started = true; + String pdbid = ""; + // todo - record which pdbids were successfuly imported. + StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer(); + List fileToLoad=new ArrayList(); + List filePDB = new ArrayList(); + List filePDBpos =new ArrayList(); + try + { + String[] curfiles = jmb.getPdbFile(); // files currently in viewer + // TODO: replace with reference fetching/transfer code (validate PDBentry + // as a DBRef?) + jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb(); + for (int pi = 0; pi < jmb.pdbentry.length; pi++) + { + String file = new File(jmb.pdbentry[pi].getFile()) + .getAbsoluteFile().getPath(); + if (file == null) + { + // retrieve the pdb and store it locally + AlignmentI pdbseq = null; + pdbid = jmb.pdbentry[pi].getId(); + long hdl = pdbid.hashCode() - System.currentTimeMillis(); + if (progressBar != null) + { + progressBar.setProgressBar("Fetching PDB " + pdbid, hdl); + } + try + { + pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi] + .getId()); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("Retrieving PDB id " + pdbid, oomerror); + } catch (Exception ex) + { + ex.printStackTrace(); + errormsgs.append("'" + pdbid + "'"); + } + if (progressBar != null) + { + progressBar.setProgressBar("Finished.", hdl); + } + if (pdbseq != null) + { + // just transfer the file name from the first sequence's first + // PDBEntry + file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() + .elementAt(0)).getFile()).getAbsolutePath(); + jmb.pdbentry[pi].setFile(file); + + files.append(" \"" + Platform.escapeString(file) + "\""); + } + else + { + errormsgs.append("'" + pdbid + "' "); + } + } + else + { + if (curfiles != null && curfiles.length > 0) + { + addingStructures = true; // already files loaded. + for (int c = 0; c < curfiles.length; c++) + { + if (curfiles[c].equals(file)) + { + file = null; + break; + } + } + } + + if (file != null) + { + fileToLoad.add(file); + filePDB.add(jmb.pdbentry[pi]); + filePDBpos.add(Integer.valueOf(pi)); + files.append(" \"" + Platform.escapeString(file) + "\""); + } + } + } + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("Retrieving PDB files: " + pdbid, oomerror); + } catch (Exception ex) + { + ex.printStackTrace(); + errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid + + "'"); + } + if (errormsgs.length() > 0) + { + + JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + .formatMessage("label.pdb_entries_couldnt_be_retrieved", + new String[] + { errormsgs.toString() }), MessageManager + .getString("label.couldnt_load_file"), + JOptionPane.ERROR_MESSAGE); + + } + long lastnotify = jmb.getLoadNotifiesHandled(); + if (files.length() > 0) + { + if (!addingStructures) + { + try + { + initChimera(""); + } catch (Exception ex) + { + Cache.log.error("Couldn't open Chimera viewer!", ex); + } + } + int num=-1; + for (PDBEntry pe : filePDB) + { + num++; + if (pe.getFile() != null) + { + try + { + int pos=filePDBpos.get(num).intValue(); + jmb.openFile(pe); + jmb.addSequence(pos, jmb.sequence[pos]); + File fl=new File(pe.getFile()); + String protocol = AppletFormatAdapter.URL; + try + { + if (fl.exists()) + { + protocol = AppletFormatAdapter.FILE; + } + } catch (Exception e) + { + } catch (Error e) + { + } + // Explicitly map to the filename used by Jmol ; + jmb.ssm.setMapping(jmb.sequence[pos], null, pe.getFile(), + protocol); + // pdbentry[pe].getFile(), protocol); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning( + "When trying to open and map structures from Chimera!", + oomerror); + } catch (Exception ex) + { + Cache.log.error("Couldn't open " + pe.getFile() + + " in Chimera viewer!", ex); + } finally + { + Cache.log.debug("File locations are " + files); + } + } + } + // jmb.getPdbFile(); + jmb.setFinishedInit(true); + jmb.setLoadingFromArchive(false); + + // refresh the sequence colours for the new structure(s) + for (AlignmentPanel ap : _colourwith) + { + jmb.updateColours(ap); + } + // do superposition if asked to + if (alignAddedStructures) + { + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + alignStructs_withAllAlignPanels(); + } + }); + alignAddedStructures = false; + } + addingStructures = false; + } + _started = false; + worker = null; + } + + 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(MessageManager.getString("action.save")); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + try + { + // TODO: cope with multiple PDB files in view + BufferedReader in = new BufferedReader(new FileReader( + jmb.getPdbFile()[0])); + 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(); + try + { + for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) + { + cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile())); + cap.appendText("\n"); + } + } catch (OutOfMemoryError e) + { + new OOMWarning( + "composing sequence-structure alignments for display in text box.", + e); + cap.dispose(); + return; + } + jalview.gui.Desktop.addInternalFrame(cap, + MessageManager.getString("label.pdb_sequence_mapping"), 550, + 600); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void eps_actionPerformed(ActionEvent e) + { + throw new Error("EPS Generation not yet implemented."); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void png_actionPerformed(ActionEvent e) + { + throw new Error("PNG Generation not yet implemented."); + } + + public void jmolColour_actionPerformed(ActionEvent actionEvent) + { + if (jmolColour.isSelected()) + { + // disable automatic sequence colouring. + jmb.setColourBySequence(false); + } + } + + public void seqColour_actionPerformed(ActionEvent actionEvent) + { + jmb.setColourBySequence(seqColour.isSelected()); + if (_colourwith == null) + { + _colourwith = new Vector(); + } + if (jmb.isColourBySequence()) + { + if (!jmb.isLoadingFromArchive()) + { + if (_colourwith.size() == 0 && ap != null) + { + // Make the currently displayed alignment panel the associated view + _colourwith.add(ap.alignFrame.alignPanel); + } + } + // Set the colour using the current view for the associated alignframe + for (AlignmentPanel ap : _colourwith) + { + jmb.colourBySequence(ap.av.showSequenceFeatures, ap); + } + } + } + + public void chainColour_actionPerformed(ActionEvent actionEvent) + { + chainColour.setSelected(true); + jmb.colourByChain(); + } + + public void chargeColour_actionPerformed(ActionEvent actionEvent) + { + chargeColour.setSelected(true); + jmb.colourByCharge(); + } + + public void zappoColour_actionPerformed(ActionEvent actionEvent) + { + zappoColour.setSelected(true); + jmb.setJalviewColourScheme(new ZappoColourScheme()); + } + + public void taylorColour_actionPerformed(ActionEvent actionEvent) + { + taylorColour.setSelected(true); + jmb.setJalviewColourScheme(new TaylorColourScheme()); + } + + public void hydroColour_actionPerformed(ActionEvent actionEvent) + { + hydroColour.setSelected(true); + jmb.setJalviewColourScheme(new HydrophobicColourScheme()); + } + + public void helixColour_actionPerformed(ActionEvent actionEvent) + { + helixColour.setSelected(true); + jmb.setJalviewColourScheme(new HelixColourScheme()); + } + + public void strandColour_actionPerformed(ActionEvent actionEvent) + { + strandColour.setSelected(true); + jmb.setJalviewColourScheme(new StrandColourScheme()); + } + + public void turnColour_actionPerformed(ActionEvent actionEvent) + { + turnColour.setSelected(true); + jmb.setJalviewColourScheme(new TurnColourScheme()); + } + + public void buriedColour_actionPerformed(ActionEvent actionEvent) + { + buriedColour.setSelected(true); + jmb.setJalviewColourScheme(new BuriedColourScheme()); + } + + public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) + { + setJalviewColourScheme(new PurinePyrimidineColourScheme()); + } + + public void userColour_actionPerformed(ActionEvent actionEvent) + { + userColour.setSelected(true); + new UserDefinedColours(this, null); + } + + public void backGround_actionPerformed(ActionEvent actionEvent) + { + java.awt.Color col = JColorChooser.showDialog(this, + "Select Background Colour", null); + if (col != null) + { + jmb.setBackgroundColour(col); + } + } + + public void jmolHelp_actionPerformed(ActionEvent actionEvent) + { + try + { + jalview.util.BrowserLauncher + .openURL("https://www.cgl.ucsf.edu/chimera/docs/UsersGuide"); + } catch (Exception ex) + { + } + } + + String viewId = null; + + public String getViewId() + { + if (viewId == null) + { + viewId = System.currentTimeMillis() + "." + this.hashCode(); + } + return viewId; + } + + public void updateTitleAndMenus() + { + if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) + { + repaint(); + return; + } + setChainMenuItems(jmb.chainNames); + + this.setTitle(jmb.getViewerTitle()); + if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1) + { + jmolActionMenu.setVisible(true); + } + if (!jmb.isLoadingFromArchive()) + { + seqColour_actionPerformed(null); + } + } + + protected