X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=358cca6d0b8dcf536dc89b67aee6a796ba5fd3dd;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=5fb8e6260b5fbe827479b9af5b898b6e3b207a48;hpb=f47cbc54ccc008c3e4eefd4b0e514036b7ace708;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 5fb8e62..358cca6 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import jalview.analysis.Conservation; +import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; @@ -27,14 +29,19 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.GraphLine; import jalview.datamodel.PDBEntry; import jalview.datamodel.RnaViewerModel; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.datamodel.StructureViewerModel; import jalview.datamodel.StructureViewerModel.StructureData; import jalview.ext.varna.RnaModel; import jalview.gui.StructureViewer.ViewerType; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; +import jalview.renderer.ResidueShaderI; import jalview.schemabinding.version2.AlcodMap; import jalview.schemabinding.version2.AlcodonFrame; import jalview.schemabinding.version2.Annotation; @@ -71,8 +78,7 @@ import jalview.schemabinding.version2.Viewport; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.GraduatedColor; -import jalview.schemes.ResidueColourScheme; +import jalview.schemes.FeatureColour; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; import jalview.structure.StructureSelectionManager; @@ -82,6 +88,7 @@ import jalview.util.Platform; import jalview.util.StringUtils; import jalview.util.jarInputStreamProvider; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import jalview.ws.jws2.Jws2Discoverer; @@ -107,6 +114,7 @@ import java.lang.reflect.InvocationTargetException; import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; +import java.util.Arrays; import java.util.Enumeration; import java.util.HashMap; import java.util.HashSet; @@ -124,7 +132,6 @@ import java.util.jar.JarInputStream; import java.util.jar.JarOutputStream; import javax.swing.JInternalFrame; -import javax.swing.JOptionPane; import javax.swing.SwingUtilities; import org.exolab.castor.xml.Marshaller; @@ -164,7 +171,9 @@ public class Jalview2XML */ Map seqRefIds = null; - Vector frefedSequence = null; + Map incompleteSeqs = null; + + List frefedSequence = null; boolean raiseGUI = true; // whether errors are raised in dialog boxes or not @@ -219,6 +228,10 @@ public class Jalview2XML { seqsToIds.clear(); } + if (incompleteSeqs != null) + { + incompleteSeqs.clear(); + } // seqRefIds = null; // seqsToIds = null; } @@ -241,6 +254,14 @@ public class Jalview2XML { seqRefIds = new HashMap(); } + if (incompleteSeqs == null) + { + incompleteSeqs = new HashMap(); + } + if (frefedSequence == null) + { + frefedSequence = new ArrayList(); + } } public Jalview2XML() @@ -252,78 +273,185 @@ public class Jalview2XML this.raiseGUI = raiseGUI; } + /** + * base class for resolving forward references to sequences by their ID + * + * @author jprocter + * + */ + abstract class SeqFref + { + String sref; + + String type; + + public SeqFref(String _sref, String type) + { + sref = _sref; + this.type = type; + } + + public String getSref() + { + return sref; + } + + public SequenceI getSrefSeq() + { + return seqRefIds.get(sref); + } + + public boolean isResolvable() + { + return seqRefIds.get(sref) != null; + } + + public SequenceI getSrefDatasetSeq() + { + SequenceI sq = seqRefIds.get(sref); + if (sq != null) + { + while (sq.getDatasetSequence() != null) + { + sq = sq.getDatasetSequence(); + } + } + return sq; + } + + /** + * @return true if the forward reference was fully resolved + */ + abstract boolean resolve(); + + @Override + public String toString() + { + return type + " reference to " + sref; + } + } + + /** + * create forward reference for a mapping + * + * @param sref + * @param _jmap + * @return + */ + public SeqFref newMappingRef(final String sref, + final jalview.datamodel.Mapping _jmap) + { + SeqFref fref = new SeqFref(sref, "Mapping") + { + public jalview.datamodel.Mapping jmap = _jmap; + + @Override + boolean resolve() + { + SequenceI seq = getSrefDatasetSeq(); + if (seq == null) + { + return false; + } + jmap.setTo(seq); + return true; + } + }; + return fref; + } + + public SeqFref newAlcodMapRef(final String sref, + final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap) + { + + SeqFref fref = new SeqFref(sref, "Codon Frame") + { + AlignedCodonFrame cf = _cf; + + public jalview.datamodel.Mapping mp = _jmap; + + @Override + public boolean isResolvable() + { + return super.isResolvable() && mp.getTo() != null; + }; + + @Override + boolean resolve() + { + SequenceI seq = getSrefDatasetSeq(); + if (seq == null) + { + return false; + } + cf.addMap(seq, mp.getTo(), mp.getMap()); + return true; + } + }; + return fref; + } + public void resolveFrefedSequences() { - if (frefedSequence.size() > 0) + Iterator nextFref = frefedSequence.iterator(); + int toresolve = frefedSequence.size(); + int unresolved = 0, failedtoresolve = 0; + while (nextFref.hasNext()) { - int r = 0, rSize = frefedSequence.size(); - while (r < rSize) + SeqFref ref = nextFref.next(); + if (ref.isResolvable()) { - Object[] ref = frefedSequence.elementAt(r); - if (ref != null) + try { - String sref = (String) ref[0]; - if (seqRefIds.containsKey(sref)) + if (ref.resolve()) { - if (ref[1] instanceof jalview.datamodel.Mapping) - { - SequenceI seq = seqRefIds.get(sref); - while (seq.getDatasetSequence() != null) - { - seq = seq.getDatasetSequence(); - } - ((jalview.datamodel.Mapping) ref[1]).setTo(seq); - } - else - { - if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame) - { - SequenceI seq = 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--; + nextFref.remove(); } else { - System.err - .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string " - + ref[0] - + " with objecttype " - + ref[1].getClass()); - r++; + failedtoresolve++; } + } catch (Exception x) + { + System.err + .println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence " + + ref.getSref()); + x.printStackTrace(); + failedtoresolve++; } - else + } + else + { + unresolved++; + } + } + if (unresolved > 0) + { + System.err.println("Jalview Project Import: There were " + unresolved + + " forward references left unresolved on the stack."); + } + if (failedtoresolve > 0) + { + System.err.println("SERIOUS! " + failedtoresolve + + " resolvable forward references failed to resolve."); + } + if (incompleteSeqs != null && incompleteSeqs.size() > 0) + { + System.err.println("Jalview Project Import: There are " + + incompleteSeqs.size() + + " sequences which may have incomplete metadata."); + if (incompleteSeqs.size() < 10) + { + for (SequenceI s : incompleteSeqs.values()) { - // empty reference - frefedSequence.remove(r); - rSize--; + System.err.println(s.toString()); } } + else + { + System.err + .println("Too many to report. Skipping output of incomplete sequences."); + } } } @@ -395,7 +523,20 @@ public class Jalview2XML { return; } + saveAllFrames(Arrays.asList(frames), jout); + } + /** + * core method for storing state for a set of AlignFrames. + * + * @param frames + * - frames involving all data to be exported (including containing + * splitframes) + * @param jout + * - project output stream + */ + private void saveAllFrames(List frames, JarOutputStream jout) + { Hashtable dsses = new Hashtable(); /* @@ -415,9 +556,9 @@ public class Jalview2XML List viewIds = new ArrayList(); // REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) + for (int i = frames.size() - 1; i > -1; i--) { - AlignFrame af = frames[i]; + AlignFrame af = frames.get(i); // skip ? if (skipList != null && skipList @@ -520,30 +661,20 @@ public class Jalview2XML { try { - int ap = 0; - int apSize = af.alignPanels.size(); FileOutputStream fos = new FileOutputStream(jarFile); JarOutputStream jout = new JarOutputStream(fos); - Hashtable dsses = new Hashtable(); - List viewIds = new ArrayList(); + List frames = new ArrayList(); - for (AlignmentPanel apanel : af.alignPanels) + // resolve splitframes + if (af.getViewport().getCodingComplement() != null) { - String jfileName = apSize == 1 ? fileName : fileName + ap; - ap++; - if (!jfileName.endsWith(".xml")) - { - jfileName = jfileName + ".xml"; - } - saveState(apanel, jfileName, jout, viewIds); - String dssid = getDatasetIdRef(af.getViewport().getAlignment() - .getDataset()); - if (!dsses.containsKey(dssid)) - { - dsses.put(dssid, af); - } + frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames(); + } + else + { + frames.add(af); } - writeDatasetFor(dsses, fileName, jout); + saveAllFrames(frames, jout); try { jout.flush(); @@ -626,6 +757,7 @@ public class Jalview2XML List userColours = new ArrayList(); AlignViewport av = ap.av; + ViewportRanges vpRanges = av.getRanges(); JalviewModel object = new JalviewModel(); object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); @@ -677,38 +809,42 @@ public class Jalview2XML JSeq jseq; Set calcIdSet = new HashSet(); - + // record the set of vamsas sequence XML POJO we create. + HashMap vamsasSetIds = new HashMap(); // SAVE SEQUENCES - for (int i = 0; i < rjal.getHeight(); i++) + for (final SequenceI jds : rjal.getSequences()) { - final SequenceI jds = rjal.getSequenceAt(i); final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds : jds.getDatasetSequence(); String id = seqHash(jds); - - 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)); - } - else - { - vamsasSeq = createVamsasSequence(id, jds); - vamsasSet.addSequence(vamsasSeq); - seqRefIds.put(id, jds); + if (vamsasSetIds.get(id) == null) + { + if (seqRefIds.get(id) != null && !storeDS) + { + // 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 + { + vamsasSeq = createVamsasSequence(id, jds); + vamsasSet.addSequence(vamsasSeq); + vamsasSetIds.put(id, vamsasSeq); + seqRefIds.put(id, jds); + } } - jseq = new JSeq(); jseq.setStart(jds.getStart()); jseq.setEnd(jds.getEnd()); @@ -724,65 +860,66 @@ public class Jalview2XML jseq.setHidden(av.getAlignment().getHiddenSequences() .isHidden(jds)); - if (av.isHiddenRepSequence(rjal.getSequenceAt(i))) + if (av.isHiddenRepSequence(jds)) { jalview.datamodel.SequenceI[] reps = av - .getRepresentedSequences(rjal.getSequenceAt(i)) - .getSequencesInOrder(rjal); + .getRepresentedSequences(jds).getSequencesInOrder(rjal); for (int h = 0; h < reps.length; h++) { - if (reps[h] != rjal.getSequenceAt(i)) + if (reps[h] != jds) { jseq.addHiddenSequences(rjal.findIndex(reps[h])); } } } } + // mark sequence as reference - if it is the reference for this view + if (jal.hasSeqrep()) + { + jseq.setViewreference(jds == jal.getSeqrep()); + } } - if (jds.getSequenceFeatures() != null) + // TODO: omit sequence features from each alignment view's XML dump if we + // are storing dataset + List sfs = jds + .getSequenceFeatures(); + for (SequenceFeature sf : sfs) { - jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures(); - int index = 0; - while (index < sf.length) - { - Features features = new Features(); + Features features = new Features(); - features.setBegin(sf[index].getBegin()); - features.setEnd(sf[index].getEnd()); - features.setDescription(sf[index].getDescription()); - features.setType(sf[index].getType()); - features.setFeatureGroup(sf[index].getFeatureGroup()); - features.setScore(sf[index].getScore()); - if (sf[index].links != null) + features.setBegin(sf.getBegin()); + features.setEnd(sf.getEnd()); + features.setDescription(sf.getDescription()); + features.setType(sf.getType()); + features.setFeatureGroup(sf.getFeatureGroup()); + features.setScore(sf.getScore()); + if (sf.links != null) + { + for (int l = 0; l < sf.links.size(); l++) { - for (int l = 0; l < sf[index].links.size(); l++) - { - OtherData keyValue = new OtherData(); - keyValue.setKey("LINK_" + l); - keyValue.setValue(sf[index].links.elementAt(l).toString()); - features.addOtherData(keyValue); - } + OtherData keyValue = new OtherData(); + keyValue.setKey("LINK_" + l); + keyValue.setValue(sf.links.elementAt(l).toString()); + features.addOtherData(keyValue); } - if (sf[index].otherDetails != null) + } + if (sf.otherDetails != null) + { + String key; + Iterator keys = sf.otherDetails.keySet().iterator(); + while (keys.hasNext()) { - String key; - Iterator keys = sf[index].otherDetails.keySet() - .iterator(); - while (keys.hasNext()) - { - key = keys.next(); - OtherData keyValue = new OtherData(); - keyValue.setKey(key); - keyValue.setValue(sf[index].otherDetails.get(key).toString()); - features.addOtherData(keyValue); - } + key = keys.next(); + OtherData keyValue = new OtherData(); + keyValue.setKey(key); + keyValue.setValue(sf.otherDetails.get(key).toString()); + features.addOtherData(keyValue); } - - jseq.addFeatures(features); - index++; } + + jseq.addFeatures(features); } if (jdatasq.getAllPDBEntries() != null) @@ -855,17 +992,16 @@ public class Jalview2XML } } - if (entry.getProperty() != null && !entry.getProperty().isEmpty()) + Enumeration props = entry.getProperties(); + if (props.hasMoreElements()) { PdbentryItem item = new PdbentryItem(); - Hashtable properties = entry.getProperty(); - Enumeration en2 = properties.keys(); - while (en2.hasMoreElements()) + while (props.hasMoreElements()) { Property prop = new Property(); - String key = en2.nextElement().toString(); + String key = props.nextElement(); prop.setName(key); - prop.setValue(properties.get(key).toString()); + prop.setValue(entry.getProperty(key).toString()); item.addProperty(prop); } pdb.addPdbentryItem(item); @@ -885,16 +1021,17 @@ public class Jalview2XML jal = av.getAlignment(); } // SAVE MAPPINGS - if (jal.getCodonFrames() != null) + // FOR DATASET + if (storeDS && jal.getCodonFrames() != null) { List jac = jal.getCodonFrames(); for (AlignedCodonFrame acf : jac) { AlcodonFrame alc = new AlcodonFrame(); - vamsasSet.addAlcodonFrame(alc); if (acf.getProtMappings() != null && acf.getProtMappings().length > 0) { + boolean hasMap = false; SequenceI[] dnas = acf.getdnaSeqs(); jalview.datamodel.Mapping[] pmaps = acf.getProtMappings(); for (int m = 0; m < pmaps.length; m++) @@ -904,9 +1041,14 @@ public class Jalview2XML alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, false)); alc.addAlcodMap(alcmap); + hasMap = true; + } + if (hasMap) + { + vamsasSet.addAlcodonFrame(alc); } } - + // TODO: delete this ? dead code from 2.8.3->2.9 ? // { // AlcodonFrame alc = new AlcodonFrame(); // vamsasSet.addAlcodonFrame(alc); @@ -961,7 +1103,7 @@ public class Jalview2XML Tree tree = new Tree(); tree.setTitle(tp.getTitle()); tree.setCurrentTree((av.currentTree == tp.getTree())); - tree.setNewick(tp.getTree().toString()); + tree.setNewick(tp.getTree().print()); tree.setThreshold(tp.treeCanvas.threshold); tree.setFitToWindow(tp.fitToWindow.getState()); @@ -1031,38 +1173,43 @@ public class Jalview2XML // group has references so set its ID field jGroup.setId(groupRefs.get(sg)); } - if (sg.cs != null) + ColourSchemeI colourScheme = sg.getColourScheme(); + if (colourScheme != null) { - if (sg.cs.conservationApplied()) + ResidueShaderI groupColourScheme = sg + .getGroupColourScheme(); + if (groupColourScheme.conservationApplied()) { - jGroup.setConsThreshold(sg.cs.getConservationInc()); + jGroup.setConsThreshold(groupColourScheme.getConservationInc()); - if (sg.cs instanceof jalview.schemes.UserColourScheme) + if (colourScheme instanceof jalview.schemes.UserColourScheme) { - jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); + jGroup.setColour(setUserColourScheme(colourScheme, + userColours, jms)); } else { - jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs)); + jGroup.setColour(colourScheme.getSchemeName()); } } - else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient) + else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient) { jGroup.setColour("AnnotationColourGradient"); jGroup.setAnnotationColours(constructAnnotationColours( - (jalview.schemes.AnnotationColourGradient) sg.cs, + (jalview.schemes.AnnotationColourGradient) colourScheme, userColours, jms)); } - else if (sg.cs instanceof jalview.schemes.UserColourScheme) + else if (colourScheme instanceof jalview.schemes.UserColourScheme) { - jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); + jGroup.setColour(setUserColourScheme(colourScheme, + userColours, jms)); } else { - jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs)); + jGroup.setColour(colourScheme.getSchemeName()); } - jGroup.setPidThreshold(sg.cs.getThreshold()); + jGroup.setPidThreshold(groupColourScheme.getThreshold()); } jGroup.setOutlineColour(sg.getOutlineColour().getRGB()); @@ -1121,8 +1268,8 @@ public class Jalview2XML view.setWidth(size.width); view.setHeight(size.height); - view.setStartRes(av.startRes); - view.setStartSeq(av.startSeq); + view.setStartRes(vpRanges.getStartRes()); + view.setStartSeq(vpRanges.getStartSeq()); if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) { @@ -1145,23 +1292,20 @@ public class Jalview2XML .getGlobalColourScheme())); } + ResidueShaderI vcs = av.getResidueShading(); ColourSchemeI cs = av.getGlobalColourScheme(); if (cs != null) { - if (cs.conservationApplied()) + if (vcs.conservationApplied()) { - view.setConsThreshold(cs.getConservationInc()); + view.setConsThreshold(vcs.getConservationInc()); if (cs instanceof jalview.schemes.UserColourScheme) { view.setBgColour(setUserColourScheme(cs, userColours, jms)); } } - - if (cs instanceof ResidueColourScheme) - { - view.setPidThreshold(cs.getThreshold()); - } + view.setPidThreshold(vcs.getThreshold()); } view.setConservationSelected(av.getConservationSelected()); @@ -1202,31 +1346,30 @@ public class Jalview2XML .toArray(new String[0]); Vector settingsAdded = new Vector(); - Object gstyle = null; - GraduatedColor gcol = null; if (renderOrder != null) { for (String featureType : renderOrder) { - gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getFeatureStyle(featureType); + FeatureColourI fcol = ap.getSeqPanel().seqCanvas + .getFeatureRenderer().getFeatureStyle(featureType); Setting setting = new Setting(); setting.setType(featureType); - if (gstyle instanceof GraduatedColor) + if (!fcol.isSimpleColour()) { - 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()); + setting.setColour(fcol.getMaxColour().getRGB()); + setting.setMincolour(fcol.getMinColour().getRGB()); + setting.setMin(fcol.getMin()); + setting.setMax(fcol.getMax()); + setting.setColourByLabel(fcol.isColourByLabel()); + setting.setAutoScale(fcol.isAutoScaled()); + setting.setThreshold(fcol.getThreshold()); + // -1 = No threshold, 0 = Below, 1 = Above + setting.setThreshstate(fcol.isAboveThreshold() ? 1 : (fcol + .isBelowThreshold() ? 0 : -1)); } else { - setting.setColour(((Color) gstyle).getRGB()); + setting.setColour(fcol.getColour().getRGB()); } setting.setDisplay(av.getFeaturesDisplayed().isVisible( @@ -1244,8 +1387,7 @@ public class Jalview2XML // is groups actually supposed to be a map here ? Iterator en = ap.getSeqPanel().seqCanvas - .getFeatureRenderer() - .getFeatureGroups().iterator(); + .getFeatureRenderer().getFeatureGroups().iterator(); Vector groupsAdded = new Vector(); while (en.hasNext()) { @@ -1263,22 +1405,22 @@ public class Jalview2XML groupsAdded.addElement(grp); } jms.setFeatureSettings(fs); - } if (av.hasHiddenColumns()) { - if (av.getColumnSelection() == null - || av.getColumnSelection().getHiddenColumns() == null) + jalview.datamodel.HiddenColumns hidden = av.getAlignment() + .getHiddenColumns(); + if (hidden == null || hidden.getHiddenRegions() == null) { warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this."); } else { - for (int c = 0; c < av.getColumnSelection().getHiddenColumns() + for (int c = 0; c < hidden.getHiddenRegions() .size(); c++) { - int[] region = av.getColumnSelection().getHiddenColumns() + int[] region = hidden.getHiddenRegions() .get(c); HiddenColumns hc = new HiddenColumns(); hc.setStart(region[0]); @@ -1568,6 +1710,15 @@ public class Jalview2XML return matchedFile; } + /** + * Populates the AnnotationColours xml for save. This captures the settings of + * the options in the 'Colour by Annotation' dialog. + * + * @param acg + * @param userColours + * @param jms + * @return + */ private AnnotationColours constructAnnotationColours( AnnotationColourGradient acg, List userColours, JalviewModelSequence jms) @@ -1575,16 +1726,16 @@ public class Jalview2XML AnnotationColours ac = new AnnotationColours(); ac.setAboveThreshold(acg.getAboveThreshold()); ac.setThreshold(acg.getAnnotationThreshold()); - ac.setAnnotation(acg.getAnnotation()); - if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme) + // 2.10.2 save annotationId (unique) not annotation label + ac.setAnnotation(acg.getAnnotation().annotationId); + if (acg.getBaseColour() instanceof UserColourScheme) { ac.setColourScheme(setUserColourScheme(acg.getBaseColour(), userColours, jms)); } else { - ac.setColourScheme(ColourSchemeProperty.getColourName(acg - .getBaseColour())); + ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour())); } ac.setMaxColour(acg.getMaxColour().getRGB()); @@ -1929,16 +2080,17 @@ public class Jalview2XML if (jds.getDatasetSequence() != null) { vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); - if (jds.getDatasetSequence().getDBRefs() != null) - { - dbrefs = jds.getDatasetSequence().getDBRefs(); - } } else { - vamsasSeq.setDsseqid(id); // so we can tell which sequences really are + // seqId==dsseqid so we can tell which sequences really are // dataset sequences only + vamsasSeq.setDsseqid(id); dbrefs = jds.getDBRefs(); + if (parentseq == null) + { + parentseq = jds; + } } if (dbrefs != null) { @@ -1990,38 +2142,32 @@ public class Jalview2XML if (jmp.getTo() != null) { MappingChoice mpc = new MappingChoice(); - if (recurse - && (parentseq != jmp.getTo() || parentseq - .getDatasetSequence() != jmp.getTo())) + + // check/create ID for the sequence referenced by getTo() + + String jmpid = ""; + SequenceI ps = null; + if (parentseq != jmp.getTo() + && parentseq.getDatasetSequence() != jmp.getTo()) { - mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()), - jmp.getTo(), jds)); + // chaining dbref rather than a handshaking one + jmpid = seqHash(ps = jmp.getTo()); } else { - String jmpid = ""; - SequenceI ps = null; - if (parentseq != jmp.getTo() - && parentseq.getDatasetSequence() != jmp.getTo()) - { - // chaining dbref rather than a handshaking one - jmpid = seqHash(ps = jmp.getTo()); - } - else - { - jmpid = seqHash(ps = parentseq); - } - mpc.setDseqFor(jmpid); - if (!seqRefIds.containsKey(mpc.getDseqFor())) - { - jalview.bin.Cache.log.debug("creatign new DseqFor ID"); - seqRefIds.put(mpc.getDseqFor(), ps); - } - else - { - jalview.bin.Cache.log.debug("reusing DseqFor ID"); - } + jmpid = seqHash(ps = parentseq); + } + mpc.setDseqFor(jmpid); + if (!seqRefIds.containsKey(mpc.getDseqFor())) + { + jalview.bin.Cache.log.debug("creatign new DseqFor ID"); + seqRefIds.put(mpc.getDseqFor(), ps); + } + else + { + jalview.bin.Cache.log.debug("reusing DseqFor ID"); } + mp.setMappingChoice(mpc); } } @@ -2230,14 +2376,10 @@ public class Jalview2XML } if (seqRefIds == null) { - seqRefIds = new HashMap(); - } - if (frefedSequence == null) - { - frefedSequence = new Vector(); + initSeqRefs(); } - AlignFrame af = null, _af = null; + IdentityHashMap importedDatasets = new IdentityHashMap(); Map gatherToThisFrame = new HashMap(); final String file = jprovider.getFilename(); try @@ -2265,13 +2407,24 @@ public class Jalview2XML if (true) // !skipViewport(object)) { _af = loadFromObject(object, file, true, jprovider); - if (object.getJalviewModelSequence().getViewportCount() > 0) + if (_af != null + && object.getJalviewModelSequence().getViewportCount() > 0) { - af = _af; - if (af.viewport.isGatherViewsHere()) + if (af == null) { - gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); + // store a reference to the first view + af = _af; } + if (_af.viewport.isGatherViewsHere()) + { + // if this is a gathered view, keep its reference since + // after gathering views, only this frame will remain + af = _af; + gatherToThisFrame.put(_af.viewport.getSequenceSetId(), _af); + } + // Save dataset to register mappings once all resolved + importedDatasets.put(af.viewport.getAlignment().getDataset(), + af.viewport.getAlignment().getDataset()); } } entryCount++; @@ -2327,11 +2480,6 @@ public class Jalview2XML e.printStackTrace(); } - if (Desktop.instance != null) - { - Desktop.instance.stopLoading(); - } - /* * Regather multiple views (with the same sequence set id) to the frame (if * any) that is flagged as the one to gather to, i.e. convert them to tabbed @@ -2345,11 +2493,24 @@ public class Jalview2XML } restoreSplitFrames(); - + for (AlignmentI ds : importedDatasets.keySet()) + { + if (ds.getCodonFrames() != null) + { + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).registerMappings(ds.getCodonFrames()); + } + } if (errorMessage != null) { reportErrors(); } + + if (Desktop.instance != null) + { + Desktop.instance.stopLoading(); + } + return af; } @@ -2394,6 +2555,8 @@ public class Jalview2XML SplitFrame sf = createSplitFrame(dnaFrame, af); addedToSplitFrames.add(dnaFrame); addedToSplitFrames.add(af); + dnaFrame.setMenusForViewport(); + af.setMenusForViewport(); if (af.viewport.isGatherViewsHere()) { gatherTo.add(sf); @@ -2415,6 +2578,7 @@ public class Jalview2XML Viewport view = candidate.getKey(); Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view.getHeight()); + af.setMenusForViewport(); System.err.println("Failed to restore view " + view.getTitle() + " to split frame"); } @@ -2484,10 +2648,12 @@ public class Jalview2XML @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - finalErrorMessage, "Error " - + (saving ? "saving" : "loading") - + " Jalview file", JOptionPane.WARNING_MESSAGE); + JvOptionPane + .showInternalMessageDialog(Desktop.desktop, + finalErrorMessage, "Error " + + (saving ? "saving" : "loading") + + " Jalview file", + JvOptionPane.WARNING_MESSAGE); } }); } @@ -2518,14 +2684,16 @@ public class Jalview2XML * @param pdbId * @return */ - String loadPDBFile(jarInputStreamProvider jprovider, String pdbId) + String loadPDBFile(jarInputStreamProvider jprovider, String pdbId, + String origFile) { if (alreadyLoadedPDB.containsKey(pdbId)) { return alreadyLoadedPDB.get(pdbId).toString(); } - String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb"); + String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb", + origFile); if (tempFile != null) { alreadyLoadedPDB.put(pdbId, tempFile); @@ -2542,14 +2710,26 @@ public class Jalview2XML * @param prefix * a prefix for the temporary file name, must be at least three * characters long + * @param origFile + * null or original file - so new file can be given the same suffix + * as the old one * @return */ protected String copyJarEntry(jarInputStreamProvider jprovider, - String jarEntryName, String prefix) + String jarEntryName, String prefix, String origFile) { BufferedReader in = null; PrintWriter out = null; - + String suffix = ".tmp"; + if (origFile == null) + { + origFile = jarEntryName; + } + int sfpos = origFile.lastIndexOf("."); + if (sfpos > -1 && sfpos < (origFile.length() - 3)) + { + suffix = "." + origFile.substring(sfpos + 1); + } try { JarInputStream jin = jprovider.getJarInputStream(); @@ -2567,7 +2747,7 @@ public class Jalview2XML if (entry != null) { in = new BufferedReader(new InputStreamReader(jin, UTF_8)); - File outFile = File.createTempFile(prefix, ".tmp"); + File outFile = File.createTempFile(prefix, suffix); outFile.deleteOnExit(); out = new PrintWriter(new FileOutputStream(outFile)); String data; @@ -2655,36 +2835,71 @@ public class Jalview2XML // LOAD SEQUENCES List hiddenSeqs = null; - jalview.datamodel.Sequence jseq; List tmpseqs = new ArrayList(); boolean multipleView = false; - + SequenceI referenceseqForView = null; JSeq[] jseqs = object.getJalviewModelSequence().getJSeq(); int vi = 0; // counter