X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=b899ae91286069efd7693efbf31071f4f44d2cd1;hb=6403068c0c328cfb63af451f7fa1bd568fa0fdd3;hp=22977a99d893fbe296487a5d3c44056a8ee6fc7c;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java old mode 100755 new mode 100644 index 22977a9..b899ae9 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,5 +1,5 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) + * 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. @@ -19,8 +19,10 @@ 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.*; @@ -30,6 +32,7 @@ import org.exolab.castor.xml.*; import uk.ac.vamsas.objects.utils.MapList; import jalview.bin.Cache; import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.SequenceI; import jalview.schemabinding.version2.*; @@ -45,7 +48,7 @@ import jalview.util.jarInputStreamProvider; * will be :) * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.134 $ */ public class Jalview2XML { @@ -412,7 +415,7 @@ public class Jalview2XML JarOutputStream jout) { initSeqRefs(); - + Vector jmolViewIds = new Vector(); // Vector userColours = new Vector(); AlignViewport av = ap.av; @@ -579,32 +582,62 @@ public class Jalview2XML if (frames[f] instanceof AppJmol) { jmol = (AppJmol) frames[f]; - if (!jmol.pdbentry.getId().equals(entry.getId()) - && !(entry.getId().length() > 4 && entry.getId() - .toLowerCase().startsWith( - jmol.pdbentry.getId().toLowerCase()))) - continue; - matchedFile = jmol.pdbentry.getFile(); // record the file so we - // can get at it if the ID - // match is ambiguous (e.g. - // 1QIP==1qipA) - 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()); - 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) { - pdb.addStructureState(state); + 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++) + { + 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()); + state.setAlignwithAlignPanel(jmol.isUsedforaligment(ap)); + state.setColourwithAlignPanel(jmol + .isUsedforcolourby(ap)); + state.setColourByJmol(jmol.isColouredByJmol()); + 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); + } } } } @@ -803,18 +836,12 @@ public class Jalview2XML } 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; - } + + // store all visualization attributes for annotation + an.setGraphHeight(aa[i].graphHeight); + an.setCentreColLabels(aa[i].centreColLabels); + an.setScaleColLabels(aa[i].scaleColLabel); + an.setShowAllColLabels(aa[i].showAllColLabels); if (aa[i].graph > 0) { @@ -836,6 +863,13 @@ public class Jalview2XML } an.setLabel(aa[i].label); + + 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); + } if (aa[i].hasScore()) { an.setScore(aa[i].getScore()); @@ -863,9 +897,8 @@ 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) @@ -874,6 +907,13 @@ public class Jalview2XML } an.addAnnotationElement(ae); + if (aa[i].autoCalculated) + { + // only write one non-null entry into the annotation row - + // sufficient to get the visualization attributes necessary to + // display data + continue; + } } } else @@ -946,7 +986,7 @@ public class Jalview2XML groups[i].setTextCol1(sg.textColour.getRGB()); groups[i].setTextCol2(sg.textColour2.getRGB()); groups[i].setTextColThreshold(sg.thresholdTextColour); - groups[i].setShowUnconserved(sg.getShowunconserved()); + groups[i].setShowUnconserved(sg.getShowNonconserved()); groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram()); groups[i].setShowSequenceLogo(sg.isShowSequenceLogo()); @@ -964,8 +1004,8 @@ public class Jalview2XML // /////////SAVE VIEWPORT Viewport view = new Viewport(); view.setTitle(ap.alignFrame.getTitle()); - view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), av - .getSequenceSetId())); + view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), + av.getSequenceSetId())); view.setId(av.getViewId()); view.setViewName(av.viewName); view.setGatheredViews(av.gatherViewsHere); @@ -1079,40 +1119,43 @@ public class Jalview2XML Vector settingsAdded = new Vector(); Object gstyle = null; GraduatedColor gcol = null; - for (int ro = 0; ro < renderOrder.length; ro++) + if (renderOrder != null) { - gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer() - .getFeatureStyle(renderOrder[ro]); - Setting setting = new Setting(); - setting.setType(renderOrder[ro]); - 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 + for (int ro = 0; ro < renderOrder.length; ro++) { - setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() - .getColour(renderOrder[ro]).getRGB()); - } + gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer() + .getFeatureStyle(renderOrder[ro]); + Setting setting = new Setting(); + setting.setType(renderOrder[ro]); + 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])); - float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder( - renderOrder[ro]); - if (rorder > -1) - { - setting.setOrder(rorder); + setting.setDisplay(av.featuresDisplayed + .containsKey(renderOrder[ro])); + float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer() + .getOrder(renderOrder[ro]); + if (rorder > -1) + { + setting.setOrder(rorder); + } + fs.addSetting(setting); + settingsAdded.addElement(renderOrder[ro]); } - fs.addSetting(setting); - settingsAdded.addElement(renderOrder[ro]); } // Make sure we save none displayed feature settings @@ -1152,10 +1195,8 @@ 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); } @@ -1797,6 +1838,25 @@ public class Jalview2XML return null; } + private class JvAnnotRow + { + public JvAnnotRow(int i, AlignmentAnnotation jaa) + { + order = i; + template = jaa; + } + + /** + * persisted version of annotation row from which to take vis properties + */ + public jalview.datamodel.AlignmentAnnotation template; + + /** + * original position of the annotation row in the alignment + */ + public int order; + } + /** * Load alignment frame from jalview XML DOM object * @@ -2029,11 +2089,11 @@ public class Jalview2XML // //////////////////////////////// // LOAD ANNOTATIONS - boolean hideQuality = true, hideConservation = true, hideConsensus = true; + ArrayList autoAlan = new ArrayList(); /** * store any annotations which forward reference a group's ID */ - Hashtable groupAnnotRefs = new Hashtable(); + Hashtable> groupAnnotRefs = new Hashtable>(); if (vamsasSet.getAnnotationCount() > 0) { @@ -2041,22 +2101,29 @@ 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; - continue; - } - else if (an[i].getLabel().equals("Conservation")) - { - hideConservation = false; - continue; + /** + * test if annotation is automatically calculated for this view only + */ + boolean autoForView = false; + if (an[i].getLabel().equals("Quality") + || an[i].getLabel().equals("Conservation") + || an[i].getLabel().equals("Consensus")) + { + // Kludge for pre 2.5 projects which lacked the autocalculated flag + autoForView = true; + if (!an[i].hasAutoCalculated()) + { + an[i].setAutoCalculated(true); + } } - else if (an[i].getLabel().equals("Consensus")) + if (autoForView + || (an[i].hasAutoCalculated() && an[i].isAutoCalculated())) { - hideConsensus = false; - continue; + // remove ID - we don't recover annotation from other views for + // view-specific annotation + an[i].setId(null); } + // set visiblity for other annotation in this view if (an[i].getId() != null && annotationIds.containsKey(an[i].getId())) @@ -2079,7 +2146,6 @@ public class Jalview2XML if (!an[i].getScoreOnly()) { anot = new jalview.datamodel.Annotation[al.getWidth()]; - for (int aa = 0; aa < ae.length && aa < anot.length; aa++) { if (ae[aa].getPosition() >= anot.length) @@ -2087,10 +2153,11 @@ 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 @@ -2100,16 +2167,21 @@ public class Jalview2XML // { // anot[ae[aa].getPosition()].displayCharacter = ""; // } - anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa] - .getColour()); + anot[ae[aa].getPosition()].colour = new java.awt.Color( + ae[aa].getColour()); } } jalview.datamodel.AlignmentAnnotation jaa = null; if (an[i].getGraph()) { + float llim = 0, hlim = 0; + // if (autoForView || an[i].isAutoCalculated()) { + // hlim=11f; + // } jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot, 0, 0, an[i].getGraphType()); + an[i].getDescription(), anot, llim, hlim, + an[i].getGraphType()); jaa.graphGroup = an[i].getGraphGroup(); @@ -2121,33 +2193,49 @@ public class Jalview2XML an[i].getThresholdLine().getColour()))); } - + if (autoForView || an[i].isAutoCalculated()) + { + // Hardwire the symbol display line to ensure that labels for + // histograms are displayed + jaa.hasText = true; + } } else { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), an[i].getDescription(), anot); } - // register new annotation - if (an[i].getId() != null) + if (autoForView) { - 