X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=87b8d8739d14ffa980928d7abe43fcacca6c6f70;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=35d4685b916c569a9c0e43cdfc8190f4bb3b8d46;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 35d4685..87b8d87 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.analysis.Conservation; import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; import jalview.api.structures.JalviewStructureDisplayI; @@ -28,22 +29,31 @@ 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.datamodel.features.FeatureMatcher; +import jalview.datamodel.features.FeatureMatcherI; +import jalview.datamodel.features.FeatureMatcherSet; +import jalview.datamodel.features.FeatureMatcherSetI; 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; import jalview.schemabinding.version2.AnnotationColours; import jalview.schemabinding.version2.AnnotationElement; import jalview.schemabinding.version2.CalcIdParam; +import jalview.schemabinding.version2.Colour; +import jalview.schemabinding.version2.CompoundMatcher; import jalview.schemabinding.version2.DBRef; import jalview.schemabinding.version2.Features; import jalview.schemabinding.version2.Group; @@ -56,6 +66,8 @@ import jalview.schemabinding.version2.MapListFrom; import jalview.schemabinding.version2.MapListTo; import jalview.schemabinding.version2.Mapping; import jalview.schemabinding.version2.MappingChoice; +import jalview.schemabinding.version2.MatchCondition; +import jalview.schemabinding.version2.MatcherSet; import jalview.schemabinding.version2.OtherData; import jalview.schemabinding.version2.PdbentryItem; import jalview.schemabinding.version2.Pdbids; @@ -71,20 +83,25 @@ import jalview.schemabinding.version2.ThresholdLine; import jalview.schemabinding.version2.Tree; import jalview.schemabinding.version2.UserColours; import jalview.schemabinding.version2.Viewport; +import jalview.schemabinding.version2.types.ColourThreshTypeType; +import jalview.schemabinding.version2.types.FeatureMatcherByType; +import jalview.schemabinding.version2.types.NoValueColour; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; import jalview.schemes.FeatureColour; -import jalview.schemes.ResidueColourScheme; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; +import jalview.util.Format; import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.StringUtils; import jalview.util.jarInputStreamProvider; +import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import jalview.ws.jws2.Jws2Discoverer; @@ -111,6 +128,7 @@ import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; import java.util.Enumeration; import java.util.HashMap; import java.util.HashSet; @@ -128,7 +146,6 @@ 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; @@ -178,13 +195,13 @@ public class Jalview2XML * Map of reconstructed AlignFrame objects that appear to have come from * SplitFrame objects (have a dna/protein complement view). */ - private Map splitFrameCandidates = new HashMap(); + private Map splitFrameCandidates = new HashMap<>(); /* * Map from displayed rna structure models to their saved session state jar * entry names */ - private Map rnaSessions = new HashMap(); + private Map rnaSessions = new HashMap<>(); /** * create/return unique hash string for sq @@ -213,51 +230,23 @@ public class Jalview2XML } } - void clearSeqRefs() - { - if (_cleartables) - { - if (seqRefIds != null) - { - seqRefIds.clear(); - } - if (seqsToIds != null) - { - seqsToIds.clear(); - } - if (incompleteSeqs != null) - { - incompleteSeqs.clear(); - } - // seqRefIds = null; - // seqsToIds = null; - } - else - { - // do nothing - warn("clearSeqRefs called when _cleartables was not set. Doing nothing."); - // seqRefIds = new Hashtable(); - // seqsToIds = new IdentityHashMap(); - } - } - void initSeqRefs() { if (seqsToIds == null) { - seqsToIds = new IdentityHashMap(); + seqsToIds = new IdentityHashMap<>(); } if (seqRefIds == null) { - seqRefIds = new HashMap(); + seqRefIds = new HashMap<>(); } if (incompleteSeqs == null) { - incompleteSeqs = new HashMap(); + incompleteSeqs = new HashMap<>(); } if (frefedSequence == null) { - frefedSequence = new ArrayList(); + frefedSequence = new ArrayList<>(); } } @@ -315,6 +304,7 @@ public class Jalview2XML } return sq; } + /** * @return true if the forward reference was fully resolved */ @@ -357,7 +347,8 @@ public class Jalview2XML } public SeqFref newAlcodMapRef(final String sref, - final AlignedCodonFrame _cf, final jalview.datamodel.Mapping _jmap) + final AlignedCodonFrame _cf, + final jalview.datamodel.Mapping _jmap) { SeqFref fref = new SeqFref(sref, "Codon Frame") @@ -367,6 +358,12 @@ public class Jalview2XML public jalview.datamodel.Mapping mp = _jmap; @Override + public boolean isResolvable() + { + return super.isResolvable() && mp.getTo() != null; + }; + + @Override boolean resolve() { SequenceI seq = getSrefDatasetSeq(); @@ -383,44 +380,53 @@ public class Jalview2XML public void resolveFrefedSequences() { - Iterator nextFref=frefedSequence.iterator(); - int toresolve=frefedSequence.size(); - int unresolved=0,failedtoresolve=0; - while (nextFref.hasNext()) { + Iterator nextFref = frefedSequence.iterator(); + int toresolve = frefedSequence.size(); + int unresolved = 0, failedtoresolve = 0; + while (nextFref.hasNext()) + { SeqFref ref = nextFref.next(); if (ref.isResolvable()) { - try { + try + { if (ref.resolve()) { nextFref.remove(); - } else { + } + else + { failedtoresolve++; } - } catch (Exception x) { - System.err.println("IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "+ref.getSref()); + } 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) + if (unresolved > 0) { System.err.println("Jalview Project Import: There were " + unresolved + " forward references left unresolved on the stack."); } - if (failedtoresolve>0) + 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."); + 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()) @@ -430,8 +436,8 @@ public class Jalview2XML } else { - System.err - .println("Too many to report. Skipping output of incomplete sequences."); + System.err.println( + "Too many to report. Skipping output of incomplete sequences."); } } } @@ -440,9 +446,9 @@ public class Jalview2XML * This maintains a map of viewports, the key being the seqSetId. Important to * set historyItem and redoList for multiple views */ - Map viewportsAdded = new HashMap(); + Map viewportsAdded = new HashMap<>(); - Map annotationIds = new HashMap(); + Map annotationIds = new HashMap<>(); String uniqueSetSuffix = ""; @@ -518,7 +524,7 @@ public class Jalview2XML */ private void saveAllFrames(List frames, JarOutputStream jout) { - Hashtable dsses = new Hashtable(); + Hashtable dsses = new Hashtable<>(); /* * ensure cached data is clear before starting @@ -533,17 +539,16 @@ public class Jalview2XML // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS // ////////////////////////////////////////////////// - List shortNames = new ArrayList(); - List viewIds = new ArrayList(); + List shortNames = new ArrayList<>(); + List viewIds = new ArrayList<>(); // REVERSE ORDER for (int i = frames.size() - 1; i > -1; i--) { AlignFrame af = frames.get(i); // skip ? - if (skipList != null - && skipList - .containsKey(af.getViewport().getSequenceSetId())) + if (skipList != null && skipList + .containsKey(af.getViewport().getSequenceSetId())) { continue; } @@ -563,8 +568,8 @@ public class Jalview2XML saveState(apanel, fileName, jout, viewIds); - String dssid = getDatasetIdRef(af.getViewport().getAlignment() - .getDataset()); + String dssid = getDatasetIdRef( + af.getViewport().getAlignment().getDataset()); if (!dsses.containsKey(dssid)) { dsses.put(dssid, af); @@ -610,8 +615,8 @@ public class Jalview2XML if (shortName.indexOf(File.separatorChar) > -1) { - shortName = shortName.substring(shortName - .lastIndexOf(File.separatorChar) + 1); + shortName = shortName + .substring(shortName.lastIndexOf(File.separatorChar) + 1); } int count = 1; @@ -644,7 +649,7 @@ public class Jalview2XML { FileOutputStream fos = new FileOutputStream(jarFile); JarOutputStream jout = new JarOutputStream(fos); - List frames = new ArrayList(); + List frames = new ArrayList<>(); // resolve splitframes if (af.getViewport().getCodingComplement() != null) @@ -730,21 +735,22 @@ public class Jalview2XML { if (viewIds == null) { - viewIds = new ArrayList(); + viewIds = new ArrayList<>(); } initSeqRefs(); - List userColours = new ArrayList(); + List userColours = new ArrayList<>(); AlignViewport av = ap.av; + ViewportRanges vpRanges = av.getRanges(); JalviewModel object = new JalviewModel(); object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); object.setCreationDate(new java.util.Date(System.currentTimeMillis())); - object.setVersion(jalview.bin.Cache.getDefault("VERSION", - "Development Build")); + object.setVersion( + jalview.bin.Cache.getDefault("VERSION", "Development Build")); /** * rjal is full height alignment, jal is actual alignment with full metadata @@ -788,38 +794,43 @@ public class Jalview2XML } JSeq jseq; - Set calcIdSet = new HashSet(); - + Set calcIdSet = new HashSet<>(); + // record the set of vamsas sequence XML POJO we create. + HashMap vamsasSetIds = new HashMap<>(); // SAVE SEQUENCES for (final SequenceI jds : rjal.getSequences()) { 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()); @@ -832,14 +843,13 @@ public class Jalview2XML if (av.hasHiddenRows()) { // use rjal, contains the full height alignment - jseq.setHidden(av.getAlignment().getHiddenSequences() - .isHidden(jds)); + jseq.setHidden( + av.getAlignment().getHiddenSequences().isHidden(jds)); if (av.isHiddenRepSequence(jds)) { jalview.datamodel.SequenceI[] reps = av - .getRepresentedSequences(jds) - .getSequencesInOrder(rjal); + .getRepresentedSequences(jds).getSequencesInOrder(rjal); for (int h = 0; h < reps.length; h++) { @@ -859,48 +869,61 @@ public class Jalview2XML // TODO: omit sequence features from each alignment view's XML dump if we // are storing dataset - if (jds.getSequenceFeatures() != null) + 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) + { + /* + * save feature attributes, which may be simple strings or + * map valued (have sub-attributes) + */ + for (Entry entry : sf.otherDetails.entrySet()) { - String key; - Iterator keys = sf[index].otherDetails.keySet() - .iterator(); - while (keys.hasNext()) + String key = entry.getKey(); + Object value = entry.getValue(); + if (value instanceof Map) + { + for (Entry subAttribute : ((Map) value) + .entrySet()) + { + OtherData otherData = new OtherData(); + otherData.setKey(key); + otherData.setKey2(subAttribute.getKey()); + otherData.setValue(subAttribute.getValue().toString()); + features.addOtherData(otherData); + } + } + else { - key = keys.next(); - OtherData keyValue = new OtherData(); - keyValue.setKey(key); - keyValue.setValue(sf[index].otherDetails.get(key).toString()); - features.addOtherData(keyValue); + OtherData otherData = new OtherData(); + otherData.setKey(key); + otherData.setValue(value.toString()); + features.addOtherData(otherData); } } - - jseq.addFeatures(features); - index++; } + + jseq.addFeatures(features); } if (jdatasq.getAllPDBEntries() != null) @@ -929,8 +952,8 @@ public class Jalview2XML if (frames[f] instanceof StructureViewerBase) { StructureViewerBase viewFrame = (StructureViewerBase) frames[f]; - matchedFile = saveStructureState(ap, jds, pdb, entry, - viewIds, matchedFile, viewFrame); + matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds, + matchedFile, viewFrame); /* * Only store each structure viewer's state once in the project * jar. First time through only (storeDS==false) @@ -946,8 +969,8 @@ public class Jalview2XML viewerState.getBytes()); } catch (IOException e) { - System.err.println("Error saving viewer state: " - + e.getMessage()); + System.err.println( + "Error saving viewer state: " + e.getMessage()); } } } @@ -963,7 +986,7 @@ public class Jalview2XML pdb.setFile(matchedFile); // entry.getFile()); if (pdbfiles == null) { - pdbfiles = new ArrayList(); + pdbfiles = new ArrayList<>(); } if (!pdbfiles.contains(pdbId)) @@ -973,17 +996,16 @@ 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(); + String key = props.nextElement(); prop.setName(key); - prop.setValue(properties.get(key)); + prop.setValue(entry.getProperty(key).toString()); item.addProperty(prop); } pdb.addPdbentryItem(item); @@ -1020,8 +1042,8 @@ public class Jalview2XML { AlcodMap alcmap = new AlcodMap(); alcmap.setDnasq(seqHash(dnas[m])); - alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, - false)); + alcmap.setMapping( + createVamsasMapping(pmaps[m], dnas[m], null, false)); alc.addAlcodMap(alcmap); hasMap = true; } @@ -1066,7 +1088,7 @@ public class Jalview2XML // SAVE TREES // ///////////////////////////////// - if (!storeDS && av.currentTree != null) + if (!storeDS && av.getCurrentTree() != null) { // FIND ANY ASSOCIATED TREES // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT @@ -1080,13 +1102,13 @@ public class Jalview2XML { TreePanel tp = (TreePanel) frames[t]; - if (tp.treeCanvas.av.getAlignment() == jal) + if (tp.getTreeCanvas().getViewport().getAlignment() == jal) { Tree tree = new Tree(); tree.setTitle(tp.getTitle()); - tree.setCurrentTree((av.currentTree == tp.getTree())); - tree.setNewick(tp.getTree().toString()); - tree.setThreshold(tp.treeCanvas.threshold); + tree.setCurrentTree((av.getCurrentTree() == tp.getTree())); + tree.setNewick(tp.getTree().print()); + tree.setThreshold(tp.getTreeCanvas().getThreshold()); tree.setFitToWindow(tp.fitToWindow.getState()); tree.setFontName(tp.getTreeFont().getName()); @@ -1113,7 +1135,7 @@ public class Jalview2XML /** * store forward refs from an annotationRow to any groups */ - IdentityHashMap groupRefs = new IdentityHashMap(); + IdentityHashMap groupRefs = new IdentityHashMap<>(); if (storeDS) { for (SequenceI sq : jal.getSequences()) @@ -1155,38 +1177,42 @@ 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()); @@ -1214,14 +1240,14 @@ 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()); if (av.getCodingComplement() != null) { view.setComplementId(av.getCodingComplement().getViewId()); } - view.setViewName(av.viewName); + view.setViewName(av.getViewName()); view.setGatheredViews(av.isGatherViewsHere()); Rectangle size = ap.av.getExplodedGeometry(); @@ -1245,15 +1271,16 @@ 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) { view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(), userColours, jms)); } - else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient) + else if (av + .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient) { AnnotationColours ac = constructAnnotationColours( (jalview.schemes.AnnotationColourGradient) av @@ -1265,27 +1292,24 @@ public class Jalview2XML } else { - view.setBgColour(ColourSchemeProperty.getColourName(av - .getGlobalColourScheme())); + view.setBgColour(ColourSchemeProperty + .getColourName(av.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()); @@ -1321,20 +1345,33 @@ public class Jalview2XML { jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); - String[] renderOrder = ap.getSeqPanel().seqCanvas - .getFeatureRenderer().getRenderOrder() - .toArray(new String[0]); + FeatureRenderer fr = ap.getSeqPanel().seqCanvas + .getFeatureRenderer(); + String[] renderOrder = fr.getRenderOrder().toArray(new String[0]); - Vector settingsAdded = new Vector(); + Vector settingsAdded = new Vector<>(); if (renderOrder != null) { for (String featureType : renderOrder) { - FeatureColourI fcol = ap.getSeqPanel().seqCanvas - .getFeatureRenderer() - .getFeatureStyle(featureType); Setting setting = new Setting(); setting.setType(featureType); + + /* + * save any filter for the feature type + */ + FeatureMatcherSetI filter = fr.getFeatureFilter(featureType); + if (filter != null) { + Iterator filters = filter.getMatchers().iterator(); + FeatureMatcherI firstFilter = filters.next(); + setting.setMatcherSet(Jalview2XML.marshalFilter( + firstFilter, filters, filter.isAnded())); + } + + /* + * save colour scheme for the feature type + */ + FeatureColourI fcol = fr.getFeatureStyle(featureType); if (!fcol.isSimpleColour()) { setting.setColour(fcol.getMaxColour().getRGB()); @@ -1342,8 +1379,25 @@ public class Jalview2XML setting.setMin(fcol.getMin()); setting.setMax(fcol.getMax()); setting.setColourByLabel(fcol.isColourByLabel()); + if (fcol.isColourByAttribute()) + { + setting.setAttributeName(fcol.getAttributeName()); + } setting.setAutoScale(fcol.isAutoScaled()); setting.setThreshold(fcol.getThreshold()); + Color noColour = fcol.getNoColour(); + if (noColour == null) + { + setting.setNoValueColour(NoValueColour.NONE); + } + else if (noColour.equals(fcol.getMaxColour())) + { + setting.setNoValueColour(NoValueColour.MAX); + } + else + { + setting.setNoValueColour(NoValueColour.MIN); + } // -1 = No threshold, 0 = Below, 1 = Above setting.setThreshstate(fcol.isAboveThreshold() ? 1 : (fcol.isBelowThreshold() ? 0 : -1)); @@ -1353,9 +1407,9 @@ public class Jalview2XML setting.setColour(fcol.getColour().getRGB()); } - setting.setDisplay(av.getFeaturesDisplayed().isVisible( - featureType)); - float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() + setting.setDisplay( + av.getFeaturesDisplayed().isVisible(featureType)); + float rorder = fr .getOrder(featureType); if (rorder > -1) { @@ -1367,10 +1421,8 @@ public class Jalview2XML } // is groups actually supposed to be a map here ? - Iterator en = ap.getSeqPanel().seqCanvas - .getFeatureRenderer() - .getFeatureGroups().iterator(); - Vector groupsAdded = new Vector(); + Iterator en = fr.getFeatureGroups().iterator(); + Vector groupsAdded = new Vector<>(); while (en.hasNext()) { String grp = en.next(); @@ -1380,9 +1432,8 @@ public class Jalview2XML } Group g = new Group(); g.setName(grp); - g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas - .getFeatureRenderer().checkGroupVisibility(grp, false)) - .booleanValue()); + g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false)) + .booleanValue()); fs.addGroup(g); groupsAdded.addElement(grp); } @@ -1391,18 +1442,18 @@ public class Jalview2XML if (av.hasHiddenColumns()) { - if (av.getColumnSelection() == null - || av.getColumnSelection().getHiddenColumns() == null) + jalview.datamodel.HiddenColumns hidden = av.getAlignment() + .getHiddenColumns(); + if (hidden == null) { warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this."); } else { - for (int c = 0; c < av.getColumnSelection().getHiddenColumns() - .size(); c++) + Iterator hiddenRegions = hidden.iterator(); + while (hiddenRegions.hasNext()) { - int[] region = av.getColumnSelection().getHiddenColumns() - .get(c); + int[] region = hiddenRegions.next(); HiddenColumns hc = new HiddenColumns(); hc.setStart(region[0]); hc.setEnd(region[1]); @@ -1441,8 +1492,8 @@ public class Jalview2XML System.out.println("Writing jar entry " + fileName); JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); - PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout, - UTF_8)); + PrintWriter pout = new PrintWriter( + new OutputStreamWriter(jout, UTF_8)); Marshaller marshaller = new Marshaller(pout); marshaller.marshal(object); pout.flush(); @@ -1643,8 +1694,8 @@ public class Jalview2XML final PDBEntry pdbentry = bindingModel.getPdbEntry(peid); final String pdbId = pdbentry.getId(); if (!pdbId.equals(entry.getId()) - && !(entry.getId().length() > 4 && entry.getId() - .toLowerCase().startsWith(pdbId.toLowerCase()))) + && !