X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=b28ed0e3d9d20bdd348ad79210f1cd5cc5681105;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=97dfefd969be3330ac3f3d13594016fa7b741b04;hpb=51008f2829b2bf03318501e9b69edcda9bebd323;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 97dfefd..b28ed0e 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,26 +1,28 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; +import java.awt.Rectangle; import java.io.*; +import java.lang.reflect.InvocationTargetException; import java.net.*; import java.util.*; +import java.util.Map.Entry; import java.util.jar.*; import javax.swing.*; @@ -28,21 +30,22 @@ import javax.swing.*; import org.exolab.castor.xml.*; import uk.ac.vamsas.objects.utils.MapList; +import jalview.bin.Cache; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.schemabinding.version2.*; import jalview.schemes.*; import jalview.structure.StructureSelectionManager; +import jalview.util.jarInputStreamProvider; /** - * Write out the current jalview desktop state - * as a Jalview XML stream. + * Write out the current jalview desktop state as a Jalview XML stream. + * + * Note: the vamsas objects referred to here are primitive versions of the + * VAMSAS project schema elements - they are not the same and most likely never + * will be :) * - * Note: the vamsas objects referred to here are primitive - * versions of the VAMSAS project schema elements - they are - * not the same and most likely never will be :) - * * @author $author$ * @version $Revision$ */ @@ -50,49 +53,88 @@ public class Jalview2XML { /** * create/return unique hash string for sq + * * @param sq * @return new or existing unique string for sq */ String seqHash(SequenceI sq) { - if (seqsToIds==null) + if (seqsToIds == null) { initSeqRefs(); } if (seqsToIds.containsKey(sq)) { return (String) seqsToIds.get(sq); - } else { - // create sequential key - String key = "sq"+(seqsToIds.size()+1); + } + else + { + // create sequential key + String key = "sq" + (seqsToIds.size() + 1); + key = makeHashCode(sq, key); // check we don't have an external reference + // for it already. seqsToIds.put(sq, key); return key; } } + void clearSeqRefs() { - seqRefIds.clear(); - seqsToIds.clear(); + if (_cleartables) + { + if (seqRefIds != null) + { + seqRefIds.clear(); + } + if (seqsToIds != null) + { + seqsToIds.clear(); + } + // seqRefIds = null; + // seqsToIds = null; + } + else + { + // do nothing + warn("clearSeqRefs called when _cleartables was not set. Doing nothing."); + // seqRefIds = new Hashtable(); + // seqsToIds = new IdentityHashMap(); + } } + void initSeqRefs() { - if (seqsToIds==null) + if (seqsToIds == null) { seqsToIds = new IdentityHashMap(); } - if (seqRefIds==null) + if (seqRefIds == null) { seqRefIds = new Hashtable(); } } - java.util.IdentityHashMap seqsToIds = null; // SequenceI->key resolution + + /** + * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps + * of sequence objects are created. + */ + java.util.IdentityHashMap seqsToIds = null; + + /** + * jalview XML Sequence ID to jalview sequence object reference (both dataset + * and alignment sequences. Populated as XML reps of sequence objects are + * created.) + */ java.util.Hashtable seqRefIds = null; // key->SequenceI resolution Vector frefedSequence = null; + boolean raiseGUI = true; // whether errors are raised in dialog boxes or not + public Jalview2XML() { } + public Jalview2XML(boolean raiseGUI) { this.raiseGUI = raiseGUI; @@ -122,20 +164,50 @@ public class Jalview2XML } else { - System.err - .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for " - + ref[1].getClass() + " type objects."); + if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame) + { + SequenceI seq = (SequenceI) seqRefIds.get(sref); + while (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } + if (ref[2] != null + && ref[2] instanceof jalview.datamodel.Mapping) + { + jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2]; + ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap( + seq, mp.getTo(), mp.getMap()); + } + else + { + System.err + .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving " + + ref[2].getClass() + " type objects."); + } + } + else + { + System.err + .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for " + + ref[1].getClass() + " type objects."); + } } frefedSequence.remove(r); rSize--; } else { + System.err + .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string " + + ref[0] + + " with objecttype " + + ref[1].getClass()); r++; } } else { + // empty reference frefedSequence.remove(r); rSize--; } @@ -144,9 +216,8 @@ public class Jalview2XML } /** - * This maintains a list of viewports, the key being the - * seqSetId. Important to set historyItem and redoList - * for multiple views + * This maintains a list of viewports, the key being the seqSetId. Important + * to set historyItem and redoList for multiple views */ Hashtable viewportsAdded; @@ -162,6 +233,37 @@ public class Jalview2XML // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE public void SaveState(File statefile) { + try + { + FileOutputStream fos = new FileOutputStream(statefile); + JarOutputStream jout = new JarOutputStream(fos); + SaveState(jout); + + } catch (Exception e) + { + // TODO: inform user of the problem - they need to know if their data was + // not saved ! + if (errorMessage == null) + { + errorMessage = "Couldn't write Jalview Archive to output file '" + + statefile + "' - See console error log for details"; + } + else + { + errorMessage += "(output file was '" + statefile + "')"; + } + e.printStackTrace(); + } + reportErrors(); + } + + /** + * Writes a jalview project archive to the given Jar output stream. + * + * @param jout + */ + public void SaveState(JarOutputStream jout) + { JInternalFrame[] frames = Desktop.desktop.getAllFrames(); if (frames == null) @@ -171,22 +273,27 @@ public class Jalview2XML try { - FileOutputStream fos = new FileOutputStream(statefile); - JarOutputStream jout = new JarOutputStream(fos); - //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS - //////////////////////////////////////////////////// - //NOTE ALSO new PrintWriter must be used for each new JarEntry + // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS + // ////////////////////////////////////////////////// + // NOTE ALSO new PrintWriter must be used for each new JarEntry PrintWriter out = null; Vector shortNames = new Vector(); - //REVERSE ORDER + // REVERSE ORDER for (int i = frames.length - 1; i > -1; i--) { if (frames[i] instanceof AlignFrame) { AlignFrame af = (AlignFrame) frames[i]; + // skip ? + if (skipList != null + && skipList.containsKey(af.getViewport() + .getSequenceSetId())) + { + continue; + } String shortName = af.getTitle(); @@ -232,11 +339,22 @@ public class Jalview2XML } } } - try { jout.flush(); } catch (Exception foo) {}; + try + { + jout.flush(); + } catch (Exception foo) + { + } + ; jout.close(); } catch (Exception ex) { - //TODO: inform user of the problem - they need to know if their data was not saved ! + // TODO: inform user of the problem - they need to know if their data was + // not saved ! + if (errorMessage == null) + { + errorMessage = "Couldn't write Jalview Archive - see error output for details"; + } ex.printStackTrace(); } } @@ -262,30 +380,41 @@ public class Jalview2XML SaveState(apanel, jfileName, jout); } - try { jout.flush(); } catch (Exception foo) {}; + try + { + jout.flush(); + } catch (Exception foo) + { + } + ; jout.close(); return true; } catch (Exception ex) { + errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details"; ex.printStackTrace(); return false; } } /** - * create a JalviewModel from an algnment view and marshall it - * to a JarOutputStream - * - * @param ap panel to create jalview model for - * @param fileName name of alignment panel written to output stream - * @param jout jar output stream - * @param out jar entry name + * create a JalviewModel from an algnment view and marshall it to a + * JarOutputStream + * + * @param ap + * panel to create jalview model for + * @param fileName + * name of alignment panel written to output stream + * @param jout + * jar output stream + * @param out + * jar entry name */ public JalviewModel SaveState(AlignmentPanel ap, String fileName, JarOutputStream jout) { initSeqRefs(); - + Vector jmolViewIds = new Vector(); // Vector userColours = new Vector(); AlignViewport av = ap.av; @@ -312,7 +441,7 @@ public class Jalview2XML if (jal.getDataset() != null) { // dataset id is the dataset's hashcode - vamsasSet.setDatasetId(jal.getDataset().hashCode() + ""); + vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset())); } if (jal.getProperties() != null) { @@ -329,7 +458,7 @@ public class Jalview2XML JSeq jseq; - //SAVE SEQUENCES + // SAVE SEQUENCES String id = ""; jalview.datamodel.SequenceI jds; for (int i = 0; i < jal.getHeight(); i++) @@ -339,14 +468,19 @@ public class Jalview2XML if (seqRefIds.get(id) != null) { - // This happens for two reasons: 1. multiple views are being serialised. 