void buildChimeraActionMenu() + { + if (_alignwith == null) + { + _alignwith = new Vector(); + } + if (_alignwith.size() == 0 && ap != null) + { + _alignwith.add(ap); + } + ; + for (Component c : jmolActionMenu.getMenuComponents()) + { + if (c != alignStructs) + { + jmolActionMenu.remove((JMenuItem) c); + } + } + final ItemListener handler; + } + + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event + * .ActionEvent) + */ + @Override + protected void alignStructs_actionPerformed(ActionEvent actionEvent) + { + alignStructs_withAllAlignPanels(); + } + + private void alignStructs_withAllAlignPanels() + { + if (ap == null) + { + return; + } + ; + if (_alignwith.size() == 0) + { + _alignwith.add(ap); + } + ; + try + { + AlignmentI[] als = new Alignment[_alignwith.size()]; + ColumnSelection[] alc = new ColumnSelection[_alignwith.size()]; + int[] alm = new int[_alignwith.size()]; + int a = 0; + + for (AlignmentPanel ap : _alignwith) + { + als[a] = ap.av.getAlignment(); + alm[a] = -1; + alc[a++] = ap.av.getColumnSelection(); + } + jmb.superposeStructures(als, alm, alc); + } catch (Exception e) + { + StringBuffer sp = new StringBuffer(); + for (AlignmentPanel ap : _alignwith) + { + sp.append("'" + ap.alignFrame.getTitle() + "' "); + } + Cache.log.info("Couldn't align structures with the " + sp.toString() + + "associated alignment panels.", e); + + } + + } + + public void setJalviewColourScheme(ColourSchemeI ucs) + { + jmb.setJalviewColourScheme(ucs); + + } + + /** + * + * @param alignment + * @return first alignment panel displaying given alignment, or the default + * alignment panel + */ + public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) + { + for (AlignmentPanel ap : getAllAlignmentPanels()) + { + if (ap.av.getAlignment() == alignment) + { + return ap; + } + } + return ap; + } + + /** + * + * @param ap2 + * @return true if this Jmol instance is linked with the given alignPanel + */ + public boolean isLinkedWith(AlignmentPanel ap2) + { + return _aps.contains(ap2.av.getSequenceSetId()); + } + + public boolean isUsedforaligment(AlignmentPanel ap2) + { + + return (_alignwith != null) && _alignwith.contains(ap2); + } + + public boolean isUsedforcolourby(AlignmentPanel ap2) + { + return (_colourwith != null) && _colourwith.contains(ap2); + } + + /** + * + * @return TRUE if the view is NOT being coloured by sequence associations. + */ + public boolean isColouredByJmol() + { + return !jmb.isColourBySequence(); + } + + public SequenceStructureBinding getBinding() + { + return jmb; + } + +} diff --git a/src/jalview/gui/JalviewChimeraBindingModel.java b/src/jalview/gui/JalviewChimeraBindingModel.java new file mode 100644 index 0000000..f7c4878 --- /dev/null +++ b/src/jalview/gui/JalviewChimeraBindingModel.java @@ -0,0 +1,102 @@ +package jalview.gui; + +import jalview.api.AlignmentViewPanel; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.ext.rbvi.chimera.JalviewChimeraBinding; +import jalview.structure.StructureSelectionManager; + +public class JalviewChimeraBindingModel extends JalviewChimeraBinding +{ + private ChimeraViewFrame cvf; + + public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame, + StructureSelectionManager ssm, PDBEntry[] pdbentry, + SequenceI[][] sequenceIs, String[][] chains, String protocol) + { + super(ssm, pdbentry, sequenceIs, chains, protocol); + cvf = chimeraViewFrame; + } + + FeatureRenderer fr = null; + + @Override + public jalview.api.FeatureRenderer getFeatureRenderer( + AlignmentViewPanel alignment) + { + AlignmentPanel ap = (alignment == null) ? cvf.ap + : (AlignmentPanel) alignment; + if (ap.av.showSequenceFeatures) + { + if (fr == null) + { + fr = ap.cloneFeatureRenderer(); + } + else + { + ap.updateFeatureRenderer(fr); + } + } + + return fr; + } + + @Override + public jalview.api.SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment) + { + return new SequenceRenderer(((AlignmentPanel) alignment).av); + } + @Override + public void refreshGUI() + { + // appJmolWindow.repaint(); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + cvf.updateTitleAndMenus(); + cvf.revalidate(); + } + }); + } + + public void updateColours(Object source) + { + AlignmentPanel ap = (AlignmentPanel) source, topap; + // ignore events from panels not used to colour this view + if (!cvf.isUsedforcolourby(ap)) + return; + if (!isLoadingFromArchive()) + { + colourBySequence(ap.av.getShowSequenceFeatures(), ap); + } + } + @Override + public void releaseReferences(Object svl) + { + // TODO Auto-generated method stub + + } + + @Override + protected void releaseUIResources() + { + // TODO Auto-generated method stub + + } + + @Override + public void refreshPdbEntries() + { + // TODO Auto-generated method stub + + } + + @Override + public void showUrl(String url, String target) + { + // TODO Auto-generated method stub + + } +} diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java index ce22d84..e307aa9 100644 --- a/src/jalview/gui/StructureViewer.java +++ b/src/jalview/gui/StructureViewer.java @@ -66,17 +66,19 @@ public class StructureViewer public JalviewStructureDisplayI viewStructures(AlignmentPanel ap, PDBEntry[] pr, SequenceI[][] collateForPDB) { + return viewStructures(getViewerType(), ap, pr, collateForPDB); + } + public JalviewStructureDisplayI viewStructures(Viewer viewerType,AlignmentPanel ap, + PDBEntry[] pr, SequenceI[][] collateForPDB) + { JalviewStructureDisplayI sview = null; - switch (getViewerType()) - { - case JMOL: - + if (viewerType.equals(Viewer.JMOL)){ sview = new AppJmol(ap, pr, ap.av.collateForPDB(pr)); - - break; - case CHIMERA: - break; - default: + } else + if (viewerType.equals(Viewer.CHIMERA)) { + sview = new ChimeraViewFrame(ap, pr, ap.av.collateForPDB(pr)); + }else + { Cache.log.error("Unknown structure viewer type " + getViewerType().toString()); } diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java index 3803fa1..f719d27 100755 --- a/src/jalview/gui/UserDefinedColours.java +++ b/src/jalview/gui/UserDefinedColours.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.structures.JalviewStructureDisplayI; import jalview.datamodel.SequenceGroup; import jalview.io.JalviewFileChooser; import jalview.jbgui.GUserDefinedColours; @@ -67,7 +68,7 @@ public class UserDefinedColours extends GUserDefinedColours implements JInternalFrame frame; - AppJmol jmol; + JalviewStructureDisplayI jmol; Vector upperCaseButtons; @@ -121,7 +122,7 @@ public class UserDefinedColours extends GUserDefinedColours implements showFrame(); } - public UserDefinedColours(AppJmol jmol, ColourSchemeI oldcs) + public UserDefinedColours(JalviewStructureDisplayI jmol, ColourSchemeI oldcs) { super(); this.jmol = jmol; diff --git a/test/jalview/ext/rbvi/chimera/ChimeraConnect.java b/test/jalview/ext/rbvi/chimera/ChimeraConnect.java index 658c9c6..be4e5ea 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraConnect.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraConnect.java @@ -18,7 +18,6 @@ public class ChimeraConnect StructureManager csm; ext.edu.ucsf.rbvi.strucviz2.ChimeraManager cm = new ChimeraManager(csm = new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true)); assertTrue("Couldn't launch chimera",cm.launchChimera(csm.getChimeraPaths())); - int n=0; while (n++<100) { diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java new file mode 100644 index 0000000..1736af5 --- /dev/null +++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java @@ -0,0 +1,82 @@ +package jalview.ext.rbvi.chimera; + +import static org.junit.Assert.*; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.StructureViewer; +import jalview.gui.StructureViewer.Viewer; +import jalview.io.FormatAdapter; + +import java.awt.Desktop; +import java.io.File; + +import org.junit.After; +import org.junit.AfterClass; +import org.junit.Before; +import org.junit.BeforeClass; +import org.junit.Test; + +public class JalviewChimeraView +{ + + /** + * @throws java.lang.Exception + */ + @BeforeClass + public static void setUpBeforeClass() throws Exception + { + jalview.bin.Jalview.main(new String[] + { "-noquestionnaire -nonews -props", "test/src/jalview/ext/rbvi/chimera/testProps.jvprops" }); + } + + /** + * @throws java.lang.Exception + */ + @AfterClass + public static void tearDownAfterClass() throws Exception + { + jalview.gui.Desktop.instance.closeAll_actionPerformed(null); + + } + + + @Test + public void testSingleSeqView() + { + String inFile = "examples/1gaq.txt"; + AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded( + inFile, FormatAdapter.FILE); + assertTrue("Didn't read input file " + inFile, af != null); + for (SequenceI sq:af.getViewport().getAlignment().getSequences()) + { + SequenceI dsq=sq.getDatasetSequence(); + while (dsq.getDatasetSequence()!=null) + { + dsq=dsq.getDatasetSequence(); + } + if (dsq.getPDBId()!=null && dsq.getPDBId().size()>0) { + for (int q=0;q