(entry.getId().length() > 4 && entry.getId().toLowerCase() + .startsWith(pdbId.toLowerCase()))) { /* * not interested in a binding to a different PDB entry here @@ -1657,8 +1708,8 @@ public class Jalview2XML } else if (!matchedFile.equals(pdbentry.getFile())) { - Cache.log - .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): " + Cache.log.warn( + "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): " + pdbentry.getFile()); } // record the @@ -1667,7 +1718,8 @@ public class Jalview2XML // match is ambiguous (e.g. // 1QIP==1qipA) - for (int smap = 0; smap < viewFrame.getBinding().getSequence()[peid].length; smap++) + for (int smap = 0; smap < viewFrame.getBinding() + .getSequence()[peid].length; smap++) { // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1) if (jds == viewFrame.getBinding().getSequence()[peid][smap]) @@ -1691,6 +1743,15 @@ 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) @@ -1698,16 +1759,17 @@ 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)); + 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()); @@ -1750,11 +1812,10 @@ public class Jalview2XML if (groupIdr == null) { // make a locally unique String - groupRefs.put( - annotation.groupRef, + groupRefs.put(annotation.groupRef, groupIdr = ("" + System.currentTimeMillis() - + annotation.groupRef.getName() + groupRefs - .size())); + + annotation.groupRef.getName() + + groupRefs.size())); } an.setGroupRef(groupIdr.toString()); } @@ -1834,7 +1895,8 @@ public class Jalview2XML } if (annotation.annotations[a].displayCharacter != null) { - ae.setDisplayCharacter(annotation.annotations[a].displayCharacter); + ae.setDisplayCharacter( + annotation.annotations[a].displayCharacter); } if (!Float.isNaN(annotation.annotations[a].value)) @@ -1845,8 +1907,8 @@ public class Jalview2XML ae.setPosition(a); if (annotation.annotations[a].secondaryStructure > ' ') { - ae.setSecondaryStructure(annotation.annotations[a].secondaryStructure - + ""); + ae.setSecondaryStructure( + annotation.annotations[a].secondaryStructure + ""); } if (annotation.annotations[a].colour != null @@ -1908,8 +1970,8 @@ public class Jalview2XML // need to be able to recover 1) settings 2) user-defined presets or // recreate settings from preset 3) predefined settings provided by // service - or settings that can be transferred (or discarded) - vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n", - "|\\n|")); + vCalcIdParam.setParameters( + settings.getWsParamFile().replace("\n", "|\\n|")); vCalcIdParam.setAutoUpdate(settings.isAutoUpdate()); // todo - decide if updateImmediately is needed for any projects. @@ -1969,8 +2031,8 @@ public class Jalview2XML } } throw new Error(MessageManager.formatMessage( - "error.unsupported_version_calcIdparam", - new Object[] { calcIdParam.toString() })); + "error.unsupported_version_calcIdparam", new Object[] + { calcIdParam.toString() })); } /** @@ -2212,8 +2274,8 @@ public class Jalview2XML for (int i = 0; i < 24; i++) { - newColours[i] = new java.awt.Color(Integer.parseInt(colours - .getUserColourScheme().getColour(i).getRGB(), 16)); + newColours[i] = new java.awt.Color(Integer.parseInt( + colours.getUserColourScheme().getColour(i).getRGB(), 16)); } jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme( @@ -2224,8 +2286,9 @@ public class Jalview2XML newColours = new java.awt.Color[23]; for (int i = 0; i < 23; i++) { - newColours[i] = new java.awt.Color(Integer.parseInt(colours - .getUserColourScheme().getColour(i + 24).getRGB(), 16)); + newColours[i] = new java.awt.Color(Integer.parseInt( + colours.getUserColourScheme().getColour(i + 24).getRGB(), + 16)); } ucs.setLowerCaseColours(newColours); } @@ -2258,7 +2321,7 @@ public class Jalview2XML try { // create list to store references for any new Jmol viewers created - newStructureViewers = new Vector(); + newStructureViewers = new Vector<>(); // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING // Workaround is to make sure caller implements the JarInputStreamProvider // interface @@ -2266,6 +2329,7 @@ public class Jalview2XML jarInputStreamProvider jprovider = createjarInputStreamProvider(file); af = loadJalviewAlign(jprovider); + af.setMenusForViewport(); } catch (MalformedURLException e) { @@ -2351,8 +2415,8 @@ public class Jalview2XML initSeqRefs(); } AlignFrame af = null, _af = null; - IdentityHashMap importedDatasets = new IdentityHashMap(); - Map gatherToThisFrame = new HashMap(); + IdentityHashMap importedDatasets = new IdentityHashMap<>(); + Map gatherToThisFrame = new HashMap<>(); final String file = jprovider.getFilename(); try { @@ -2379,8 +2443,8 @@ public class Jalview2XML if (true) // !skipViewport(object)) { _af = loadFromObject(object, file, true, jprovider); - if (_af != null - && object.getJalviewModelSequence().getViewportCount() > 0) + if (_af != null && object.getJalviewModelSequence() + .getViewportCount() > 0) { if (af == null) { @@ -2412,8 +2476,8 @@ public class Jalview2XML { ex.printStackTrace(); errorMessage = "Couldn't locate Jalview XML file : " + file; - System.err.println("Exception whilst loading jalview XML file : " - + ex + "\n"); + System.err.println( + "Exception whilst loading jalview XML file : " + ex + "\n"); } catch (Exception ex) { System.err.println("Parsing as Jalview Version 2 file failed."); @@ -2442,8 +2506,8 @@ public class Jalview2XML } ex.printStackTrace(); - System.err.println("Exception whilst loading jalview XML file : " - + ex + "\n"); + System.err.println( + "Exception whilst loading jalview XML file : " + ex + "\n"); } catch (OutOfMemoryError e) { // Don't use the OOM Window here @@ -2469,8 +2533,9 @@ public class Jalview2XML { if (ds.getCodonFrames() != null) { - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).registerMappings(ds.getCodonFrames()); + StructureSelectionManager + .getStructureSelectionManager(Desktop.instance) + .registerMappings(ds.getCodonFrames()); } } if (errorMessage != null) @@ -2493,9 +2558,9 @@ public class Jalview2XML */ protected void restoreSplitFrames() { - List gatherTo = new ArrayList(); - List addedToSplitFrames = new ArrayList(); - Map dna = new HashMap(); + List gatherTo = new ArrayList<>(); + List addedToSplitFrames = new ArrayList<>(); + Map dna = new HashMap<>(); /* * Identify the DNA alignments @@ -2527,6 +2592,8 @@ 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); @@ -2548,6 +2615,7 @@ 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"); } @@ -2617,10 +2685,11 @@ 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); } }); } @@ -2632,7 +2701,7 @@ public class Jalview2XML errorMessage = null; } - Map alreadyLoadedPDB = new HashMap(); + Map alreadyLoadedPDB = new