in vamsasSeq array for (int i = 0; i < jseqs.length; i++) { String seqId = jseqs[i].getId(); - if (seqRefIds.get(seqId) != null) + SequenceI tmpSeq = seqRefIds.get(seqId); + if (tmpSeq != null) { - tmpseqs.add(seqRefIds.get(seqId)); - multipleView = true; + if (!incompleteSeqs.containsKey(seqId)) + { + // may not need this check, but keep it for at least 2.9,1 release + if (tmpSeq.getStart() != jseqs[i].getStart() + || tmpSeq.getEnd() != jseqs[i].getEnd()) + { + System.err + .println("Warning JAL-2154 regression: updating start/end for sequence " + + tmpSeq.toString() + " to " + jseqs[i]); + } + } + else + { + incompleteSeqs.remove(seqId); + } + if (vamsasSeq.length > vi && vamsasSeq[vi].getId().equals(seqId)) + { + // most likely we are reading a dataset XML document so + // update from vamsasSeq section of XML for this sequence + tmpSeq.setName(vamsasSeq[vi].getName()); + tmpSeq.setDescription(vamsasSeq[vi].getDescription()); + tmpSeq.setSequence(vamsasSeq[vi].getSequence()); + vi++; + } + else + { + // reading multiple views, so vamsasSeq set is a subset of JSeq + multipleView = true; + } + tmpSeq.setStart(jseqs[i].getStart()); + tmpSeq.setEnd(jseqs[i].getEnd()); + tmpseqs.add(tmpSeq); } else { - jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(), + tmpSeq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(), vamsasSeq[vi].getSequence()); - jseq.setDescription(vamsasSeq[vi].getDescription()); - jseq.setStart(jseqs[i].getStart()); - jseq.setEnd(jseqs[i].getEnd()); - jseq.setVamsasId(uniqueSetSuffix + seqId); - seqRefIds.put(vamsasSeq[vi].getId(), jseq); - tmpseqs.add(jseq); + tmpSeq.setDescription(vamsasSeq[vi].getDescription()); + tmpSeq.setStart(jseqs[i].getStart()); + tmpSeq.setEnd(jseqs[i].getEnd()); + tmpSeq.setVamsasId(uniqueSetSuffix + seqId); + seqRefIds.put(vamsasSeq[vi].getId(), tmpSeq); + tmpseqs.add(tmpSeq); vi++; } + if (jseqs[i].hasViewreference() && jseqs[i].getViewreference()) + { + referenceseqForView = tmpseqs.get(tmpseqs.size() - 1); + } + if (jseqs[i].getHidden()) { if (hiddenSeqs == null) @@ -2692,9 +2907,8 @@ public class Jalview2XML hiddenSeqs = new ArrayList(); } - hiddenSeqs.add(seqRefIds.get(seqId)); + hiddenSeqs.add(tmpSeq); } - } // / @@ -2703,31 +2917,51 @@ public class Jalview2XML SequenceI[] orderedSeqs = tmpseqs .toArray(new SequenceI[tmpseqs.size()]); - Alignment al = new Alignment(orderedSeqs); - - // / 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 + AlignmentI al = null; + // so we must create or recover the dataset alignment before going further // /////////////////////////////// if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "") { - // older jalview projects do not have a dataset id. + // older jalview projects do not have a dataset - so creat alignment and + // dataset + al = new Alignment(orderedSeqs); al.setDataset(null); } else { - // recover dataset - passing on flag indicating if this a 'viewless' - // sequence set (a.k.a. a stored dataset for the project) - recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence() - .getViewportCount() == 0); + boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0; + if (isdsal) + { + // we are importing a dataset record, so + // recover reference to an alignment already materialsed as dataset + al = getDatasetFor(vamsasSet.getDatasetId()); + } + if (al == null) + { + // materialse the alignment + al = new Alignment(orderedSeqs); + } + if (isdsal) + { + addDatasetRef(vamsasSet.getDatasetId(), al); + } + + // finally, verify all data in vamsasSet is actually present in al + // passing on flag indicating if it is actually a stored dataset + recoverDatasetFor(vamsasSet, al, isdsal); + } + + if (referenceseqForView != null) + { + al.setSeqrep(referenceseqForView); + } + // / Add the alignment properties + for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++) + { + SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i); + al.setProperty(ssp.getKey(), ssp.getValue()); } + // /////////////////////////////// Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this?? @@ -2735,6 +2969,12 @@ public class Jalview2XML { // load sequence features, database references and any associated PDB // structures for the alignment + // + // prior to 2.10, this part would only be executed the first time a + // sequence was encountered, but not afterwards. + // now, for 2.10 projects, this is also done if the xml doc includes + // dataset sequences not actually present in any particular view. + // for (int i = 0; i < vamsasSeq.length; i++) { if (jseqs[i].getFeaturesCount() > 0) @@ -2742,12 +2982,11 @@ public class Jalview2XML Features[] features = jseqs[i].getFeatures(); for (int f = 0; f < features.length; f++) { - jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature( - features[f].getType(), features[f].getDescription(), - features[f].getStatus(), features[f].getBegin(), - features[f].getEnd(), features[f].getFeatureGroup()); - - sf.setScore(features[f].getScore()); + SequenceFeature sf = new SequenceFeature(features[f].getType(), + features[f].getDescription(), features[f].getBegin(), + features[f].getEnd(), features[f].getScore(), + features[f].getFeatureGroup()); + sf.setStatus(features[f].getStatus()); for (int od = 0; od < features[f].getOtherDataCount(); od++) { OtherData keyValue = features[f].getOtherData(od); @@ -2761,13 +3000,17 @@ public class Jalview2XML } } - - al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); + // adds feature to datasequence's feature set (since Jalview 2.10) + al.getSequenceAt(i).addSequenceFeature(sf); } } if (vamsasSeq[i].getDBRefCount() > 0) { - addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]); + // adds dbrefs to datasequence's set (since Jalview 2.10) + addDBRefs( + al.getSequenceAt(i).getDatasetSequence() == null ? al.getSequenceAt(i) + : al.getSequenceAt(i).getDatasetSequence(), + vamsasSeq[i]); } if (jseqs[i].getPdbidsCount() > 0) { @@ -2778,29 +3021,49 @@ public class Jalview2XML entry.setId(ids[p].getId()); if (ids[p].getType() != null) { - if (ids[p].getType().equalsIgnoreCase("PDB")) + if (PDBEntry.Type.getType(ids[p].getType()) != null) { - entry.setType(PDBEntry.Type.PDB); + entry.setType(PDBEntry.Type.getType(ids[p].getType())); } else { entry.setType(PDBEntry.Type.FILE); } } - if (ids[p].getFile() != null) + // jprovider is null when executing 'New View' + if (ids[p].getFile() != null && jprovider != null) { if (!pdbloaded.containsKey(ids[p].getFile())) { - entry.setFile(loadPDBFile(jprovider, ids[p].getId())); + entry.setFile(loadPDBFile(jprovider, ids[p].getId(), + ids[p].getFile())); } else { entry.setFile(pdbloaded.get(ids[p].getId()).toString()); } } + if (ids[p].getPdbentryItem() != null) + { + for (PdbentryItem item : ids[p].getPdbentryItem()) + { + for (Property pr : item.getProperty()) + { + entry.setProperty(pr.getName(), pr.getValue()); + } + } + } StructureSelectionManager.getStructureSelectionManager( Desktop.instance).registerPDBEntry(entry); - al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + // adds PDBEntry to datasequence's set (since Jalview 2.10) + if (al.getSequenceAt(i).getDatasetSequence() != null) + { + al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + } + else + { + al.getSequenceAt(i).addPDBId(entry); + } } } } @@ -2829,20 +3092,20 @@ public class Jalview2XML if (maps[m].getMapping() != null) { mapping = addMapping(maps[m].getMapping()); - } - if (dnaseq != null && mapping.getTo() != null) - { - cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); - } - else - { - // defer to later - frefedSequence.add(new Object[] { maps[m].getDnasq(), cf, - mapping }); + if (dnaseq != null && mapping.getTo() != null) + { + cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); + } + else + { + // defer to later + frefedSequence.add(newAlcodMapRef(maps[m].getDnasq(), cf, + mapping)); + } } } + al.addCodonFrame(cf); } - al.addCodonFrame(cf); } } @@ -3090,18 +3353,13 @@ public class Jalview2XML && jGroup.getAnnotationColours() != null) { addAnnotSchemeGroup = true; - cs = null; } else { - cs = ColourSchemeProperty.getColour(al, jGroup.getColour()); - } - - if (cs != null) - { - cs.setThreshold(jGroup.getPidThreshold(), true); + cs = ColourSchemeProperty.getColourScheme(al, jGroup.getColour()); } } + int pidThreshold = jGroup.getPidThreshold(); Vector seqs = new Vector(); @@ -3124,7 +3382,8 @@ public class Jalview2XML SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs, jGroup.getDisplayBoxes(), jGroup.getDisplayText(), jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd()); - + sg.getGroupColourScheme().setThreshold(pidThreshold, true); + sg.getGroupColourScheme().setConservationInc(jGroup.getConsThreshold()); sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour())); sg.textColour = new java.awt.Color(jGroup.getTextCol1()); @@ -3151,9 +3410,8 @@ public class Jalview2XML } if (jGroup.getConsThreshold() != 0) { - jalview.analysis.Conservation c = new jalview.analysis.Conservation( - "All", ResidueProperties.propHash, 3, - sg.getSequences(null), 0, sg.getWidth() - 1); + Conservation c = new Conservation("All", sg.getSequences(null), + 0, sg.getWidth() - 1); c.calculate(); c.verdict(false, 25); sg.cs.setConservation(c); @@ -3191,8 +3449,8 @@ public class Jalview2XML if (addAnnotSchemeGroup) { // reconstruct the annotation colourscheme - sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(), - null, al, jms, false); + sg.setColourScheme(constructAnnotationColour( + jGroup.getAnnotationColours(), null, al, jms, false)); } } } @@ -3342,7 +3600,7 @@ public class Jalview2XML String rnaTitle = ss.getTitle(); String sessionState = ss.getViewerState(); String tempStateFile = copyJarEntry(jprovider, sessionState, - "varna"); + "varna", null); RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped); appVarna.addModelSession(rna, rnaTitle, tempStateFile); } @@ -3418,7 +3676,7 @@ public class Jalview2XML TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); if (tp == null) { - tp = af.ShowNewickTree( + tp = af.showNewickTree( new jalview.io.NewickFile(tree.getNewick()), tree.getTitle(), tree.getWidth(), tree.getHeight(), tree.getXpos(), tree.getYpos()); @@ -3517,7 +3775,8 @@ public class Jalview2XML // 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.setFile(loadPDBFile(jprovider, ids[p].getId(), + ids[p].getFile())); jpdb.setId(ids[p].getId()); int x = structureState.getXpos(); @@ -3528,7 +3787,8 @@ public class Jalview2XML // 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()); + String pdbFile = loadPDBFile(jprovider, ids[p].getId(), + ids[p].getFile()); jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i] .getId() + ""); if (sviewid == null) @@ -3688,7 +3948,7 @@ public class Jalview2XML */ String viewerJarEntryName = getViewerJarEntryName(data.getViewId()); chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName, - "chimera"); + "chimera", null); Set> fileData = data.getFileData() .entrySet(); @@ -3769,6 +4029,11 @@ public class Jalview2XML // filename // translation differently. StructureData filedat = oldFiles.get(new File(oldfilenam)); + if (filedat == null) + { + String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\"); + filedat = oldFiles.get(new File(reformatedOldFilename)); + } newFileLoc.append(Platform.escapeString(filedat.getFilePath())); pdbfilenames.add(filedat.getFilePath()); pdbids.add(filedat.getPdbId()); @@ -3974,8 +4239,7 @@ public class Jalview2XML StructureData filedat = oldFiles.get(id); String pdbFile = filedat.getFilePath(); SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]); - binding.getSsm().setMapping(seq, null, pdbFile, - jalview.io.AppletFormatAdapter.FILE); + binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE); binding.addSequenceForStructFile(pdbFile, seq); } // and add the AlignmentPanel's reference to the view panel @@ -4082,7 +4346,7 @@ public class Jalview2XML } AlignFrame loadViewport(String file, JSeq[] JSEQ, - List hiddenSeqs, Alignment al, + List hiddenSeqs, AlignmentI al, JalviewModelSequence jms, Viewport view, String uniqueSeqSetId, String viewId, List autoAlan) { @@ -4090,7 +4354,7 @@ public class Jalview2XML af = new AlignFrame(al, view.getWidth(), view.getHeight(), uniqueSeqSetId, viewId); - af.setFileName(file, "Jalview"); + af.setFileName(file, FileFormat.Jalview); for (int i = 0; i < JSEQ.length; i++) { @@ -4098,6 +4362,12 @@ public class Jalview2XML .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); } + if (al.hasSeqrep()) + { + af.getViewport().setColourByReferenceSeq(true); + af.getViewport().setDisplayReferenceSeq(true); + } + af.viewport.setGatherViewsHere(view.getGatheredViews()); if (view.getSequenceSetId() != null) @@ -4124,25 +4394,25 @@ public class Jalview2XML { for (int s = 0; s < JSEQ.length; s++) { - jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup(); - + SequenceGroup hidden = new SequenceGroup(); + boolean isRepresentative = false; for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++) { - hidden.addSequence( - al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false); + isRepresentative = true; + SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s] + .getHiddenSequences(r)); + hidden.addSequence(sequenceToHide, false); + // remove from hiddenSeqs list so we don't try to hide it twice + hiddenSeqs.remove(sequenceToHide); + } + if (isRepresentative) + { + SequenceI representativeSequence = al.getSequenceAt(s); + hidden.addSequence(representativeSequence, false); + af.viewport.hideRepSequences(representativeSequence, hidden); } - af.viewport.hideRepSequences(al.getSequenceAt(s), hidden); } - // jalview.datamodel.SequenceI[] hseqs = new - // jalview.datamodel.SequenceI[hiddenSeqs - // .size()]; - // - // for (int s = 0; s < hiddenSeqs.size(); s++) - // { - // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s); - // } - SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs .size()]); af.viewport.hideSequence(hseqs); @@ -4159,10 +4429,12 @@ public class Jalview2XML af.viewport.setShowAnnotation(view.getShowAnnotation()); af.viewport.setAbovePIDThreshold(view.getPidSelected()); + af.viewport.setThreshold(view.getPidThreshold()); af.viewport.setColourText(view.getShowColourText()); af.viewport.setConservationSelected(view.getConservationSelected()); + af.viewport.setIncrement(view.getConsThreshold()); af.viewport.setShowJVSuffix(view.getShowFullId()); af.viewport.setRightAlignIds(view.getRightAlignIds()); af.viewport.setFont( @@ -4186,8 +4458,8 @@ public class Jalview2XML af.viewport.setThresholdTextColour(view.getTextColThreshold()); af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view .isShowUnconserved() : false); - af.viewport.setStartRes(view.getStartRes()); - af.viewport.setStartSeq(view.getStartSeq()); + af.viewport.getRanges().setStartRes(view.getStartRes()); + // startSeq set in af.alignPanel.updateLayout below af.alignPanel.updateLayout(); ColourSchemeI cs = null; // apply colourschemes @@ -4207,22 +4479,21 @@ public class Jalview2XML } else { - cs = ColourSchemeProperty.getColour(al, view.getBgColour()); - } - - if (cs != null) - { - cs.setThreshold(view.getPidThreshold(), true); - cs.setConsensus(af.viewport.getSequenceConsensusHash()); + cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour()); } } af.viewport.setGlobalColourScheme(cs); + af.viewport.getResidueShading().setThreshold( + view.getPidThreshold(), true); + af.viewport.getResidueShading().setConsensus( + af.viewport.getSequenceConsensusHash()); af.viewport.setColourAppliesToAllGroups(false); if (view.getConservationSelected() && cs != null) { - cs.setConservationInc(view.getConsThreshold()); + af.viewport.getResidueShading().setConservationInc( + view.getConsThreshold()); } af.changeColour(cs); @@ -4301,25 +4572,33 @@ public class Jalview2XML af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; - Hashtable featureGroups = new Hashtable(); - Hashtable featureColours = new Hashtable(); - Hashtable featureOrder = new Hashtable(); + Map featureColours = new Hashtable(); + Map featureOrder = new Hashtable(); for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); 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); + FeatureColourI gc = setting.hasMin() ? new FeatureColour( + new Color(setting.getMincolour()), new Color( + setting.getColour()), setting.getMin(), + setting.getMax()) : new FeatureColour(new Color( + setting.getMincolour()), new Color(setting.getColour()), + 0, 1); if (setting.hasThreshold()) { - gc.setThresh(setting.getThreshold()); - gc.setThreshType(setting.getThreshstate()); + gc.setThreshold(setting.getThreshold()); + int threshstate = setting.getThreshstate(); + // -1 = None, 0 = Below, 1 = Above threshold + if (threshstate == 0) + { + gc.setBelowThreshold(true); + } + else if (threshstate == 1) + { + gc.setAboveThreshold(true); + } } gc.setAutoScaled(true); // default if (setting.hasAutoScale()) @@ -4335,8 +4614,8 @@ public class Jalview2XML } else { - featureColours.put(setting.getType(), - new java.awt.Color(setting.getColour())); + featureColours.put(setting.getType(), new FeatureColour( + new Color(setting.getColour()))); } renderOrder[fs] = setting.getType(); if (setting.hasOrder()) @@ -4353,7 +4632,7 @@ public class Jalview2XML fdi.setVisible(setting.getType()); } } - Hashtable fgtable = new Hashtable(); + Map fgtable = new Hashtable(); for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) { Group grp = jms.getFeatureSettings().getGroup(gs); @@ -4396,7 +4675,7 @@ public class Jalview2XML } } af.setMenusFromViewport(af.viewport); - + af.setTitle(view.getTitle()); // TODO: we don't need to do this if the viewport is aready visible. /* * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it @@ -4420,12 +4699,21 @@ public class Jalview2XML return af; } + /** + * Reads saved data to restore Colour by Annotation settings + * + * @param viewAnnColour + * @param af + * @param al + * @param jms + * @param checkGroupAnnColour + * @return + */ private ColourSchemeI constructAnnotationColour( - AnnotationColours viewAnnColour, AlignFrame af, Alignment al, + AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al, JalviewModelSequence jms, boolean checkGroupAnnColour) { boolean propagateAnnColour = false; - ColourSchemeI cs = null; AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al; if (checkGroupAnnColour && al.getGroups() != null && al.getGroups().size() > 0) @@ -4433,119 +4721,98 @@ public class Jalview2XML // pre 2.8.1 behaviour // check to see if we should transfer annotation colours propagateAnnColour = true; - for (jalview.datamodel.SequenceGroup sg : al.getGroups()) + for (SequenceGroup sg : al.getGroups()) { - if (sg.cs instanceof AnnotationColourGradient) + if (sg.getColourScheme() instanceof AnnotationColourGradient) { propagateAnnColour = false; } } } - // int find annotation - if (annAlignment.getAlignmentAnnotation() != null) + + /* + * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId + */ + String annotationId = viewAnnColour.getAnnotation(); + AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId); + + /* + * pre 2.10.2: saved annotationId is AlignmentAnnotation.label + */ + if (matchedAnnotation == null && annAlignment.getAlignmentAnnotation() != null) { for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++) { - if (annAlignment.getAlignmentAnnotation()[i].label - .equals(viewAnnColour.getAnnotation())) + if (annotationId + .equals(annAlignment.getAlignmentAnnotation()[i].label)) { - if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null) - { - annAlignment.getAlignmentAnnotation()[i] - .setThreshold(new jalview.datamodel.GraphLine( - viewAnnColour.getThreshold(), "Threshold", - java.awt.Color.black) - - ); - } - - if (viewAnnColour.getColourScheme().equals("None")) - { - cs = new AnnotationColourGradient( - annAlignment.getAlignmentAnnotation()[i], - new java.awt.Color(viewAnnColour.getMinColour()), - new java.awt.Color(viewAnnColour.getMaxColour()), - viewAnnColour.getAboveThreshold()); - } - else if (viewAnnColour.getColourScheme().startsWith("ucs")) - { - cs = new AnnotationColourGradient( - annAlignment.getAlignmentAnnotation()[i], - getUserColourScheme(jms, - viewAnnColour.getColourScheme()), - viewAnnColour.getAboveThreshold()); - } - else - { - cs = new AnnotationColourGradient( - annAlignment.getAlignmentAnnotation()[i], - ColourSchemeProperty.getColour(al, - viewAnnColour.getColourScheme()), - viewAnnColour.getAboveThreshold()); - } - if (viewAnnColour.hasPerSequence()) - { - ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour - .isPerSequence()); - } - if (viewAnnColour.hasPredefinedColours()) - { - ((AnnotationColourGradient) cs) - .setPredefinedColours(viewAnnColour - .isPredefinedColours()); - } - if (propagateAnnColour && al.getGroups() != null) - { - // Also use these settings for all the groups - for (int g = 0; g < al.getGroups().size(); g++) - { - jalview.datamodel.SequenceGroup