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) + // register new annotation + if (an[i].getId() != null) { - jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()), - 1, true); - al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); + 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) + { + jaa.createSequenceMapping( + al.findName(an[i].getSequenceRef()), 1, true); + 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); + ArrayList aal = groupAnnotRefs + .get(an[i].getGroupRef()); + if (aal == null) + { + aal = new ArrayList(); + groupAnnotRefs.put(an[i].getGroupRef(), aal); + } + aal.add(jaa); } if (an[i].hasScore()) @@ -2169,9 +2257,23 @@ public class Jalview2XML // 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. + // update at end of load. + } + if (an[i].hasGraphHeight()) + { + jaa.graphHeight = an[i].getGraphHeight(); + } + if (jaa.autoCalculated) + { + autoAlan.add(new JvAnnotRow(i, jaa)); + } + else + // if (!autoForView) + { + // add autocalculated group annotation and any user created annotation + // for the view + al.addAnnotation(jaa); } - al.addAnnotation(jaa); } } @@ -2227,25 +2329,21 @@ 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.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i] + sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i] .isShowUnconserved() : false); sg.thresholdTextColour = groups[i].getTextColThreshold(); if (groups[i].hasShowConsensusHistogram()) { - sg - .setShowConsensusHistogram(groups[i] - .isShowConsensusHistogram()); + sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram()); } ; if (groups[i].hasShowSequenceLogo()) { - sg.setIncludeAllConsSymbols(groups[i].isShowSequenceLogo()); + sg.setshowSequenceLogo(groups[i].isShowSequenceLogo()); } if (groups[i].hasIgnoreGapsinConsensus()) { @@ -2254,8 +2352,8 @@ public class Jalview2XML 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); @@ -2264,11 +2362,29 @@ public class Jalview2XML if (groups[i].getId() != null && groupAnnotRefs.size() > 0) { // re-instate unique group/annotation row reference - jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs + ArrayList jaal = groupAnnotRefs .get(groups[i].getId()); - if (jaa != null) + if (jaal != null) { - jaa.groupRef = sg; + for (jalview.datamodel.AlignmentAnnotation jaa : jaal) + { + jaa.groupRef = sg; + if (jaa.autoCalculated) + { + // match up and try to set group autocalc alignment row for this + // annotation + if (jaa.label.startsWith("Consensus for ")) + { + sg.setConsensus(jaa); + } + // match up and try to set group autocalc alignment row for this + // annotation + if (jaa.label.startsWith("Conservation for ")) + { + sg.setConservationRow(jaa); + } + } + } } } al.addGroup(sg); @@ -2346,9 +2462,8 @@ public class Jalview2XML if (isnewview) { - af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus, - hideQuality, hideConservation, jms, view, uniqueSeqSetId, - viewId); + af = loadViewport(file, JSEQ, hiddenSeqs, al, jms, view, + uniqueSeqSetId, viewId, autoAlan); av = af.viewport; ap = af.alignPanel; } @@ -2366,9 +2481,10 @@ public class Jalview2XML 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()); + 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 ? @@ -2431,6 +2547,10 @@ public class Jalview2XML // //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) @@ -2455,118 +2575,329 @@ public class Jalview2XML int y = ids[p].getStructureState(s).getYpos(); int width = ids[p].getStructureState(s).getWidth(); int height = ids[p].getStructureState(s).getHeight(); - AppJmol comp = null; - JInternalFrame[] frames = null; - do + + // 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(), new boolean[] + { false, false, true } }); + // Legacy pre-2.7 conversion JAL-823 : + // do not assume any view has to be linked for colour by + // sequence + } + + // assemble String[] { pdb files }, String[] { id for each + // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, { + // seqs_file 2}, boolean[] { + // linkAlignPanel,superposeWithAlignpanel}} from hash + Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid); + ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s) + .hasAlignwithAlignPanel() ? ids[p].getStructureState( + s).getAlignwithAlignPanel() : false; + // never colour by linked panel if not specified + ((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s) + .hasColourwithAlignPanel() ? ids[p] + .getStructureState(s).getColourwithAlignPanel() + : false; + // default for pre-2.7 projects is that Jmol colouring is enabled + ((boolean[]) jmoldat[3])[2] &= ids[p].getStructureState(s) + .hasColourByJmol() ? ids[p].getStructureState(s) + .getColourByJmol() : true; + + if (((String) jmoldat[1]).length() < ids[p] + .getStructureState(s).getContent().length()) { - 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) - { - } - ; + jmoldat[1] = ids[p].getStructureState(s).getContent(); } - } 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 (ids[p].getFile() != null) { - if (frames[f] instanceof AppJmol) + Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2]) + .get(ids[p].getFile()); + if (seqstrmaps == null) { - 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]; - } + ((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 } } - // 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()); + else + { + errorMessage = ("The Jmol views in the Jalview 2 project may\nnot be correctly bound to sequences in the alignment.\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747"); + warn(errorMessage); + } + } + } + } + } + { - jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[] - { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId() - + "") }; + // 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]; + final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring = ((boolean[]) svattrib[3])[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(); - if (comp == null) + // 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 { - // create a new Jmol window - String state = ids[p].getStructureState(s).getContent(); - StringBuffer newFileLoc = null; - if (state.indexOf("load") > -1) - { - newFileLoc = new StringBuffer(state.substring(0, state - .indexOf("\"", state.indexOf("load")) + 1)); + 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]; + } + } + } - newFileLoc.append(jpdb.getFile()); - newFileLoc.append(state.substring(state.indexOf("\"", - state.indexOf("load \"") + 6))); - } - else - { - System.err - .println("Ignoring incomplete Jmol state for PDB " - + ids[p].getId()); + 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 = new StringBuffer(state); - newFileLoc.append("; load \""); - newFileLoc.append(jpdb.getFile()); - newFileLoc.append("\";"); - } + } + newFileLoc.append(";"); + } - if (newFileLoc != null) + 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")) { - new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel, - newFileLoc.toString(), new java.awt.Rectangle(x, - y, width, height), sviewid); + if (val.trim().equals("true")) + { + val = "1"; + } + else + { + val = "0"; + } + newFileLoc.replace(histbug, diff, val); } - } - else - // if (comp != null) + // 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 { - // NOTE: if the jalview project is part of a shared session then - // view synchronization should/could be done here. - - // add mapping for this sequence to the already open Jmol - // instance (if it doesn't already exist) - // These - StructureSelectionManager.getStructureSelectionManager() - .setMapping(seq, null, pdbFile, - jalview.io.AppletFormatAdapter.FILE); + javax.swing.SwingUtilities.invokeAndWait(new Runnable() + { + public void run() + { + AppJmol sview = null; + try + { + sview = new AppJmol(pdbf, id, sq, alf.alignPanel, + useinJmolsuperpos, usetoColourbyseq, + jmolColouring, 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); - ((AppJmol) comp).addSequence(seq); + } 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]); + ((AppJmol) comp).jmb.ssm.setMapping(seq, null, pdbFile, + jalview.io.AppletFormatAdapter.FILE); + ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq); + } + // and add the AlignmentPanel's reference to the Jmol view + ((AppJmol) comp).addAlignmentPanel(ap); + if (useinJmolsuperpos) + { + ((AppJmol) comp).useAlignmentPanelForSuperposition(ap); + } + else + { + ((AppJmol) comp).excludeAlignmentPanelForSuperposition(ap); + } + if (usetoColourbyseq) + { + ((AppJmol) comp).useAlignmentPanelForColourbyseq(ap, + !jmolColouring); + } + else + { + ((AppJmol) comp).excludeAlignmentPanelForColourbyseq(ap); + } } } } } - + // 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) + Alignment al, JalviewModelSequence