HashMap<>(); /** * when set, local views will be updated from view stored in JalviewXML @@ -2651,14 +2720,16 @@ 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); @@ -2675,14 +2746,26 @@ 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(); @@ -2700,7 +2783,7 @@ 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; @@ -2789,8 +2872,7 @@ public class Jalview2XML List hiddenSeqs = null; - - List tmpseqs = new ArrayList(); + List tmpseqs = new ArrayList<>(); boolean multipleView = false; SequenceI referenceseqForView = null; @@ -2806,19 +2888,35 @@ public class Jalview2XML 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()); + 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 { + } + 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); - multipleView = true; } else { @@ -2842,7 +2940,7 @@ public class Jalview2XML { if (hiddenSeqs == null) { - hiddenSeqs = new ArrayList(); + hiddenSeqs = new ArrayList<>(); } hiddenSeqs.add(tmpSeq); @@ -2867,7 +2965,8 @@ public class Jalview2XML } else { - boolean isdsal = object.getJalviewModelSequence().getViewportCount() == 0; + boolean isdsal = object.getJalviewModelSequence() + .getViewportCount() == 0; if (isdsal) { // we are importing a dataset record, so @@ -2907,6 +3006,12 @@ 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) @@ -2914,32 +3019,63 @@ 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()); + 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()); - sf.setScore(features[f].getScore()); + /* + * load any feature attributes - include map-valued attributes + */ + Map> mapAttributes = new HashMap<>(); for (int od = 0; od < features[f].getOtherDataCount(); od++) { OtherData keyValue = features[f].getOtherData(od); - if (keyValue.getKey().startsWith("LINK")) + String attributeName = keyValue.getKey(); + String attributeValue = keyValue.getValue(); + if (attributeName.startsWith("LINK")) { - sf.addLink(keyValue.getValue()); + sf.addLink(attributeValue); } else { - sf.setValue(keyValue.getKey(), keyValue.getValue()); + String subAttribute = keyValue.getKey2(); + if (subAttribute == null) + { + // simple string-valued attribute + sf.setValue(attributeName, attributeValue); + } + else + { + // attribute 'key' has sub-attribute 'key2' + if (!mapAttributes.containsKey(attributeName)) + { + mapAttributes.put(attributeName, new HashMap<>()); + } + mapAttributes.get(attributeName).put(subAttribute, + attributeValue); + } } - + } + for (Entry> mapAttribute : mapAttributes + .entrySet()) + { + sf.setValue(mapAttribute.getKey(), mapAttribute.getValue()); } - 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) { @@ -2950,29 +3086,50 @@ 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()); } } - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).registerPDBEntry(entry); - al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + 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); + // 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); + } } } } @@ -3001,16 +3158,16 @@ 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(newAlcodMapRef(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); @@ -3020,12 +3177,12 @@ public class Jalview2XML // //////////////////////////////// // LOAD ANNOTATIONS - List autoAlan = new ArrayList(); + List autoAlan = new ArrayList<>(); /* * store any annotations which forward reference a group's ID */ - Map> groupAnnotRefs = new Hashtable>(); + Map> groupAnnotRefs = new Hashtable<>(); if (vamsasSet.getAnnotationCount() > 0) { @@ -3050,9 +3207,8 @@ public class Jalview2XML annotation.setAutoCalculated(true); } } - if (autoForView - || (annotation.hasAutoCalculated() && annotation - .isAutoCalculated())) + if (autoForView || (annotation.hasAutoCalculated() + && annotation.isAutoCalculated())) { // remove ID - we don't recover annotation from other views for // view-specific annotation @@ -3094,10 +3250,12 @@ public class Jalview2XML anot[anpos] = 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].getDisplayCharacter(), ae[aa].getDescription(), + (ae[aa].getSecondaryStructure() == null + || ae[aa].getSecondaryStructure().length() == 0) + ? ' ' + : ae[aa].getSecondaryStructure() + .charAt(0), ae[aa].getValue() ); @@ -3131,10 +3289,11 @@ public class Jalview2XML jaa._linecolour = firstColour; if (annotation.getThresholdLine() != null) { - jaa.setThreshold(new jalview.datamodel.GraphLine(annotation - .getThresholdLine().getValue(), annotation - .getThresholdLine().getLabel(), new java.awt.Color( - annotation.getThresholdLine().getColour()))); + jaa.setThreshold(new jalview.datamodel.GraphLine( + annotation.getThresholdLine().getValue(), + annotation.getThresholdLine().getLabel(), + new java.awt.Color( + annotation.getThresholdLine().getColour()))); } if (autoForView || annotation.isAutoCalculated()) @@ -3180,7 +3339,7 @@ public class Jalview2XML .get(an[i].getGroupRef()); if (aal == null) { - aal = new ArrayList(); + aal = new ArrayList<>(); groupAnnotRefs.put(an[i].getGroupRef(), aal); } aal.add(jaa); @@ -3262,20 +3421,16 @@ 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(); + Vector seqs = new Vector<>(); for (int s = 0; s < jGroup.getSeqCount(); s++) { @@ -3296,13 +3451,16 @@ 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()); sg.textColour2 = new java.awt.Color(jGroup.getTextCol2()); - sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup - .isShowUnconserved() : false); + sg.setShowNonconserved( + jGroup.hasShowUnconserved() ? jGroup.isShowUnconserved() + : false); sg.thresholdTextColour = jGroup.getTextColThreshold(); if (jGroup.hasShowConsensusHistogram()) { @@ -3323,9 +3481,8 @@ 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); @@ -3334,8 +3491,8 @@ public class Jalview2XML if (jGroup.getId() != null && groupAnnotRefs.size() > 0) { // re-instate unique group/annotation row reference - List jaal = groupAnnotRefs.get(jGroup - .getId()); + List jaal = groupAnnotRefs + .get(jGroup.getId()); if (jaal != null) { for (AlignmentAnnotation jaa : jaal) @@ -3363,8 +3520,8 @@ 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)); } } } @@ -3381,8 +3538,8 @@ public class Jalview2XML // to the same sequenceSet. We must modify this id on load // so that each load of the file gives a unique id String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; - String viewId = (view.getId() == null ? null : view.getId() - + uniqueSetSuffix); + String viewId = (view.getId() == null ? null + : view.getId() + uniqueSetSuffix); AlignFrame af = null; AlignViewport av = null; // now check to see if we really need to create a new viewport. @@ -3395,8 +3552,8 @@ public class Jalview2XML // XML. // and then recover its containing af to allow the settings to be applied. // TODO: fix for vamsas demo - System.err - .println("About to recover a viewport for existing alignment: Sequence set ID is " + System.err.println( + "About to recover a viewport for existing alignment: Sequence set ID is " + uniqueSeqSetId); Object seqsetobj = retrieveExistingObj(uniqueSeqSetId); if (seqsetobj != null) @@ -3404,14 +3561,14 @@ public class Jalview2XML if (seqsetobj instanceof String) { uniqueSeqSetId = (String) seqsetobj; - System.err - .