sg = al.getGroups().get(g); - - if (sg.cs == null) - { - continue; - } + matchedAnnotation = annAlignment.getAlignmentAnnotation()[i]; + break; + } + } + } + if (matchedAnnotation == null) + { + System.err.println("Failed to match annotation colour scheme for " + + annotationId); + return null; + } + if (matchedAnnotation.getThreshold() == null) + { + matchedAnnotation.setThreshold(new GraphLine(viewAnnColour.getThreshold(), + "Threshold", Color.black)); + } - /* - * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs = - * new AnnotationColourGradient( - * annAlignment.getAlignmentAnnotation()[i], new - * java.awt.Color(viewAnnColour. getMinColour()), new - * java.awt.Color(viewAnnColour. getMaxColour()), - * viewAnnColour.getAboveThreshold()); } else - */ - { - sg.cs = new AnnotationColourGradient( - annAlignment.getAlignmentAnnotation()[i], sg.cs, - viewAnnColour.getAboveThreshold()); - if (cs instanceof AnnotationColourGradient) - { - if (viewAnnColour.hasPerSequence()) - { - ((AnnotationColourGradient) cs) - .setSeqAssociated(viewAnnColour.isPerSequence()); - } - if (viewAnnColour.hasPredefinedColours()) - { - ((AnnotationColourGradient) cs) - .setPredefinedColours(viewAnnColour - .isPredefinedColours()); - } - } - } + AnnotationColourGradient cs = null; + if (viewAnnColour.getColourScheme().equals("None")) + { + cs = new AnnotationColourGradient(matchedAnnotation, new Color( + viewAnnColour.getMinColour()), new Color( + viewAnnColour.getMaxColour()), + viewAnnColour.getAboveThreshold()); + } + else if (viewAnnColour.getColourScheme().startsWith("ucs")) + { + cs = new AnnotationColourGradient(matchedAnnotation, getUserColourScheme( + jms, viewAnnColour.getColourScheme()), + viewAnnColour.getAboveThreshold()); + } + else + { + cs = new AnnotationColourGradient(matchedAnnotation, + ColourSchemeProperty.getColourScheme(al, + viewAnnColour.getColourScheme()), + viewAnnColour.getAboveThreshold()); + } - } - } + boolean perSequenceOnly = viewAnnColour.isPerSequence(); + boolean useOriginalColours = viewAnnColour.isPredefinedColours(); + cs.setSeqAssociated(perSequenceOnly); + cs.setPredefinedColours(useOriginalColours); - break; + if (propagateAnnColour && al.getGroups() != null) + { + // Also use these settings for all the groups + for (int g = 0; g < al.getGroups().size(); g++) + { + SequenceGroup sg = al.getGroups().get(g); + if (sg.getGroupColourScheme() == null) + { + continue; } + AnnotationColourGradient groupScheme = new AnnotationColourGradient( + matchedAnnotation, sg.getColourScheme(), + viewAnnColour.getAboveThreshold()); + sg.setColourScheme(groupScheme); + groupScheme.setSeqAssociated(perSequenceOnly); + groupScheme.setPredefinedColours(useOriginalColours); } } return cs; } - private void reorderAutoannotation(AlignFrame af, Alignment al, + private void reorderAutoannotation(AlignFrame af, AlignmentI al, List autoAlan) { // copy over visualization settings for autocalculated annotation in the @@ -4700,10 +4967,11 @@ public class Jalview2XML } } - private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al, + private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al, boolean ignoreUnrefed) { - jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId()); + jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet + .getDatasetId()); Vector dseqs = null; if (ds == null) { @@ -4713,7 +4981,7 @@ public class Jalview2XML for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++) { Sequence vamsasSeq = vamsasSet.getSequence(i); - ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed); + ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed, i); } // create a new dataset if (ds == null) @@ -4740,18 +5008,29 @@ public class Jalview2XML * dataset alignment * @param dseqs * vector to add new dataset sequence to + * @param ignoreUnrefed + * - when true, don't create new sequences from vamsasSeq if it's id + * doesn't already have an asssociated Jalview sequence. + * @param vseqpos + * - used to reorder the sequence in the alignment according to the + * vamsasSeq array ordering, to preserve ordering of dataset */ private void ensureJalviewDatasetSequence(Sequence vamsasSeq, - AlignmentI ds, Vector dseqs, boolean ignoreUnrefed) + AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos) { // JBP TODO: Check this is called for AlCodonFrames to support recovery of // xRef Codon Maps SequenceI sq = seqRefIds.get(vamsasSeq.getId()); + boolean reorder = false; SequenceI dsq = null; if (sq != null && sq.getDatasetSequence() != null) { dsq = sq.getDatasetSequence(); } + else + { + reorder = true; + } if (sq == null && ignoreUnrefed) { return; @@ -4847,21 +5126,50 @@ public class Jalview2XML // + (post ? "appended" : "")); } } + else + { + // sequence refs are identical. We may need to update the existing dataset + // alignment with this one, though. + if (ds != null && dseqs == null) + { + int opos = ds.findIndex(dsq); + SequenceI tseq = null; + if (opos != -1 && vseqpos != opos) + { + // remove from old position + ds.deleteSequence(dsq); + } + if (vseqpos < ds.getHeight()) + { + if (vseqpos != opos) + { + // save sequence at destination position + tseq = ds.getSequenceAt(vseqpos); + ds.replaceSequenceAt(vseqpos, dsq); + ds.addSequence(tseq); + } + } + else + { + ds.addSequence(dsq); + } + } + } } /* * TODO use AlignmentI here and in related methods - needs * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment */ - Hashtable datasetIds = null; + Hashtable datasetIds = null; - IdentityHashMap dataset2Ids = null; + IdentityHashMap dataset2Ids = null; - private Alignment getDatasetFor(String datasetId) + private AlignmentI getDatasetFor(String datasetId) { if (datasetIds == null) { - datasetIds = new Hashtable(); + datasetIds = new Hashtable(); return null; } if (datasetIds.containsKey(datasetId)) @@ -4871,11 +5179,11 @@ public class Jalview2XML return null; } - private void addDatasetRef(String datasetId, Alignment dataset) + private void addDatasetRef(String datasetId, AlignmentI dataset) { if (datasetIds == null) { - datasetIds = new Hashtable(); + datasetIds = new Hashtable(); } datasetIds.put(datasetId, dataset); } @@ -4886,7 +5194,7 @@ public class Jalview2XML * @param dataset * @return */ - private String getDatasetIdRef(Alignment dataset) + private String getDatasetIdRef(AlignmentI dataset) { if (dataset.getDataset() != null) { @@ -4898,7 +5206,7 @@ public class Jalview2XML // make a new datasetId and record it if (dataset2Ids == null) { - dataset2Ids = new IdentityHashMap(); + dataset2Ids = new IdentityHashMap(); } else { @@ -4966,7 +5274,7 @@ public class Jalview2XML } else { - frefedSequence.add(new Object[] { dsfor, jmap }); + frefedSequence.add(newMappingRef(dsfor, jmap)); } } else @@ -5004,6 +5312,7 @@ public class Jalview2XML djs.setEnd(jmap.getMap().getToHighest()); djs.setVamsasId(uniqueSetSuffix + sqid); jmap.setTo(djs); + incompleteSeqs.put(sqid, djs); seqRefIds.put(sqid, djs); }