2. the hashCode has collided with another sequence's code. This DOES HAPPEN! (PF00072.15.stk does this) - // JBPNote: Uncomment to debug writing out of files that do not read back in due to ArrayOutOfBoundExceptions. - //System.err.println("vamsasSeq backref: "+id+""); - //System.err.println(jds.getName()+" "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString()); - //System.err.println("Hashcode: "+seqHash(jds)); - //SequenceI rsq = (SequenceI) seqRefIds.get(id + ""); - //System.err.println(rsq.getName()+" "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString()); - //System.err.println("Hashcode: "+seqHash(rsq)); + // This happens for two reasons: 1. multiple views are being serialised. + // 2. the hashCode has collided with another sequence's code. This DOES + // HAPPEN! (PF00072.15.stk does this) + // JBPNote: Uncomment to debug writing out of files that do not read + // back in due to ArrayOutOfBoundExceptions. + // System.err.println("vamsasSeq backref: "+id+""); + // System.err.println(jds.getName()+" + // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString()); + // System.err.println("Hashcode: "+seqHash(jds)); + // SequenceI rsq = (SequenceI) seqRefIds.get(id + ""); + // System.err.println(rsq.getName()+" + // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString()); + // System.err.println("Hashcode: "+seqHash(rsq)); } else { @@ -439,41 +573,80 @@ public class Jalview2XML pdb.setType(entry.getType()); AppJmol jmol; - //This must have been loaded, is it still visible? + // This must have been loaded, is it still visible? JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + String matchedFile = null; for (int f = frames.length - 1; f > -1; f--) { if (frames[f] instanceof AppJmol) { + // TODO: revise schema to allow many:one PDB id binding to viewer jmol = (AppJmol) frames[f]; - if (!jmol.pdbentry.getId().equals(entry.getId())) - continue; - - StructureState state = new StructureState(); - state.setVisible(true); - state.setXpos(jmol.getX()); - state.setYpos(jmol.getY()); - state.setWidth(jmol.getWidth()); - state.setHeight(jmol.getHeight()); - - String statestring = jmol.viewer.getStateInfo(); - if (state != null) - { - state.setContent(statestring.replaceAll("\n", "")); - } - for (int s = 0; s < jmol.sequence.length; s++) + for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++) { - if (jal.findIndex(jmol.sequence[s]) > -1) + if (!jmol.jmb.pdbentry[peid].getId().equals(entry.getId()) + && !(entry.getId().length() > 4 && entry + .getId() + .toLowerCase() + .startsWith( + jmol.jmb.pdbentry[peid].getId() + .toLowerCase()))) + continue; + if (matchedFile == null) + { + matchedFile = jmol.jmb.pdbentry[peid].getFile(); + } + else if (!matchedFile.equals(jmol.jmb.pdbentry[peid] + .getFile())) + { + Cache.log + .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): " + + jmol.jmb.pdbentry[peid].getFile()); + ; // record the + } + // file so we + // can get at it if the ID + // match is ambiguous (e.g. + // 1QIP==1qipA) + String statestring = jmol.jmb.viewer.getStateInfo(); + + for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++) { - pdb.addStructureState(state); + if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1) + { + StructureState state = new StructureState(); + state.setVisible(true); + state.setXpos(jmol.getX()); + state.setYpos(jmol.getY()); + state.setWidth(jmol.getWidth()); + state.setHeight(jmol.getHeight()); + state.setViewId(jmol.getViewId()); + if (!jmolViewIds.contains(state.getViewId())) + { + // Make sure we only store a Jmol state once in each XML + // document. + jmolViewIds.addElement(state.getViewId()); + state.setContent(statestring.replaceAll("\n", "")); + } + else + { + state.setContent("# duplicate state"); + } + pdb.addStructureState(state); + } } } } } - if (entry.getFile() != null) + if (matchedFile != null || entry.getFile() != null) { - pdb.setFile(entry.getFile()); + if (entry.getFile() != null) + { + // use entry's file + matchedFile = entry.getFile(); + } + pdb.setFile(matchedFile); // entry.getFile()); if (pdbfiles == null) { pdbfiles = new Vector(); @@ -484,7 +657,7 @@ public class Jalview2XML pdbfiles.addElement(entry.getId()); try { - File file = new File(entry.getFile()); + File file = new File(matchedFile); if (file.exists() && jout != null) { byte[] data = new byte[(int) file.length()]; @@ -544,9 +717,14 @@ public class Jalview2XML for (int p = 0; p < jac[i].aaWidth; p++) { Alcodon cmap = new Alcodon(); - cmap.setPos1(jac[i].codons[p][0]); - cmap.setPos2(jac[i].codons[p][1]); - cmap.setPos3(jac[i].codons[p][2]); + if (jac[i].codons[p] != null) + { + // Null codons indicate a gapped column in the translated peptide + // alignment. + cmap.setPos1(jac[i].codons[p][0]); + cmap.setPos2(jac[i].codons[p][1]); + cmap.setPos3(jac[i].codons[p][2]); + } alc.addAlcodon(cmap); } if (jac[i].getProtMappings() != null @@ -557,7 +735,7 @@ public class Jalview2XML for (int m = 0; m < pmaps.length; m++) { AlcodMap alcmap = new AlcodMap(); - alcmap.setDnasq("" + dnas[m].hashCode()); + alcmap.setDnasq(seqHash(dnas[m])); alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, false)); alc.addAlcodMap(alcmap); @@ -566,8 +744,8 @@ public class Jalview2XML } } - //SAVE TREES - /////////////////////////////////// + // SAVE TREES + // ///////////////////////////////// if (av.currentTree != null) { // FIND ANY ASSOCIATED TREES @@ -603,7 +781,7 @@ public class Jalview2XML tree.setWidth(tp.getWidth()); tree.setXpos(tp.getX()); tree.setYpos(tp.getY()); - + tree.setId(makeHashCode(tp, null)); jms.addTree(tree); } } @@ -611,7 +789,11 @@ public class Jalview2XML } } - //SAVE ANNOTATIONS + // SAVE ANNOTATIONS + /** + * store forward refs from an annotationRow to any groups + */ + IdentityHashMap groupRefs = new IdentityHashMap(); if (jal.getAlignmentAnnotation() != null) { jalview.datamodel.AlignmentAnnotation[] aa = jal @@ -628,23 +810,40 @@ public class Jalview2XML an.setId(aa[i].annotationId); - if (aa[i] == av.quality || aa[i] == av.conservation - || aa[i] == av.consensus) - { - an.setLabel(aa[i].label); - an.setGraph(true); - vamsasSet.addAnnotation(an); - continue; - } - an.setVisible(aa[i].visible); an.setDescription(aa[i].description); if (aa[i].sequenceRef != null) { + // TODO later annotation sequenceRef should be the XML ID of the + // sequence rather than its display name an.setSequenceRef(aa[i].sequenceRef.getName()); } + if (aa[i].groupRef != null) + { + Object groupIdr = groupRefs.get(aa[i].groupRef); + if (groupIdr == null) + { + // make a locally unique String + groupRefs.put(aa[i].groupRef, + groupIdr = ("" + System.currentTimeMillis() + + aa[i].groupRef.getName() + groupRefs.size())); + } + an.setGroupRef(groupIdr.toString()); + } + if (aa[i] == av.quality || aa[i] == av.conservation + || aa[i] == av.consensus || aa[i].autoCalculated) + { + // new way of indicating autocalculated annotation - + an.setAutoCalculated(aa[i].autoCalculated); + // write a stub for this annotation - indicate presence of autocalc + // rows + an.setLabel(aa[i].label); + an.setGraph(true); + vamsasSet.addAnnotation(an); + continue; + } if (aa[i].graph > 0) { @@ -693,9 +892,8 @@ public class Jalview2XML ae.setPosition(a); if (aa[i].annotations[a].secondaryStructure != ' ' && aa[i].annotations[a].secondaryStructure != '\0') - ae - .setSecondaryStructure(aa[i].annotations[a].secondaryStructure - + ""); + ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure + + ""); if (aa[i].annotations[a].colour != null && aa[i].annotations[a].colour != java.awt.Color.black) @@ -713,8 +911,7 @@ public class Jalview2XML vamsasSet.addAnnotation(an); } } - - //SAVE GROUPS + // SAVE GROUPS if (jal.getGroups() != null) { JGroup[] groups = new JGroup[jal.getGroups().size()]; @@ -728,6 +925,11 @@ public class Jalview2XML groups[i].setStart(sg.getStartRes()); groups[i].setEnd(sg.getEndRes()); groups[i].setName(sg.getName()); + if (groupRefs.containsKey(sg)) + { + // group has references so set it's ID field + groups[i].setId(groupRefs.get(sg).toString()); + } if (sg.cs != null) { if (sg.cs.conservationApplied()) @@ -772,7 +974,10 @@ public class Jalview2XML groups[i].setTextCol1(sg.textColour.getRGB()); groups[i].setTextCol2(sg.textColour2.getRGB()); groups[i].setTextColThreshold(sg.thresholdTextColour); - + groups[i].setShowUnconserved(sg.getShowNonconserved()); + groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); + groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram()); + groups[i].setShowSequenceLogo(sg.isShowSequenceLogo()); for (int s = 0; s < sg.getSize(); s++) { jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg @@ -784,10 +989,12 @@ public class Jalview2XML jms.setJGroup(groups); } - ///////////SAVE VIEWPORT + // /////////SAVE VIEWPORT Viewport view = new Viewport(); view.setTitle(ap.alignFrame.getTitle()); - view.setSequenceSetId(av.getSequenceSetId()); + view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), + av.getSequenceSetId())); + view.setId(av.getViewId()); view.setViewName(av.viewName); view.setGatheredViews(av.gatherViewsHere); @@ -877,11 +1084,20 @@ public class Jalview2XML view.setRightAlignIds(av.rightAlignIds); view.setShowSequenceFeatures(av.showSequenceFeatures); view.setShowText(av.getShowText()); + view.setShowUnconserved(av.getShowUnconserved()); view.setWrapAlignment(av.getWrapAlignment()); view.setTextCol1(av.textColour.getRGB()); view.setTextCol2(av.textColour2.getRGB()); view.setTextColThreshold(av.thresholdTextColour); - + view.setShowConsensusHistogram(av.isShowConsensusHistogram()); + view.setShowSequenceLogo(av.isShowSequenceLogo()); + view.setShowGroupConsensus(av.isShowGroupConsensus()); + view.setShowGroupConservation(av.isShowGroupConservation()); + view.setShowNPfeatureTooltip(av.isShowNpFeats()); + view.setShowDbRefTooltip(av.isShowDbRefs()); + view.setFollowHighlight(av.followHighlight); + view.setFollowSelection(av.followSelection); + view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus()); if (av.featuresDisplayed != null) { jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); @@ -889,12 +1105,31 @@ public class Jalview2XML String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; Vector settingsAdded = new Vector(); + Object gstyle = null; + GraduatedColor gcol = null; for (int ro = 0; ro < renderOrder.length; ro++) { + gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer() + .getFeatureStyle(renderOrder[ro]); Setting setting = new Setting(); setting.setType(renderOrder[ro]); - setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() - .getColour(renderOrder[ro]).getRGB()); + if (gstyle instanceof GraduatedColor) + { + gcol = (GraduatedColor) gstyle; + setting.setColour(gcol.getMaxColor().getRGB()); + setting.setMincolour(gcol.getMinColor().getRGB()); + setting.setMin(gcol.getMin()); + setting.setMax(gcol.getMax()); + setting.setColourByLabel(gcol.isColourByLabel()); + setting.setAutoScale(gcol.isAutoScale()); + setting.setThreshold(gcol.getThresh()); + setting.setThreshstate(gcol.getThreshType()); + } + else + { + setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() + .getColour(renderOrder[ro]).getRGB()); + } setting.setDisplay(av.featuresDisplayed .containsKey(renderOrder[ro])); @@ -908,7 +1143,7 @@ public class Jalview2XML settingsAdded.addElement(renderOrder[ro]); } - //Make sure we save none displayed feature settings + // Make sure we save none displayed feature settings Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours .keys(); while (en.hasMoreElements()) @@ -945,10 +1180,8 @@ public class Jalview2XML } Group g = new Group(); g.setName(grp); - g - .setDisplay(((Boolean) ap.seqPanel.seqCanvas - .getFeatureRenderer().featureGroups.get(grp)) - .booleanValue()); + g.setDisplay(((Boolean) ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups + .get(grp)).booleanValue()); fs.addGroup(g); groupsAdded.addElement(grp); } @@ -958,14 +1191,23 @@ public class Jalview2XML if (av.hasHiddenColumns) { - for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++) + if (av.getColumnSelection() == null + || av.getColumnSelection().getHiddenColumns() == null) + { + warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this."); + } + else { - int[] region = (int[]) av.getColumnSelection().getHiddenColumns() - .elementAt(c); - HiddenColumns hc = new HiddenColumns(); - hc.setStart(region[0]); - hc.setEnd(region[1]); - view.addHiddenColumns(hc); + for (int c = 0; c < av.getColumnSelection().getHiddenColumns() + .size(); c++) + { + int[] region = (int[]) av.getColumnSelection().getHiddenColumns() + .elementAt(c); + HiddenColumns hc = new HiddenColumns(); + hc.setStart(region[0]); + hc.setEnd(region[1]); + view.addHiddenColumns(hc); + } } } @@ -974,18 +1216,19 @@ public class Jalview2XML object.setJalviewModelSequence(jms); object.getVamsasModel().addSequenceSet(vamsasSet); - if (jout!=null && fileName!=null) + if (jout != null && fileName != null) { - //We may not want to write the object to disk, - //eg we can copy the alignViewport to a new view object - //using save and then load + // We may not want to write the object to disk, + // eg we can copy the alignViewport to a new view object + // using save and then load try { JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout, - "UTF-8")); - org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(pout); + "UTF-8")); + org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller( + pout); marshaller.marshal(object); pout.flush(); jout.closeEntry(); @@ -998,6 +1241,68 @@ public class Jalview2XML return object; } + /** + * External mapping between jalview objects and objects yielding a valid and + * unique object ID string. This is null for normal Jalview project IO, but + * non-null when a jalview project is being read or written as part of a + * vamsas session. + */ + IdentityHashMap jv2vobj = null; + + /** + * Construct a unique ID for jvobj using either existing bindings or if none + * exist, the result of the hashcode call for the object. + * + * @param jvobj + * jalview data object + * @return unique ID for referring to jvobj + */ + private String makeHashCode(Object jvobj, String altCode) + { + if (jv2vobj != null) + { + Object id = jv2vobj.get(jvobj); + if (id != null) + { + return id.toString(); + } + // check string ID mappings + if (jvids2vobj != null && jvobj instanceof String) + { + id = jvids2vobj.get(jvobj); + } + if (id != null) + { + return id.toString(); + } + // give up and warn that something has gone wrong + warn("Cannot find ID for object in external mapping : " + jvobj); + } + return altCode; + } + + /** + * return local jalview object mapped to ID, if it exists + * + * @param idcode + * (may be null) + * @return null or object bound to idcode + */ + private Object retrieveExistingObj(String idcode) + { + if (idcode != null && vobj2jv != null) + { + return vobj2jv.get(idcode); + } + return null; + } + + /** + * binding from ID strings from external mapping table to jalview data model + * objects. + */ + private Hashtable vobj2jv; + private Sequence createVamsasSequence(String id, SequenceI jds) { return createVamsasSequence(true, id, jds, null); @@ -1022,7 +1327,8 @@ public class Jalview2XML } else { - vamsasSeq.setDsseqid(id); // so we can tell which sequences really are dataset sequences only + vamsasSeq.setDsseqid(id); // so we can tell which sequences really are + // dataset sequences only dbrefs = jds.getDBRef(); } if (dbrefs != null) @@ -1079,8 +1385,8 @@ public class Jalview2XML && (parentseq != jmp.getTo() || parentseq .getDatasetSequence() != jmp.getTo())) { - mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()) - , jmp.getTo(), jds)); + mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()), + jmp.getTo(), jds)); } else { @@ -1118,11 +1424,16 @@ public class Jalview2XML { String id = null; jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; - + boolean newucs = false; if (!userColours.contains(ucs)) { userColours.add(ucs); - + newucs = true; + } + id = "ucs" + userColours.indexOf(ucs); + if (newucs) + { + // actually create the scheme's entry in the XML model java.awt.Color[] colours = ucs.getColours(); jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours(); jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme(); @@ -1146,7 +1457,6 @@ public class Jalview2XML } } - id = "ucs" + userColours.indexOf(ucs); uc.setId(id); uc.setUserColourScheme(jbucs); jms.addUserColours(uc); @@ -1197,48 +1507,122 @@ public class Jalview2XML } /** - * DOCUMENT ME! - * - * @param file DOCUMENT ME! + * contains last error message (if any) encountered by XML loader. + */ + String errorMessage = null; + + /** + * flag to control whether the Jalview2XML_V1 parser should be deferred to if + * exceptions are raised during project XML parsing + */ + public boolean attemptversion1parse = true; + + /** + * Load a jalview project archive from a jar file + * + * @param file + * - HTTP URL or filename */ public AlignFrame LoadJalviewAlign(final String file) { - uniqueSetSuffix = System.currentTimeMillis() % 100000 + ""; jalview.gui.AlignFrame af = null; - seqRefIds = new Hashtable(); - viewportsAdded = new Hashtable(); - frefedSequence = new Vector(); - Hashtable gatherToThisFrame = new Hashtable(); + try + { + // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING + // Workaround is to make sure caller implements the JarInputStreamProvider + // interface + // so we can re-open the jar input stream for each entry. - String errorMessage = null; + jarInputStreamProvider jprovider = createjarInputStreamProvider(file); + af = LoadJalviewAlign(jprovider); + } catch (MalformedURLException e) + { + errorMessage = "Invalid URL format for '" + file + "'"; + reportErrors(); + } + return af; + } - try + private jarInputStreamProvider createjarInputStreamProvider( + final String file) throws MalformedURLException + { + URL url = null; + errorMessage = null; + uniqueSetSuffix = null; + seqRefIds = null; + viewportsAdded = null; + frefedSequence = null; + + if (file.startsWith("http://")) + { + url = new URL(file); + } + final URL _url = url; + return new jarInputStreamProvider() { - //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING - URL url = null; - if (file.startsWith("http://")) + public JarInputStream getJarInputStream() throws IOException + { + if (_url != null) + { + return new JarInputStream(_url.openStream()); + } + else + { + return new JarInputStream(new FileInputStream(file)); + } + } + + public String getFilename() { - url = new URL(file); + return file; } + }; + } + + /** + * Recover jalview session from a jalview project archive. Caller may + * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence + * themselves. Any null fields will be initialised with default values, + * non-null fields are left alone. + * + * @param jprovider + * @return + */ + public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider) + { + errorMessage = null; + if (uniqueSetSuffix == null) + { + uniqueSetSuffix = System.currentTimeMillis() % 100000 + ""; + } + if (seqRefIds == null) + { + seqRefIds = new Hashtable(); + } + if (viewportsAdded == null) + { + viewportsAdded = new Hashtable(); + } + if (frefedSequence == null) + { + frefedSequence = new Vector(); + } + jalview.gui.AlignFrame af = null; + Hashtable gatherToThisFrame = new Hashtable(); + final String file = jprovider.getFilename(); + try + { JarInputStream jin = null; JarEntry jarentry = null; int entryCount = 1; do { - if (url != null) - { - jin = new JarInputStream(url.openStream()); - } - else - { - jin = new JarInputStream(new FileInputStream(file)); - } - + jin = jprovider.getJarInputStream(); for (int i = 0; i < entryCount; i++) { jarentry = jin.getNextJarEntry(); @@ -1252,17 +1636,19 @@ public class Jalview2XML Unmarshaller unmar = new Unmarshaller(object); unmar.setValidation(false); object = (JalviewModel) unmar.unmarshal(in); - - af = LoadFromObject(object, file, true); - if (af.viewport.gatherViewsHere) + if (true) // !skipViewport(object)) { - gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); + af = LoadFromObject(object, file, true, jprovider); + if (af.viewport.gatherViewsHere) + { + gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); + } } entryCount++; } else if (jarentry != null) { - //Some other file here. + // Some other file here. entryCount++; } } while (jarentry != null); @@ -1283,16 +1669,19 @@ public class Jalview2XML { System.err.println("Parsing as Jalview Version 2 file failed."); ex.printStackTrace(System.err); - - //Is Version 1 Jar file? - try { - af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file); - } catch (Exception ex2) { - System.err.println("Exception whilst loading as jalviewXMLV1:"); - ex2.printStackTrace(); - af = null; + if (attemptversion1parse) + { + // Is Version 1 Jar file? + try + { + af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider); + } catch (Exception ex2) + { + System.err.println("Exception whilst loading as jalviewXMLV1:"); + ex2.printStackTrace(); + af = null; + } } - if (Desktop.instance != null) { Desktop.instance.stopLoading(); @@ -1306,6 +1695,12 @@ public class Jalview2XML System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); + } catch (OutOfMemoryError