jms, Viewport view, + String uniqueSeqSetId, String viewId, + ArrayList autoAlan) { AlignFrame af = null; af = new AlignFrame(al, view.getWidth(), view.getHeight(), @@ -2611,8 +2942,8 @@ 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); } @@ -2628,35 +2959,14 @@ public class Jalview2XML af.viewport.hideSequence(hseqs); } - // set visibility of annotation in view - if ((hideConsensus || hideQuality || hideConservation) - && al.getAlignmentAnnotation() != null) - { - int hSize = al.getAlignmentAnnotation().length; - for (int h = 0; h < hSize; h++) - { - if ((hideConsensus && al.getAlignmentAnnotation()[h].label - .equals("Consensus")) - || (hideQuality && al.getAlignmentAnnotation()[h].label - .equals("Quality")) - || (hideConservation && al.getAlignmentAnnotation()[h].label - .equals("Conservation"))) - { - al.deleteAnnotation(al.getAlignmentAnnotation()[h]); - hSize--; - h--; - } - } - 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()); @@ -2698,85 +3008,91 @@ public class Jalview2XML else if (view.getBgColour().startsWith("Annotation")) { // int find annotation - for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++) + 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")) { - jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al - .getGroups().elementAt(g); + 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()); + } - 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 @@ -2835,11 +3151,11 @@ public class Jalview2XML } if (view.hasShowSequenceLogo()) { - af.viewport.setShowSequenceLogo(view.getShowSequenceLogo()); + af.viewport.showSequenceLogo = view.getShowSequenceLogo(); } else { - af.viewport.setShowSequenceLogo(false); + af.viewport.showSequenceLogo = false; } if (view.hasShowDbRefTooltip()) { @@ -2942,13 +3258,88 @@ public class Jalview2XML } af.setMenusFromViewport(af.viewport); - af.alignPanel.updateAnnotation(false); // recompute any autoannotation // TODO: we don't need to do this if the viewport is aready visible. - Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view - .getHeight()); + Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), + view.getHeight()); + af.alignPanel.updateAnnotation(false); // recompute any autoannotation + reorderAutoannotation(af, al, autoAlan); return af; } + private void reorderAutoannotation(AlignFrame af, Alignment al, + ArrayList autoAlan) + { + // copy over visualization settings for autocalculated annotation in the + // view + if (al.getAlignmentAnnotation() != null) + { + /** + * Kludge for magic autoannotation names (see JAL-811) + */ + String[] magicNames = new String[] + { "Consensus", "Quality", "Conservation" }; + JvAnnotRow nullAnnot = new JvAnnotRow(-1, null); + Hashtable visan = new Hashtable(); + for (String nm : magicNames) + { + visan.put(nm, nullAnnot); + } + for (JvAnnotRow auan : autoAlan) + { + visan.put(auan.template.label, auan); + } + int hSize = al.getAlignmentAnnotation().length; + ArrayList reorder = new ArrayList(); + for (int h = 0; h < hSize; h++) + { + jalview.datamodel.AlignmentAnnotation jalan = al + .getAlignmentAnnotation()[h]; + if (jalan.autoCalculated) + { + JvAnnotRow valan = visan.get(jalan.label); + if (valan != null) + { + // delete the auto calculated row from the alignment + al.deleteAnnotation(al.getAlignmentAnnotation()[h], false); + hSize--; + h--; + if (valan != nullAnnot) + { + if (jalan != valan.template) + { + // newly created autoannotation row instance + // so keep a reference to the visible annotation row + // and copy over all relevant attributes + if (valan.template.graphHeight >= 0) + + { + jalan.graphHeight = valan.template.graphHeight; + } + jalan.visible = valan.template.visible; + } + reorder.add(new JvAnnotRow(valan.order, jalan)); + } + } + } + } + int s = 0, srt[] = new int[reorder.size()]; + JvAnnotRow[] rws = new JvAnnotRow[reorder.size()]; + for (JvAnnotRow jvar : reorder) + { + rws[s] = jvar; + srt[s++] = jvar.order; + } + reorder.clear(); + jalview.util.QuickSort.sort(srt, rws); + // and re-insert the annotation at its correct position + for (JvAnnotRow jvar : rws) + { + al.addAnnotation(jvar.template, jvar.order); + } + af.alignPanel.adjustAnnotationHeight(); + } + } + Hashtable skipList = null; /** @@ -3278,8 +3669,8 @@ public class Jalview2XML /** * 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);