e) + { + // Don't use the OOM Window here + errorMessage = "Out of memory loading jalview XML file"; + System.err.println("Out of memory whilst loading jalview XML file"); + e.printStackTrace(); } if (Desktop.instance != null) @@ -1318,32 +1713,59 @@ public class Jalview2XML { Desktop.instance.gatherViews((AlignFrame) en.nextElement()); } + if (errorMessage != null) + { + reportErrors(); + } + return af; + } + + /** + * check errorMessage for a valid error message and raise an error box in the + * GUI or write the current errorMessage to stderr and then clear the error + * state. + */ + protected void reportErrors() + { + reportErrors(false); + } + protected void reportErrors(final boolean saving) + { if (errorMessage != null) { final String finalErrorMessage = errorMessage; if (raiseGUI) - { + { javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - finalErrorMessage, "Error loading Jalview file", - JOptionPane.WARNING_MESSAGE); - } - }); - } else { - System.err.println("Problem loading Jalview file: "+errorMessage); - } + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + finalErrorMessage, "Error " + + (saving ? "saving" : "loading") + + " Jalview file", JOptionPane.WARNING_MESSAGE); + } + }); + } + else + { + System.err.println("Problem loading Jalview file: " + errorMessage); + } } - - return af; + errorMessage = null; } Hashtable alreadyLoadedPDB; - String loadPDBFile(String file, String pdbId) + /** + * when set, local views will be updated from view stored in JalviewXML + * Currently (28th Sep 2008) things will go horribly wrong in vamsas document + * sync if this is set to true. + */ + private boolean updateLocalViews = false; + + String loadPDBFile(jarInputStreamProvider jprovider, String pdbId) { if (alreadyLoadedPDB == null) alreadyLoadedPDB = new Hashtable(); @@ -1353,39 +1775,46 @@ public class Jalview2XML try { - JarInputStream jin = null; - - if (file.startsWith("http://")) - { - jin = new JarInputStream(new URL(file).openStream()); - } - else - { - jin = new JarInputStream(new FileInputStream(file)); - } + JarInputStream jin = jprovider.getJarInputStream(); + /* + * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new + * URL(jprovider).openStream()); } else { jin = new JarInputStream(new + * FileInputStream(jprovider)); } + */ JarEntry entry = null; do { entry = jin.getNextJarEntry(); - } while (!entry.getName().equals(pdbId)); + } while (entry != null && !entry.getName().equals(pdbId)); + if (entry != null) + { + BufferedReader in = new BufferedReader(new InputStreamReader(jin)); + File outFile = File.createTempFile("jalview_pdb", ".txt"); + outFile.deleteOnExit(); + PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); + String data; - BufferedReader in = new BufferedReader(new InputStreamReader(jin)); - File outFile = File.createTempFile("jalview_pdb", ".txt"); - outFile.deleteOnExit(); - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; + while ((data = in.readLine()) != null) + { + out.println(data); + } + try + { + out.flush(); + } catch (Exception foo) + { + } + ; + out.close(); - while ((data = in.readLine()) != null) + alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath()); + return outFile.getAbsolutePath(); + } + else { - out.println(data); + warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId); } - try { out.flush(); } catch (Exception foo) {}; - out.close(); - - alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath()); - return outFile.getAbsolutePath(); - } catch (Exception ex) { ex.printStackTrace(); @@ -1394,8 +1823,21 @@ public class Jalview2XML return null; } + /** + * Load alignment frame from jalview XML DOM object + * + * @param object + * DOM + * @param file + * filename source string + * @param loadTreesAndStructures + * when false only create Viewport + * @param jprovider + * data source provider + * @return alignment frame created from view stored in DOM + */ AlignFrame LoadFromObject(JalviewModel object, String file, - boolean loadTreesAndStructures) + boolean loadTreesAndStructures, jarInputStreamProvider jprovider) { SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); Sequence[] vamsasSeq = vamsasSet.getSequence(); @@ -1403,9 +1845,8 @@ public class Jalview2XML JalviewModelSequence jms = object.getJalviewModelSequence(); Viewport view = jms.getViewport(0); - - ////////////////////////////////// - //LOAD SEQUENCES + // //////////////////////////////// + // LOAD SEQUENCES Vector hiddenSeqs = null; jalview.datamodel.Sequence jseq; @@ -1415,10 +1856,10 @@ public class Jalview2XML boolean multipleView = false; JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); - int vi=0; // counter in vamsasSeq array + int vi = 0; // counter in vamsasSeq array for (int i = 0; i < JSEQ.length; i++) { - String seqId = JSEQ[i].getId() + ""; + String seqId = JSEQ[i].getId(); if (seqRefIds.get(seqId) != null) { @@ -1433,7 +1874,7 @@ public class Jalview2XML jseq.setStart(JSEQ[i].getStart()); jseq.setEnd(JSEQ[i].getEnd()); jseq.setVamsasId(uniqueSetSuffix + seqId); - seqRefIds.put(vamsasSeq[vi].getId()+"", jseq); + seqRefIds.put(vamsasSeq[vi].getId(), jseq); tmpseqs.add(jseq); vi++; } @@ -1451,9 +1892,9 @@ public class Jalview2XML } - /// + // / // Create the alignment object from the sequence set - ///////////////////////////////// + // /////////////////////////////// jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs .size()]; @@ -1462,17 +1903,17 @@ public class Jalview2XML jalview.datamodel.Alignment al = new jalview.datamodel.Alignment( orderedSeqs); - /// Add the alignment properties + // / Add the alignment properties for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++) { SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i); al.setProperty(ssp.getKey(), ssp.getValue()); } - /// + // / // SequenceFeatures are added to the DatasetSequence, // so we must create or recover the dataset before loading features - ///////////////////////////////// + // /////////////////////////////// if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "") { // older jalview projects do not have a dataset id. @@ -1482,11 +1923,13 @@ public class Jalview2XML { recoverDatasetFor(vamsasSet, al); } - ///////////////////////////////// + // /////////////////////////////// Hashtable pdbloaded = new Hashtable(); if (!multipleView) { + // load sequence features, database references and any associated PDB + // structures for the alignment for (int i = 0; i < vamsasSeq.length; i++) { if (JSEQ[i].getFeaturesCount() > 0) @@ -1533,7 +1976,7 @@ public class Jalview2XML { if (!pdbloaded.containsKey(ids[p].getFile())) { - entry.setFile(loadPDBFile(file, ids[p].getId())); + entry.setFile(loadPDBFile(jprovider, ids[p].getId())); } else { @@ -1545,12 +1988,15 @@ public class Jalview2XML } } } - } + } // end !multipleview - ///////////////////////////////// + // /////////////////////////////// // LOAD SEQUENCE MAPPINGS + if (vamsasSet.getAlcodonFrameCount() > 0) { + // TODO Potentially this should only be done once for all views of an + // alignment AlcodonFrame[] alc = vamsasSet.getAlcodonFrame(); for (int i = 0; i < alc.length; i++) { @@ -1561,10 +2007,19 @@ public class Jalview2XML Alcodon[] alcods = alc[i].getAlcodon(); for (int p = 0; p < cf.codons.length; p++) { - cf.codons[p] = new int[3]; - cf.codons[p][0] = (int) alcods[p].getPos1(); - cf.codons[p][1] = (int) alcods[p].getPos2(); - cf.codons[p][2] = (int) alcods[p].getPos3(); + if (alcods[p].hasPos1() && alcods[p].hasPos2() + && alcods[p].hasPos3()) + { + // translated codons require three valid positions + cf.codons[p] = new int[3]; + cf.codons[p][0] = (int) alcods[p].getPos1(); + cf.codons[p][1] = (int) alcods[p].getPos2(); + cf.codons[p][2] = (int) alcods[p].getPos3(); + } + else + { + cf.codons[p] = null; + } } } if (alc[i].getAlcodMapCount() > 0) @@ -1575,15 +2030,21 @@ public class Jalview2XML SequenceI dnaseq = (SequenceI) seqRefIds .get(maps[m].getDnasq()); // Load Mapping + jalview.datamodel.Mapping mapping = null; // attach to dna sequence reference. + if (maps[m].getMapping() != null) + { + mapping = addMapping(maps[m].getMapping()); + } if (dnaseq != null) { - if (maps[m].getMapping() != null) - { - jalview.datamodel.Mapping mapping = addMapping(maps[m] - .getMapping()); - cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); - } + cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); + } + else + { + // defer to later + frefedSequence.add(new Object[] + { maps[m].getDnasq(), cf, mapping }); } } } @@ -1592,9 +2053,13 @@ public class Jalview2XML } - ////////////////////////////////// - //LOAD ANNOTATIONS + // //////////////////////////////// + // LOAD ANNOTATIONS boolean hideQuality = true, hideConservation = true, hideConsensus = true; + /** + * store any annotations which forward reference a group's ID + */ + Hashtable groupAnnotRefs = new Hashtable(); if (vamsasSet.getAnnotationCount() > 0) { @@ -1602,6 +2067,7 @@ public class Jalview2XML for (int i = 0; i < an.length; i++) { + // set visibility for automatic annotation for this view if (an[i].getLabel().equals("Quality")) { hideQuality = false; @@ -1617,12 +2083,14 @@ public class Jalview2XML hideConsensus = false; continue; } - + // set visiblity for other annotation in this view if (an[i].getId() != null && annotationIds.containsKey(an[i].getId())) { jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds .get(an[i].getId()); + // in principle Visible should always be true for annotation displayed + // in multiple views if (an[i].hasVisible()) jda.visible = an[i].getVisible(); @@ -1630,7 +2098,7 @@ public class Jalview2XML continue; } - + // Construct new annotation from model. AnnotationElement[] ae = an[i].getAnnotationElement(); jalview.datamodel.Annotation[] anot = null; @@ -1645,20 +2113,22 @@ public class Jalview2XML anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation( - ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa] - .getSecondaryStructure() == null || ae[aa] - .getSecondaryStructure().length() == 0) ? ' ' : ae[aa] - .getSecondaryStructure().charAt(0), ae[aa].getValue() - + ae[aa].getDisplayCharacter(), ae[aa].getDescription(), + (ae[aa].getSecondaryStructure() == null || ae[aa] + .getSecondaryStructure().length() == 0) ? ' ' + : ae[aa].getSecondaryStructure().charAt(0), + ae[aa].getValue() + ); - // JBPNote: Consider verifying dataflow for IO of secondary structure annotation read from Stockholm files - // this was added to try to ensure that - //if (anot[ae[aa].getPosition()].secondaryStructure>' ') - //{ - // anot[ae[aa].getPosition()].displayCharacter = ""; - //} - anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa] - .getColour()); + // JBPNote: Consider verifying dataflow for IO of secondary + // structure annotation read from Stockholm files + // this was added to try to ensure that + // if (anot[ae[aa].getPosition()].secondaryStructure>' ') + // { + // anot[ae[aa].getPosition()].displayCharacter = ""; + // } + anot[ae[aa].getPosition()].colour = new java.awt.Color( + ae[aa].getColour()); } } jalview.datamodel.AlignmentAnnotation jaa = null; @@ -1685,13 +2155,13 @@ public class Jalview2XML jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot); } - + // register new annotation if (an[i].getId() != null) { annotationIds.put(an[i].getId(), jaa); jaa.annotationId = an[i].getId(); } - + // recover sequence association if (an[i].getSequenceRef() != null) { if (al.findName(an[i].getSequenceRef()) != null) @@ -1701,20 +2171,40 @@ public class Jalview2XML al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); } } + // and make a note of any group association + if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0) + { + groupAnnotRefs.put(an[i].getGroupRef(), jaa); + } + if (an[i].hasScore()) { jaa.setScore(an[i].getScore()); } - if (an[i].hasVisible()) jaa.visible = an[i].getVisible(); + if (an[i].hasCentreColLabels()) + jaa.centreColLabels = an[i].getCentreColLabels(); + + if (an[i].hasScaleColLabels()) + { + jaa.scaleColLabel = an[i].getScaleColLabels(); + } + if (an[i].hasAutoCalculated() && an[i].isAutoCalculated()) + { + // newer files have an 'autoCalculated' flag and store calculation + // state in viewport properties + jaa.autoCalculated = true; // means annotation will be marked for + // update at end of load. + } al.addAnnotation(jaa); } } - ///////////////////////// - //LOAD GROUPS + // /////////////////////// + // LOAD GROUPS + // Create alignment markup and styles for this view if (jms.getJGroupCount() > 0) { JGroup[] groups = jms.getJGroup(); @@ -1764,32 +2254,514 @@ public class Jalview2XML groups[i].getDisplayText(), groups[i].getColourText(), groups[i].getStart(), groups[i].getEnd()); - sg - .setOutlineColour(new java.awt.Color(groups[i] - .getOutlineColour())); + sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour())); sg.textColour = new java.awt.Color(groups[i].getTextCol1()); sg.textColour2 = new java.awt.Color(groups[i].getTextCol2()); + sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i] + .isShowUnconserved() : false); sg.thresholdTextColour = groups[i].getTextColThreshold(); - + if (groups[i].hasShowConsensusHistogram()) + { + sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram()); + } + ; + if (groups[i].hasShowSequenceLogo()) + { + sg.setshowSequenceLogo(groups[i].isShowSequenceLogo()); + } + if (groups[i].hasIgnoreGapsinConsensus()) + { + sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus()); + } if (groups[i].getConsThreshold() != 0) { jalview.analysis.Conservation c = new jalview.analysis.Conservation( - "All", ResidueProperties.propHash, 3, sg - .getSequences(null), 0, sg.getWidth() - 1); + "All", ResidueProperties.propHash, 3, + sg.getSequences(null), 0, sg.getWidth() - 1); c.calculate(); c.verdict(false, 25); sg.cs.setConservation(c); } + if (groups[i].getId() != null && groupAnnotRefs.size() > 0) + { + // re-instate unique group/annotation row reference + jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs + .get(groups[i].getId()); + if (jaa != null) + { + jaa.groupRef = sg; + } + } al.addGroup(sg); + } } - ///////////////////////////////// + // /////////////////////////////// // LOAD VIEWPORT - AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight()); + // If we just load in the same jar file again, the sequenceSetId + // will be the same, and we end up with multiple references + // to the same sequenceSet. We must modify this id on load + // so that each load of the file gives a unique id + String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; + String viewId = (view.getId() == null ? null : view.getId() + + uniqueSetSuffix); + AlignFrame af = null; + AlignViewport av = null; + // now check to see if we really need to create a new viewport. + if (multipleView && viewportsAdded.size() == 0) + { + // We recovered an alignment for which a viewport already exists. + // TODO: fix up any settings necessary for overlaying stored state onto + // state recovered from another document. (may not be necessary). + // we may need a binding from a viewport in memory to one recovered from + // XML. + // and then recover its containing af to allow the settings to be applied. + // TODO: fix for vamsas demo + System.err + .println("About to recover a viewport for existing alignment: Sequence set ID is " + + uniqueSeqSetId); + Object seqsetobj = retrieveExistingObj(uniqueSeqSetId); + if (seqsetobj != null) + { + if (seqsetobj instanceof String) + { + uniqueSeqSetId = (String) seqsetobj; + System.err + .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is " + + uniqueSeqSetId); + } + else + { + System.err + .println("Warning : Collision between sequence set ID string and existing jalview object mapping."); + } + + } + } + AlignmentPanel ap = null; + boolean isnewview = true; + if (viewId != null) + { + // Check to see if this alignment already has a view id == viewId + jalview.gui.AlignmentPanel views[] = Desktop + .getAlignmentPanels(uniqueSeqSetId); + if (views != null && views.length > 0) + { + for (int v = 0; v < views.length; v++) + { + if (views[v].av.getViewId().equalsIgnoreCase(viewId)) + { + // recover the existing alignpanel, alignframe, viewport + af = views[v].alignFrame; + av = views[v].av; + ap = views[v]; + // TODO: could even skip resetting view settings if we don't want to + // change the local settings from other jalview processes + isnewview = false; + } + } + } + } + + if (isnewview) + { + af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus, + hideQuality, hideConservation, jms, view, uniqueSeqSetId, + viewId); + av = af.viewport; + ap = af.alignPanel; + } + // LOAD TREES + // ///////////////////////////////////// + if (loadTreesAndStructures && jms.getTreeCount() > 0) + { + try + { + for (int t = 0; t < jms.getTreeCount(); t++) + { + + Tree tree = jms.getTree(t); + + TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); + if (tp == null) + { + tp = af.ShowNewickTree( + new jalview.io.NewickFile(tree.getNewick()), + tree.getTitle(), tree.getWidth(), tree.getHeight(), + tree.getXpos(), tree.getYpos()); + if (tree.getId() != null) + { + // perhaps bind the tree id to something ? + } + } + else + { + // update local tree attributes ? + // TODO: should check if tp has been manipulated by user - if so its + // settings shouldn't be modified + tp.setTitle(tree.getTitle()); + tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree + .getWidth(), tree.getHeight())); + tp.av = av; // af.viewport; // TODO: verify 'associate with all + // views' + // works still + tp.treeCanvas.av = av; // af.viewport; + tp.treeCanvas.ap = ap; // af.alignPanel; + + } + if (tp == null) + { + warn("There was a problem recovering stored Newick tree: \n" + + tree.getNewick()); + continue; + } + + tp.fitToWindow.setState(tree.getFitToWindow()); + tp.fitToWindow_actionPerformed(null); + + if (tree.getFontName() != null) + { + tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree + .getFontStyle(), tree.getFontSize())); + } + else + { + tp.setTreeFont(new java.awt.Font(view.getFontName(), view + .getFontStyle(), tree.getFontSize())); + } + + tp.showPlaceholders(tree.getMarkUnlinked()); + tp.showBootstrap(tree.getShowBootstrap()); + tp.showDistances(tree.getShowDistances()); + + tp.treeCanvas.threshold = tree.getThreshold(); + + if (tree.getCurrentTree()) + { + af.viewport.setCurrentTree(tp.getTree()); + } + } + + } catch (Exception ex) + { + ex.printStackTrace(); + } + } + + // //LOAD STRUCTURES + if (loadTreesAndStructures) + { + // run through all PDB ids on the alignment, and collect mappings between + // jmol view ids and all sequences referring to it + Hashtable jmolViewIds = new Hashtable(); + + for (int i = 0; i < JSEQ.length; i++) + { + if (JSEQ[i].getPdbidsCount() > 0) + { + Pdbids[] ids = JSEQ[i].getPdbids(); + for (int p = 0; p < ids.length; p++) + { + for (int s = 0; s < ids[p].getStructureStateCount(); s++) + { + // check to see if we haven't already created this structure view + String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null + : ids[p].getStructureState(s).getViewId() + + uniqueSetSuffix; + jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry(); + // Originally : ids[p].getFile() + // : TODO: verify external PDB file recovery still works in normal + // jalview project load + jpdb.setFile(loadPDBFile(jprovider, ids[p].getId())); + jpdb.setId(ids[p].getId()); + + int x = ids[p].getStructureState(s).getXpos(); + int y = ids[p].getStructureState(s).getYpos(); + int width = ids[p].getStructureState(s).getWidth(); + int height = ids[p].getStructureState(s).getHeight(); + + // Probably don't need to do this anymore... + // Desktop.desktop.getComponentAt(x, y); + // TODO: NOW: check that this recovers the PDB file correctly. + String pdbFile = loadPDBFile(jprovider, ids[p].getId()); + jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds + .get(JSEQ[i].getId() + ""); + if (sviewid == null) + { + sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + + "," + height; + } + if (!jmolViewIds.containsKey(sviewid)) + { + jmolViewIds.put(sviewid, new Object[] + { new int[] + { x, y, width, height }, "", + new Hashtable() }); + } + // TODO: assemble String[] { pdb files }, String[] { id for each + // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { + // seqs_file 2}} from hash + Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid); + if (((String) jmoldat[1]).length() < ids[p] + .getStructureState(s).getContent().length()) + { + { + jmoldat[1] = ids[p].getStructureState(s).getContent(); + } + } + Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2]) + .get(ids[p].getFile()); + if (seqstrmaps == null) + { + ((Hashtable) jmoldat[2]).put( + new File(ids[p].getFile()).toString(), + seqstrmaps = new Object[] + { pdbFile, ids[p].getId(), new Vector(), + new Vector() }); + } + if (!((Vector) seqstrmaps[2]).contains(seq)) + { + ((Vector) seqstrmaps[2]).addElement(seq); + // ((Vector)seqstrmaps[3]).addElement(n) : in principle, chains + // should be stored here : do we need to + // TODO: store and recover seq/pdb_id : chain mappings + } + } + } + } + } + { + + // Instantiate the associated Jmol views + for (Entry entry : jmolViewIds.entrySet()) + { + String sviewid = entry.getKey(); + Object[] svattrib = entry.getValue(); + int[] geom = (int[]) svattrib[0]; + String state = (String) svattrib[1]; + Hashtable oldFiles = (Hashtable) svattrib[2]; + + int x = geom[0], y = geom[1], width = geom[2], height = geom[3]; + // collate the pdbfile -> sequence mappings from this view + Vector pdbfilenames = new Vector(); + Vector seqmaps = new Vector(); + Vector pdbids = new Vector(); + + // Search to see if we've already created this Jmol view + AppJmol comp = null; + JInternalFrame[] frames = null; + do + { + try + { + frames = Desktop.desktop.getAllFrames(); + } catch (ArrayIndexOutOfBoundsException e) + { + // occasional No such child exceptions are thrown here... + frames = null; + try + { + Thread.sleep(10); + } catch (Exception f) + { + } + ; + } + } while (frames == null); + // search for any Jmol windows already open from other + // alignment views that exactly match the stored structure state + for (int f = 0; comp == null && f < frames.length; f++) + { + if (frames[f] instanceof AppJmol) + { + if (sviewid != null + && ((AppJmol) frames[f]).getViewId().equals(sviewid)) + { + // post jalview 2.4 schema includes structure view id + comp = (AppJmol) frames[f]; + } + else if (frames[f].getX() == x && frames[f].getY() == y + && frames[f].getHeight() == height + && frames[f].getWidth() == width) + { + comp = (AppJmol) frames[f]; + } + } + } + + if (comp == null) + { + // create a new Jmol window. + // First parse the Jmol state to translate filenames loaded into the + // view, and record the order in which files are shown in the Jmol + // view, so we can add the sequence mappings in same order. + StringBuffer newFileLoc = null; + int cp = 0, ncp, ecp; + while ((ncp = state.indexOf("load ", cp)) > -1) + { + if (newFileLoc == null) + { + newFileLoc = new StringBuffer(); + } + newFileLoc.append(state.substring(cp, + ncp = (state.indexOf("\"", ncp + 1) + 1))); + String oldfilenam = state.substring(ncp, + ecp = state.indexOf("\"", ncp)); + // recover the new mapping data for this old filename + // have to normalize filename - since Jmol and jalview do filename + // translation differently. + Object[] filedat = oldFiles.get(new File(oldfilenam) + .toString()); + newFileLoc.append(((String) filedat[0])); + pdbfilenames.addElement((String) filedat[0]); + pdbids.addElement((String) filedat[1]); + seqmaps.addElement((SequenceI[]) ((Vector) filedat[2]) + .toArray(new SequenceI[0])); + newFileLoc.append("\""); + cp = ecp + 1; // advance beyond last \" and set cursor so we can + // look for next file statement. + } + if (cp > 0) + { + // just append rest of state + newFileLoc.append(state.substring(cp)); + } + else + { + System.err + .print("Ignoring incomplete Jmol state for PDB ids: "); + newFileLoc = new StringBuffer(state); + newFileLoc.append("; load append "); + for (String id : oldFiles.keySet()) + { + // add this and any other pdb files that should be present in + // the viewer + Object[] filedat = oldFiles.get(id); + String nfilename; + newFileLoc.append(((String) filedat[0])); + pdbfilenames.addElement((String) filedat[0]); + pdbids.addElement((String) filedat[1]); + seqmaps.addElement((SequenceI[]) ((Vector) filedat[2]) + .toArray(new SequenceI[0])); + newFileLoc.append(" \""); + newFileLoc.append((String) filedat[0]); + newFileLoc.append("\""); + + } + newFileLoc.append(";"); + } + + if (newFileLoc != null) + { + int histbug = newFileLoc.indexOf("history = "); + histbug += 10; + int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", + histbug); + String val = (diff == -1) ? null : newFileLoc.substring( + histbug, diff); + if (val != null && val.length() >= 4) + { + if (val.contains("e")) + { + if (val.trim().equals("true")) + { + val = "1"; + } + else + { + val = "0"; + } + newFileLoc.replace(histbug, diff, val); + } + } + // TODO: assemble String[] { pdb files }, String[] { id for each + // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { + // seqs_file 2}} from hash + final String[] pdbf = (String[]) pdbfilenames + .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids + .toArray(new String[pdbids.size()]); + final SequenceI[][] sq = (SequenceI[][]) seqmaps + .toArray(new SequenceI[seqmaps.size()][]); + final String fileloc = newFileLoc.toString(), vid = sviewid; + final AlignFrame alf = af; + final java.awt.Rectangle rect = new java.awt.Rectangle(x, y, + width, height); + try + { + javax.swing.SwingUtilities.invokeAndWait(new Runnable() + { + public void run() + { + AppJmol sview=null; + try { + sview=new AppJmol(pdbf, id, sq, alf.alignPanel, fileloc, + + rect, vid); + } + catch (OutOfMemoryError ex) + { + new OOMWarning("restoring structure view for PDB id "+id,(OutOfMemoryError) ex.getCause()); + if (sview!=null && sview.isVisible()) + { + sview.closeViewer(); + sview.setVisible(false); + sview.dispose(); + } + } + } + }); + } catch (InvocationTargetException ex) + { + warn("Unexpected error when opening Jmol view.",ex); + + } catch (InterruptedException e) + { + // e.printStackTrace(); + } + } + + } + else + // if (comp != null) + { + // NOTE: if the jalview project is part of a shared session then + // view synchronization should/could be done here. + + // add mapping for sequences in this view to an already open Jmol + // instance + for (String id : oldFiles.keySet()) + { + // add this and any other pdb files that should be present in the + // viewer + Object[] filedat = oldFiles.get(id); + String pdbFile = (String) filedat[0]; + SequenceI[] seq = (SequenceI[]) ((Vector) filedat[2]) + .toArray(new SequenceI[0]); + StructureSelectionManager.getStructureSelectionManager() + .setMapping(seq, null, pdbFile, + jalview.io.AppletFormatAdapter.FILE); + ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq); + } + } + } + } + } + // and finally return. + return af; + } + + AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs, + Alignment al, boolean hideConsensus, boolean hideQuality, + boolean hideConservation, JalviewModelSequence jms, + Viewport view, String uniqueSeqSetId, String viewId) + { + AlignFrame af = null; + af = new AlignFrame(al, view.getWidth(), view.getHeight(), + uniqueSeqSetId, viewId); af.setFileName(file, "Jalview"); @@ -1799,12 +2771,6 @@ public class Jalview2XML new java.awt.Color(JSEQ[i].getColour())); } - //If we just load in the same jar file again, the sequenceSetId - //will be the same, and we end up with multiple references - //to the same sequenceSet. We must modify this id on load - //so that each load of the file gives a unique id - String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; - af.viewport.gatherViewsHere = view.getGatheredViews(); if (view.getSequenceSetId() != null) @@ -1815,7 +2781,7 @@ public class Jalview2XML af.viewport.sequenceSetID = uniqueSeqSetId; if (av != null) { - + // propagate shared settings to this new view af.viewport.historyList = av.historyList; af.viewport.redoList = av.redoList; } @@ -1823,9 +2789,11 @@ public class Jalview2XML { viewportsAdded.put(uniqueSeqSetId, af.viewport); } - + // TODO: check if this method can be called repeatedly without + // side-effects if alignpanel already registered. PaintRefresher.Register(af.alignPanel, uniqueSeqSetId); } + // apply Hidden regions to view. if (hiddenSeqs != null) { for (int s = 0; s < JSEQ.length; s++) @@ -1834,8 +2802,8 @@ public class Jalview2XML for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++) { - hidden.addSequence(al - .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false); + hidden.addSequence( + al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false); } af.viewport.hideRepSequences(al.getSequenceAt(s), hidden); } @@ -1851,7 +2819,7 @@ public class Jalview2XML af.viewport.hideSequence(hseqs); } - + // set visibility of annotation in view if ((hideConsensus || hideQuality || hideConservation) && al.getAlignmentAnnotation() != null) { @@ -1872,14 +2840,14 @@ public class Jalview2XML } af.alignPanel.adjustAnnotationHeight(); } - + // recover view properties and display parameters if (view.getViewName() != null) { af.viewport.viewName = view.getViewName(); af.setInitialTabVisible(); } - af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view - .getHeight()); + af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), + view.getHeight()); af.viewport.setShowAnnotation(view.getShowAnnotation()); af.viewport.setAbovePIDThreshold(view.getPidSelected()); @@ -1905,12 +2873,13 @@ public class Jalview2XML af.viewport.textColour = new java.awt.Color(view.getTextCol1()); af.viewport.textColour2 = new java.awt.Color(view.getTextCol2()); af.viewport.thresholdTextColour = view.getTextColThreshold(); - + af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view + .isShowUnconserved() : false); af.viewport.setStartRes(view.getStartRes()); af.viewport.setStartSeq(view.getStartSeq()); ColourSchemeI cs = null; - + // apply colourschemes if (view.getBgColour() != null) { if (view.getBgColour().startsWith("ucs")) @@ -1919,87 +2888,92 @@ public class Jalview2XML } else if (view.getBgColour().startsWith("Annotation")) { - //int find annotation - for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++) + // int find annotation + if (af.viewport.alignment.getAlignmentAnnotation() != null) { - if (af.viewport.alignment.getAlignmentAnnotation()[i].label - .equals(view.getAnnotationColours().getAnnotation())) + for (int i = 0; i < af.viewport.alignment + .getAlignmentAnnotation().length; i++) { - if (af.viewport.alignment.getAlignmentAnnotation()[i] - .getThreshold() == null) + if (af.viewport.alignment.getAlignmentAnnotation()[i].label + .equals(view.getAnnotationColours().getAnnotation())) { - af.viewport.alignment.getAlignmentAnnotation()[i] - .setThreshold(new jalview.datamodel.GraphLine(view - .getAnnotationColours().getThreshold(), - "Threshold", java.awt.Color.black) - - ); - } + if (af.viewport.alignment.getAlignmentAnnotation()[i] + .getThreshold() == null) + { + af.viewport.alignment.getAlignmentAnnotation()[i] + .setThreshold(new jalview.datamodel.GraphLine(view + .getAnnotationColours().getThreshold(), + "Threshold", java.awt.Color.black) - if (view.getAnnotationColours().getColourScheme() - .equals("None")) - { - cs = new AnnotationColourGradient(af.viewport.alignment - .getAlignmentAnnotation()[i], new java.awt.Color(view - .getAnnotationColours().getMinColour()), - new java.awt.Color(view.getAnnotationColours() - .getMaxColour()), view.getAnnotationColours() - .getAboveThreshold()); - } - else if (view.getAnnotationColours().getColourScheme() - .startsWith("ucs")) - { - cs = new AnnotationColourGradient(af.viewport.alignment - .getAlignmentAnnotation()[i], GetUserColourScheme( - jms, view.getAnnotationColours().getColourScheme()), - view.getAnnotationColours().getAboveThreshold()); - } - else - { - cs = new AnnotationColourGradient(af.viewport.alignment - .getAlignmentAnnotation()[i], ColourSchemeProperty - .getColour(al, view.getAnnotationColours() - .getColourScheme()), view - .getAnnotationColours().getAboveThreshold()); - } + ); + } - // Also use these settings for all the groups - if (al.getGroups() != null) - { - for (int g = 0; g < al.getGroups().size(); g++) + if (view.getAnnotationColours().getColourScheme() + .equals("None")) + { + cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + new java.awt.Color(view.getAnnotationColours() + .getMinColour()), new java.awt.Color(view + .getAnnotationColours().getMaxColour()), + view.getAnnotationColours().getAboveThreshold()); + } + else if (view.getAnnotationColours().getColourScheme() + .startsWith("ucs")) + { + cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + GetUserColourScheme(jms, view + .getAnnotationColours().getColourScheme()), + view.getAnnotationColours().getAboveThreshold()); + } + else { - jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al - .getGroups().elementAt(g); + cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + ColourSchemeProperty.getColour(al, view + .getAnnotationColours().getColourScheme()), + view.getAnnotationColours().getAboveThreshold()); + } - if (sg.cs == null) + // Also use these settings for all the groups + if (al.getGroups() != null) + { + for (int g = 0; g < al.getGroups().size(); g++) { - continue; - } + jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al + .getGroups().elementAt(g); - /* if (view.getAnnotationColours().getColourScheme().equals("None")) - { - sg.cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], - new java.awt.Color(view.getAnnotationColours(). - getMinColour()), - new java.awt.Color(view.getAnnotationColours(). - getMaxColour()), - view.getAnnotationColours().getAboveThreshold()); - } - else*/ - { - sg.cs = new AnnotationColourGradient( - af.viewport.alignment.getAlignmentAnnotation()[i], - sg.cs, view.getAnnotationColours() - .getAboveThreshold()); - } + if (sg.cs == null) + { + continue; + } + + /* + * if + * (view.getAnnotationColours().getColourScheme().equals("None" + * )) { sg.cs = new AnnotationColourGradient( + * af.viewport.alignment.getAlignmentAnnotation()[i], new + * java.awt.Color(view.getAnnotationColours(). + * getMinColour()), new + * java.awt.Color(view.getAnnotationColours(). + * getMaxColour()), + * view.getAnnotationColours().getAboveThreshold()); } else + */ + { + sg.cs = new AnnotationColourGradient( + af.viewport.alignment.getAlignmentAnnotation()[i], + sg.cs, view.getAnnotationColours() + .getAboveThreshold()); + } + } } + + break; } - break; } - } } else @@ -2030,7 +3004,66 @@ public class Jalview2XML { af.viewport.showSequenceFeatures = true; } + if (view.hasCentreColumnLabels()) + { + af.viewport.setCentreColumnLabels(view.getCentreColumnLabels()); + } + if (view.hasIgnoreGapsinConsensus()) + { + af.viewport.ignoreGapsInConsensusCalculation = view + .getIgnoreGapsinConsensus(); + } + if (view.hasFollowHighlight()) + { + af.viewport.followHighlight = view.getFollowHighlight(); + } + if (view.hasFollowSelection()) + { + af.viewport.followSelection = view.getFollowSelection(); + } + if (view.hasShowConsensusHistogram()) + { + af.viewport.setShowConsensusHistogram(view + .getShowConsensusHistogram()); + } + else + { + af.viewport.setShowConsensusHistogram(true); + } + if (view.hasShowSequenceLogo()) + { + af.viewport.showSequenceLogo = view.getShowSequenceLogo(); + } + else + { + af.viewport.showSequenceLogo = false; + } + if (view.hasShowDbRefTooltip()) + { + af.viewport.setShowDbRefs(view.getShowDbRefTooltip()); + } + if (view.hasShowNPfeatureTooltip()) + { + af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip()); + } + if (view.hasShowGroupConsensus()) + { + af.viewport.setShowGroupConsensus(view.getShowGroupConsensus()); + } + else + { + af.viewport.setShowGroupConsensus(false); + } + if (view.hasShowGroupConservation()) + { + af.viewport.setShowGroupConservation(view.getShowGroupConservation()); + } + else + { + af.viewport.setShowGroupConservation(false); + } + // recover featre settings if (jms.getFeatureSettings() != null) { af.viewport.featuresDisplayed = new Hashtable(); @@ -2039,9 +3072,38 @@ public class Jalview2XML for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); - - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( - setting.getType(), new java.awt.Color(setting.getColour())); + if (setting.hasMincolour()) + { + GraduatedColor gc = setting.hasMin() ? new GraduatedColor( + new java.awt.Color(setting.getMincolour()), + new java.awt.Color(setting.getColour()), + setting.getMin(), setting.getMax()) : new GraduatedColor( + new java.awt.Color(setting.getMincolour()), + new java.awt.Color(setting.getColour()), 0, 1); + if (setting.hasThreshold()) + { + gc.setThresh(setting.getThreshold()); + gc.setThreshType(setting.getThreshstate()); + } + gc.setAutoScaled(true); // default + if (setting.hasAutoScale()) + { + gc.setAutoScaled(setting.getAutoScale()); + } + if (setting.hasColourByLabel()) + { + gc.setColourByLabel(setting.getColourByLabel()); + } + // and put in the feature colour table. + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( + setting.getType(), gc); + } + else + { + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( + setting.getType(), + new java.awt.Color(setting.getColour())); + } renderOrder[fs] = setting.getType(); if (setting.hasOrder()) af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( @@ -2071,154 +3133,73 @@ public class Jalview2XML for (int c = 0; c < view.getHiddenColumnsCount(); c++) { af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view - .getHiddenColumns(c).getEnd() //+1 + .getHiddenColumns(c).getEnd() // +1 ); } } af.setMenusFromViewport(af.viewport); + // TODO: we don't need to do this if the viewport is aready visible. + Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), + view.getHeight()); + af.alignPanel.updateAnnotation(false); // recompute any autoannotation + return af; + } - Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view - .getHeight()); - - //LOAD TREES - /////////////////////////////////////// - if (loadTreesAndStructures && jms.getTreeCount() > 0) - { - try - { - for (int t = 0; t < jms.getTreeCount(); t++) - { - - Tree tree = jms.getTree(t); - - TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree - .getNewick()), tree.getTitle(), tree.getWidth(), tree - .getHeight(), tree.getXpos(), tree.getYpos()); - - tp.fitToWindow.setState(tree.getFitToWindow()); - tp.fitToWindow_actionPerformed(null); - - if (tree.getFontName() != null) - { - tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree - .getFontStyle(), tree.getFontSize())); - } - else - { - tp.setTreeFont(new java.awt.Font(view.getFontName(), view - .getFontStyle(), tree.getFontSize())); - } - - tp.showPlaceholders(tree.getMarkUnlinked()); - tp.showBootstrap(tree.getShowBootstrap()); - tp.showDistances(tree.getShowDistances()); - - tp.treeCanvas.threshold = tree.getThreshold(); + Hashtable skipList = null; - if (tree.getCurrentTree()) - { - af.viewport.setCurrentTree(tp.getTree()); - } - } + /** + * TODO remove this method + * + * @param view + * @return AlignFrame bound to sequenceSetId from view, if one exists. private + * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) { + * throw new Error("Implementation Error. No skipList defined for this + * Jalview2XML instance."); } return (AlignFrame) + * skipList.get(view.getSequenceSetId()); } + */ - } catch (Exception ex) + /** + * Check if the Jalview view contained in object should be skipped or not. + * + * @param object + * @return true if view's sequenceSetId is a key in skipList + */ + private boolean skipViewport(JalviewModel object) + { + if (skipList == null) + { + return false; + } + String id; + if (skipList.containsKey(id = object.getJalviewModelSequence() + .getViewport()[0].getSequenceSetId())) + { + if (Cache.log != null && Cache.log.isDebugEnabled()) { - ex.printStackTrace(); + Cache.log.debug("Skipping seuqence set id " + id); } + return true; } + return false; + } - ////LOAD STRUCTURES - if (loadTreesAndStructures) + public void AddToSkipList(AlignFrame af) + { + if (skipList == null) { - for (int i = 0; i < JSEQ.length; i++) - { - if (JSEQ[i].getPdbidsCount() > 0) - { - Pdbids[] ids = JSEQ[i].getPdbids(); - for (int p = 0; p < ids.length; p++) - { - for (int s = 0; s < ids[p].getStructureStateCount(); s++) - { - jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry(); - - jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId())); - jpdb.setId(ids[p].getId()); - - int x = ids[p].getStructureState(s).getXpos(); - int y = ids[p].getStructureState(s).getYpos(); - int width = ids[p].getStructureState(s).getWidth(); - int height = ids[p].getStructureState(s).getHeight(); - - java.awt.Component comp = null; - - JInternalFrame[] frames = null; - do { - try { - frames = Desktop.desktop.getAllFrames(); - } - catch (ArrayIndexOutOfBoundsException e) - { - // occasional No such child exceptions are thrown here... - frames = null; - try { - Thread.sleep(10); - } catch (Exception f) {}; - } - } while (frames==null); - for (int f = 0; f < frames.length; f++) - { - if (frames[f] instanceof AppJmol) - { - if (frames[f].getX() == x && frames[f].getY() == y - && frames[f].getHeight() == height - && frames[f].getWidth() == width) - { - comp = frames[f]; - break; - } - } - } - - Desktop.desktop.getComponentAt(x, y); - - String pdbFile = loadPDBFile(file, ids[p].getId()); - - jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[] - { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId() - + "") }; - - if (comp == null) - { - String state = ids[p].getStructureState(s).getContent(); - - StringBuffer newFileLoc = new StringBuffer(state.substring( - 0, state.indexOf("\"", state.indexOf("load")) + 1)); - - newFileLoc.append(jpdb.getFile()); - newFileLoc.append(state.substring(state.indexOf("\"", state - .indexOf("load \"") + 6))); - - new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel, - newFileLoc.toString(), new java.awt.Rectangle(x, y, - width, height)); - - } - else if (comp != null) - { - StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, null, pdbFile, - jalview.io.AppletFormatAdapter.FILE); - - ((AppJmol) comp).addSequence(seq); - } - } - } - } - } + skipList = new Hashtable(); } + skipList.put(af.getViewport().getSequenceSetId(), af); + } - return af; + public void clearSkipList() + { + if (skipList != null) + { + skipList.clear(); + skipList = null; + } } private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al) @@ -2241,6 +3222,8 @@ public class Jalview2XML SequenceI[] dsseqs = new SequenceI[dseqs.size()]; dseqs.copyInto(dsseqs); ds = new jalview.datamodel.Alignment(dsseqs); + debug("Created new dataset " + vamsasSet.getDatasetId() + + " for alignment " + System.identityHashCode(al)); addDatasetRef(vamsasSet.getDatasetId(), ds); } // set the dataset for the newly imported alignment. @@ -2249,25 +3232,31 @@ public class Jalview2XML al.setDataset(ds); } } - /** * - * @param vamsasSeq sequence definition to create/merge dataset sequence for - * @param ds dataset alignment - * @param dseqs vector to add new dataset sequence to + * @param vamsasSeq + * sequence definition to create/merge dataset sequence for + * @param ds + * dataset alignment + * @param dseqs + * vector to add new dataset sequence to */ - private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs) + private void ensureJalviewDatasetSequence(Sequence vamsasSeq, + AlignmentI ds, Vector dseqs) { - jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId()); + // JBP TODO: Check this is called for AlCodonFrames to support recovery of + // xRef Codon Maps + jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds + .get(vamsasSeq.getId()); jalview.datamodel.SequenceI dsq = null; - if (sq!=null && sq.getDatasetSequence()!=null) + if (sq != null && sq.getDatasetSequence() != null) { dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence(); } - + String sqid = vamsasSeq.getDsseqid(); - if (dsq==null) + if (dsq == null) { // need to create or add a new dataset sequence reference to this sequence if (sqid != null) @@ -2288,7 +3277,7 @@ public class Jalview2XML seqRefIds.put(sqid, dsq); if (ds == null) { - if (dseqs!=null) + if (dseqs != null) { dseqs.addElement(dsq); } @@ -2297,54 +3286,53 @@ public class Jalview2XML { ds.addSequence(dsq); } - } else { - if (sq!=dsq) - { // make this dataset sequence sq's dataset sequence + } + else + { + if (sq != dsq) + { // make this dataset sequence sq's dataset sequence sq.setDatasetSequence(dsq); } } } // TODO: refactor this as a merge dataset sequence function - // now check that sq (the dataset sequence) sequence really is the union of all references to it - //boolean pre = sq.getStart() < dsq.getStart(); - //boolean post = sq.getEnd() > dsq.getEnd(); - //if (pre || post) - if (sq!=dsq) + // now check that sq (the dataset sequence) sequence really is the union of + // all references to it + // boolean pre = sq.getStart() < dsq.getStart(); + // boolean post = sq.getEnd() > dsq.getEnd(); + // if (pre || post) + if (sq != dsq) { StringBuffer sb = new StringBuffer(); String newres = jalview.analysis.AlignSeq.extractGaps( jalview.util.Comparison.GapChars, sq.getSequenceAsString()); - if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length()>dsq.getLength()) + if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) + && newres.length() > dsq.getLength()) { // Update with the longer sequence. synchronized (dsq) { - /*if (pre) - { - sb.insert(0, newres - .substring(0, dsq.getStart() - sq.getStart())); - dsq.setStart(sq.getStart()); - } - if (post) - { - sb.append(newres.substring(newres.length() - sq.getEnd() - - dsq.getEnd())); - dsq.setEnd(sq.getEnd()); - } - */ - dsq.setSequence(sb.toString()); + /* + * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() - + * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) { + * sb.append(newres.substring(newres.length() - sq.getEnd() - + * dsq.getEnd())); dsq.setEnd(sq.getEnd()); } + */ + dsq.setSequence(sb.toString()); } - //TODO: merges will never happen if we 'know' we have the real dataset sequence - this should be detected when id==dssid - System.err - .println("DEBUG Notice: Merged dataset sequence"); // (" - // + (pre ? "prepended" : "") + " " - //+ (post ? "appended" : "")); + // TODO: merges will never happen if we 'know' we have the real dataset + // sequence - this should be detected when id==dssid + System.err.println("DEBUG Notice: Merged dataset sequence"); // (" + // + (pre ? "prepended" : "") + " " + // + (post ? "appended" : "")); } } } java.util.Hashtable datasetIds = null; + java.util.IdentityHashMap dataset2Ids = null; + private Alignment getDatasetFor(String datasetId) { if (datasetIds == null) @@ -2368,6 +3356,39 @@ public class Jalview2XML datasetIds.put(datasetId, dataset); } + /** + * make a new dataset ID for this jalview dataset alignment + * + * @param dataset + * @return + */ + private String getDatasetIdRef(jalview.datamodel.Alignment dataset) + { + if (dataset.getDataset() != null) + { + warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment..."); + } + String datasetId = makeHashCode(dataset, null); + if (datasetId == null) + { + // make a new datasetId and record it + if (dataset2Ids == null) + { + dataset2Ids = new IdentityHashMap(); + } + else + { + datasetId = (String) dataset2Ids.get(dataset); + } + if (datasetId == null) + { + datasetId = "ds" + dataset2Ids.size() + 1; + dataset2Ids.put(dataset, datasetId); + } + } + return datasetId; + } + private void addDBRefs(SequenceI datasetSequence, Sequence sequence) { for (int d = 0; d < sequence.getDBRefCount(); d++) @@ -2411,17 +3432,18 @@ public class Jalview2XML MappingChoice mc = m.getMappingChoice(); if (mc.getDseqFor() != null) { - if (seqRefIds.containsKey(mc.getDseqFor())) + String dsfor = "" + mc.getDseqFor(); + if (seqRefIds.containsKey(dsfor)) { /** * recover from hash */ - jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor())); + jmap.setTo((SequenceI) seqRefIds.get(dsfor)); } else { frefedSequence.add(new Object[] - { mc.getDseqFor(), jmap }); + { dsfor, jmap }); } } else @@ -2430,35 +3452,41 @@ public class Jalview2XML * local sequence definition */ Sequence ms = mc.getSequence(); - jalview.datamodel.Sequence djs=null; + jalview.datamodel.Sequence djs = null; String sqid = ms.getDsseqid(); - if (sqid!=null && sqid.length()>0) + if (sqid != null && sqid.length() > 0) { /* * recover dataset sequence */ djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid); - } else { - System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference"); - sqid = ((Object)ms).toString(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen) } - - if (djs==null) { + else + { + System.err + .println("Warning - making up dataset sequence id for DbRef sequence map reference"); + sqid = ((Object) ms).toString(); // make up a new hascode for + // undefined dataset sequence hash + // (unlikely to happen) + } + + if (djs == null) + { /** * make a new dataset sequence and add it to refIds hash */ - djs = new jalview.datamodel.Sequence(ms - .getName(), ms.getSequence()); + djs = new jalview.datamodel.Sequence(ms.getName(), + ms.getSequence()); djs.setStart(jmap.getMap().getToLowest()); djs.setEnd(jmap.getMap().getToHighest()); djs.setVamsasId(uniqueSetSuffix + sqid); jmap.setTo(djs); seqRefIds.put(sqid, djs); - + } jalview.bin.Cache.log.debug("about to recurse on addDBRefs."); addDBRefs(djs, ms); - + } } return (jmap); @@ -2468,8 +3496,9 @@ public class Jalview2XML public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs) { - jalview.schemabinding.version2.JalviewModel jm = - SaveState(ap, null, null); + initSeqRefs(); + jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null, + null); if (!keepSeqRefs) { @@ -2479,38 +3508,216 @@ public class Jalview2XML else { uniqueSetSuffix = ""; + jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't + // overwrite the + // view we just + // copied + } + if (this.frefedSequence == null) + { + frefedSequence = new Vector(); } viewportsAdded = new Hashtable(); - AlignFrame af = LoadFromObject(jm, null, false); + AlignFrame af = LoadFromObject(jm, null, false, null); af.alignPanels.clear(); af.closeMenuItem_actionPerformed(true); - /* if(ap.av.alignment.getAlignmentAnnotation()!=null) - { - for(int i=0; i