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is " + System.err.println( + "Recovered extant sequence set ID mapping for ID : New Sequence set ID is " + uniqueSeqSetId); } else { - System.err - .println("Warning : Collision between sequence set ID string and existing jalview object mapping."); + System.err.println( + "Warning : Collision between sequence set ID string and existing jalview object mapping."); } } @@ -3420,8 +3577,8 @@ public class Jalview2XML * indicate that annotation colours are applied across all groups (pre * Jalview 2.8.1 behaviour) */ - boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan( - "2.8.1", object.getVersion()); + boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1", + object.getVersion()); AlignmentPanel ap = null; boolean isnewview = true; @@ -3496,15 +3653,15 @@ public class Jalview2XML for (int i = 0; i < jseq.getRnaViewerCount(); i++) { RnaViewer viewer = jseq.getRnaViewer(i); - AppVarna appVarna = findOrCreateVarnaViewer(viewer, - uniqueSetSuffix, ap); + AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix, + ap); for (int j = 0; j < viewer.getSecondaryStructureCount(); j++) { SecondaryStructure ss = viewer.getSecondaryStructure(j); SequenceI seq = seqRefIds.get(jseq.getId()); - AlignmentAnnotation ann = this.annotationIds.get(ss - .getAnnotationId()); + AlignmentAnnotation ann = this.annotationIds + .get(ss.getAnnotationId()); /* * add the structure to the Varna display (with session state copied @@ -3514,7 +3671,7 @@ 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); } @@ -3558,10 +3715,9 @@ public class Jalview2XML /* * viewer not found - make it */ - RnaViewerModel model = new RnaViewerModel(postLoadId, - viewer.getTitle(), viewer.getXpos(), viewer.getYpos(), - viewer.getWidth(), viewer.getHeight(), - viewer.getDividerLocation()); + RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(), + viewer.getXpos(), viewer.getYpos(), viewer.getWidth(), + viewer.getHeight(), viewer.getDividerLocation()); AppVarna varna = new AppVarna(model, ap); return varna; @@ -3590,7 +3746,7 @@ 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()); @@ -3605,13 +3761,13 @@ public class Jalview2XML // TODO: should check if tp has been manipulated by user - if so its // settings shouldn't be modified tp.setTitle(tree.getTitle()); - tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree - .getWidth(), tree.getHeight())); - tp.av = av; // af.viewport; // TODO: verify 'associate with all + tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), + tree.getWidth(), tree.getHeight())); + tp.setViewport(av); // af.viewport; // TODO: verify 'associate with all // views' // works still - tp.treeCanvas.av = av; // af.viewport; - tp.treeCanvas.ap = ap; // af.alignPanel; + tp.getTreeCanvas().setViewport(av); // af.viewport; + tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel; } if (tp == null) @@ -3626,20 +3782,20 @@ public class Jalview2XML if (tree.getFontName() != null) { - tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree - .getFontStyle(), tree.getFontSize())); + tp.setTreeFont(new java.awt.Font(tree.getFontName(), + tree.getFontStyle(), tree.getFontSize())); } else { - tp.setTreeFont(new java.awt.Font(view.getFontName(), view - .getFontStyle(), tree.getFontSize())); + tp.setTreeFont(new java.awt.Font(view.getFontName(), + view.getFontStyle(), tree.getFontSize())); } tp.showPlaceholders(tree.getMarkUnlinked()); tp.showBootstrap(tree.getShowBootstrap()); tp.showDistances(tree.getShowDistances()); - tp.treeCanvas.threshold = tree.getThreshold(); + tp.getTreeCanvas().setThreshold(tree.getThreshold()); if (tree.getCurrentTree()) { @@ -3668,7 +3824,7 @@ public class Jalview2XML * Run through all PDB ids on the alignment, and collect mappings between * distinct view ids and all sequences referring to that view. */ - Map structureViewers = new LinkedHashMap(); + Map structureViewers = new LinkedHashMap<>(); for (int i = 0; i < jseqs.length; i++) { @@ -3689,7 +3845,8 @@ 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(); @@ -3700,13 +3857,14 @@ 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()); - jalview.datamodel.SequenceI seq = seqRefIds.get(jseqs[i] - .getId() + ""); + String pdbFile = loadPDBFile(jprovider, ids[p].getId(), + ids[p].getFile()); + jalview.datamodel.SequenceI seq = seqRefIds + .get(jseqs[i].getId() + ""); if (sviewid == null) { - sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width - + "," + height; + sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + "," + + height; } if (!structureViewers.containsKey(sviewid)) { @@ -3725,8 +3883,9 @@ public class Jalview2XML // linkAlignPanel,superposeWithAlignpanel}} from hash StructureViewerModel jmoldat = structureViewers.get(sviewid); jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel() - | (structureState.hasAlignwithAlignPanel() ? structureState - .getAlignwithAlignPanel() : false)); + | (structureState.hasAlignwithAlignPanel() + ? structureState.getAlignwithAlignPanel() + : false)); /* * Default colour by linked panel to false if not specified (e.g. @@ -3734,8 +3893,9 @@ public class Jalview2XML */ boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel(); colourWithAlignPanel |= (structureState - .hasColourwithAlignPanel() ? structureState - .getColourwithAlignPanel() : false); + .hasColourwithAlignPanel() + ? structureState.getColourwithAlignPanel() + : false); jmoldat.setColourWithAlignPanel(colourWithAlignPanel); /* @@ -3743,8 +3903,9 @@ public class Jalview2XML * pre-2.7 projects) */ boolean colourByViewer = jmoldat.isColourByViewer(); - colourByViewer &= structureState.hasColourByJmol() ? structureState - .getColourByJmol() : true; + colourByViewer &= structureState.hasColourByJmol() + ? structureState.getColourByJmol() + : true; jmoldat.setColourByViewer(colourByViewer); if (jmoldat.getStateData().length() < structureState @@ -3760,8 +3921,7 @@ public class Jalview2XML StructureData seqstrmaps = jmoldat.getFileData().get(mapkey); if (seqstrmaps == null) { - jmoldat.getFileData().put( - mapkey, + jmoldat.getFileData().put(mapkey, seqstrmaps = jmoldat.new StructureData(pdbFile, ids[p].getId())); } @@ -3789,8 +3949,8 @@ public class Jalview2XML createOrLinkStructureViewer(entry, af, ap, jprovider); } catch (Exception e) { - System.err.println("Error loading structure viewer: " - + e.getMessage()); + System.err.println( + "Error loading structure viewer: " + e.getMessage()); // failed - try the next one } } @@ -3860,12 +4020,12 @@ public class Jalview2XML */ String viewerJarEntryName = getViewerJarEntryName(data.getViewId()); chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName, - "chimera"); + "chimera", null); Set> fileData = data.getFileData() .entrySet(); - List pdbs = new ArrayList(); - List allseqs = new ArrayList(); + List pdbs = new ArrayList<>(); + List allseqs = new ArrayList<>(); for (Entry pdb : fileData) { String filePath = pdb.getValue().getFilePath(); @@ -3882,8 +4042,8 @@ public class Jalview2XML // TODO use StructureViewer as a factory here, see JAL-1761 final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]); - final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs - .size()][]); + final SequenceI[][] seqsArray = allseqs + .toArray(new SequenceI[allseqs.size()][]); String newViewId = viewerData.getKey(); ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile, @@ -3921,9 +4081,9 @@ public class Jalview2XML getViewerJarEntryName(svattrib.getViewId())); } - List pdbfilenames = new ArrayList(); - List seqmaps = new ArrayList(); - List pdbids = new ArrayList(); + List pdbfilenames = new ArrayList<>(); + List seqmaps = new ArrayList<>(); + List pdbids = new ArrayList<>(); StringBuilder newFileLoc = new StringBuilder(64); int cp = 0, ncp, ecp; Map oldFiles = svattrib.getFileData(); @@ -3941,6 +4101,11 @@ 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()); @@ -3989,8 +4154,8 @@ public class Jalview2XML */ histbug += 10; int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug); - String val = (diff == -1) ? null : newFileLoc - .substring(histbug, diff); + String val = (diff == -1) ? null + : newFileLoc.substring(histbug, diff); if (val != null && val.length() >= 4) { if (val.contains("e")) // eh? what can it be? @@ -4008,8 +4173,8 @@ public class Jalview2XML } } - final String[] pdbf = pdbfilenames.toArray(new String[pdbfilenames - .size()]); + final String[] pdbf = pdbfilenames + .toArray(new String[pdbfilenames.size()]); final String[] id = pdbids.toArray(new String[pdbids.size()]); final SequenceI[][] sq = seqmaps .toArray(new SequenceI[seqmaps.size()][]); @@ -4028,10 +4193,11 @@ public class Jalview2XML JalviewStructureDisplayI sview = null; try { - sview = new StructureViewer(alf.alignPanel - .getStructureSelectionManager()).createView( - StructureViewer.ViewerType.JMOL, pdbf, id, sq, - alf.alignPanel, svattrib, fileloc, rect, sviewid); + sview = new StructureViewer( + alf.alignPanel.getStructureSelectionManager()) + .createView(StructureViewer.ViewerType.JMOL, + pdbf, id, sq, alf.alignPanel, svattrib, + fileloc, rect, sviewid); addNewStructureViewer(sview); } catch (OutOfMemoryError ex) { @@ -4091,9 +4257,8 @@ public class Jalview2XML /* * Post jalview 2.4 schema includes structure view id */ - if (sviewid != null - && ((StructureViewerBase) frame).getViewId() - .equals(sviewid)) + if (sviewid != null && ((StructureViewerBase) frame).getViewId() + .equals(sviewid)) { comp = (StructureViewerBase) frame; break; // break added in 2.9 @@ -4146,7 +4311,8 @@ 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, DataSourceType.FILE); + binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE, + null); binding.addSequenceForStructFile(pdbFile, seq); } // and add the AlignmentPanel's reference to the view panel @@ -4265,8 +4431,9 @@ public class Jalview2XML for (int i = 0; i < JSEQ.length; i++) { - af.viewport.setSequenceColour(af.viewport.getAlignment() - .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); + af.viewport.setSequenceColour( + af.viewport.getAlignment().getSequenceAt(i), + new java.awt.Color(JSEQ[i].getColour())); } if (al.hasSeqrep()) @@ -4306,8 +4473,8 @@ public class Jalview2XML for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++) { isRepresentative = true; - SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s] - .getHiddenSequences(r)); + 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); @@ -4320,31 +4487,25 @@ public class Jalview2XML } } - SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs - .size()]); + SequenceI[] hseqs = hiddenSeqs + .toArray(new SequenceI[hiddenSeqs.size()]); af.viewport.hideSequence(hseqs); } // 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.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( - new java.awt.Font(view.getFontName(), view.getFontStyle(), view - .getFontSize()), true); + af.viewport.setFont(new java.awt.Font(view.getFontName(), + view.getFontStyle(), view.getFontSize()), true); ViewStyleI vs = af.viewport.getViewStyle(); vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna()); af.viewport.setViewStyle(vs); @@ -4361,10 +4522,18 @@ public class Jalview2XML af.viewport.setTextColour(new java.awt.Color(view.getTextCol1())); af.viewport.setTextColour2(new java.awt.Color(view.getTextCol2())); 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.setShowUnconserved( + view.hasShowUnconserved() ? view.isShowUnconserved() : false); + af.viewport.getRanges().setStartRes(view.getStartRes()); + + if (view.getViewName() != null) + { + af.viewport.setViewName(view.getViewName()); + af.setInitialTabVisible(); + } + af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), + view.getHeight()); + // startSeq set in af.alignPanel.updateLayout below af.alignPanel.updateLayout(); ColourSchemeI cs = null; // apply colourschemes @@ -4384,22 +4553,21 @@ 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(), + view.getIgnoreGapsinConsensus()); + 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); @@ -4427,8 +4595,8 @@ public class Jalview2XML } if (view.hasShowConsensusHistogram()) { - af.viewport.setShowConsensusHistogram(view - .getShowConsensusHistogram()); + af.viewport + .setShowConsensusHistogram(view.getShowConsensusHistogram()); } else { @@ -4471,27 +4639,67 @@ public class Jalview2XML af.viewport.setShowGroupConservation(false); } - // recover featre settings + // recover feature settings if (jms.getFeatureSettings() != null) { + FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas + .getFeatureRenderer(); FeaturesDisplayed fdi; af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; - Map featureColours = new Hashtable(); - Map featureOrder = new Hashtable(); + Map featureColours = new Hashtable<>(); + Map featureOrder = new Hashtable<>(); - for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) + for (int fs = 0; fs < jms.getFeatureSettings() + .getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); + String featureType = setting.getType(); + + /* + * restore feature filters (if any) + */ + MatcherSet filters = setting.getMatcherSet(); + if (filters != null) + { + FeatureMatcherSetI filter = Jalview2XML + .unmarshalFilter(featureType, filters); + if (!filter.isEmpty()) + { + fr.setFeatureFilter(featureType, filter); + } + } + + /* + * restore feature colour scheme + */ + Color maxColour = new Color(setting.getColour()); if (setting.hasMincolour()) { - 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); + /* + * minColour is always set unless a simple colour + * (including for colour by label though it doesn't use it) + */ + Color minColour = new Color(setting.getMincolour()); + Color noValueColour = minColour; + NoValueColour noColour = setting.getNoValueColour(); + if (noColour == NoValueColour.NONE) + { + noValueColour = null; + } + else if (noColour == NoValueColour.MAX) + { + noValueColour = maxColour; + } + float min = setting.hasMin() ? setting.getMin() : 0f; + float max = setting.hasMin() ? setting.getMax() : 1f; + FeatureColourI gc = new FeatureColour(minColour, maxColour, + noValueColour, min, max); + if (setting.getAttributeNameCount() > 0) + { + gc.setAttributeName(setting.getAttributeName()); + } if (setting.hasThreshold()) { gc.setThreshold(setting.getThreshold()); @@ -4516,29 +4724,29 @@ public class Jalview2XML gc.setColourByLabel(setting.getColourByLabel()); } // and put in the feature colour table. - featureColours.put(setting.getType(), gc); + featureColours.put(featureType, gc); } else { - featureColours.put(setting.getType(), new FeatureColour( - new Color(setting.getColour()))); + featureColours.put(featureType, + new FeatureColour(maxColour)); } - renderOrder[fs] = setting.getType(); + renderOrder[fs] = featureType; if (setting.hasOrder()) { - featureOrder.put(setting.getType(), setting.getOrder()); + featureOrder.put(featureType, setting.getOrder()); } else { - featureOrder.put(setting.getType(), new Float(fs - / jms.getFeatureSettings().getSettingCount())); + featureOrder.put(featureType, new Float( + fs / jms.getFeatureSettings().getSettingCount())); } if (setting.getDisplay()) { - fdi.setVisible(setting.getType()); + fdi.setVisible(featureType); } } - Map fgtable = new Hashtable(); + Map fgtable = new Hashtable<>(); for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) { Group grp = jms.getFeatureSettings().getGroup(gs); @@ -4547,20 +4755,18 @@ public class Jalview2XML // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ? // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder); - FeatureRendererSettings frs = new FeatureRendererSettings( - renderOrder, fgtable, featureColours, 1.0f, featureOrder); - af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings(frs); - + FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, + fgtable, featureColours, 1.0f, featureOrder); + fr.transferSettings(frs); } if (view.getHiddenColumnsCount() > 0) { for (int c = 0; c < view.getHiddenColumnsCount(); c++) { - af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view - .getHiddenColumns(c).getEnd() // +1 - ); + af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), + view.getHiddenColumns(c).getEnd() // +1 + ); } } if (view.getCalcIdParam() != null) @@ -4605,12 +4811,21 @@ 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, 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) @@ -4618,113 +4833,93 @@ 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; @@ -4743,7 +4938,7 @@ public class Jalview2XML String[] magicNames = new String[] { "Consensus", "Quality", "Conservation" }; JvAnnotRow nullAnnot = new JvAnnotRow(-1, null); - Hashtable visan = new Hashtable(); + Hashtable visan = new Hashtable<>(); for (String nm : magicNames) { visan.put(nm, nullAnnot); @@ -4751,15 +4946,16 @@ public class Jalview2XML for (JvAnnotRow auan : autoAlan) { visan.put(auan.template.label - + (auan.template.getCalcId() == null ? "" : "\t" - + auan.template.getCalcId()), auan); + + (auan.template.getCalcId() == null ? "" + : "\t" + auan.template.getCalcId()), + auan); } int hSize = al.getAlignmentAnnotation().length; - List reorder = new ArrayList(); + List reorder = new ArrayList<>(); // work through any autoCalculated annotation already on the view // removing it if it should be placed in a different location on the // annotation panel. - List remains = new ArrayList(visan.keySet()); + List remains = new ArrayList<>(visan.keySet()); for (int h = 0; h < hSize; h++) { jalview.datamodel.AlignmentAnnotation jalan = al @@ -4855,8 +5051,9 @@ public class Jalview2XML return false; } String id; - if (skipList.containsKey(id = object.getJalviewModelSequence() - .getViewport()[0].getSequenceSetId())) + if (skipList.containsKey( + id = object.getJalviewModelSequence().getViewport()[0] + .getSequenceSetId())) { if (Cache.log != null && Cache.log.isDebugEnabled()) { @@ -4888,8 +5085,8 @@ public class Jalview2XML private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al, boolean ignoreUnrefed) { - jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet - .getDatasetId()); + jalview.datamodel.AlignmentI ds = getDatasetFor( + vamsasSet.getDatasetId()); Vector dseqs = null; if (ds == null) { @@ -4899,7 +5096,7 @@ 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) @@ -4926,18 +5123,29 @@ 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; @@ -5027,12 +5235,41 @@ public class Jalview2XML } // TODO: merges will never happen if we 'know' we have the real dataset // sequence - this should be detected when id==dssid - System.err - .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // (" + System.err.println( + "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // (" // + (pre ? "prepended" : "") + " " // + (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); + } + } + } } /* @@ -5047,7 +5284,7 @@ public class Jalview2XML { if (datasetIds == null) { - datasetIds = new Hashtable(); + datasetIds = new Hashtable<>(); return null; } if (datasetIds.containsKey(datasetId)) @@ -5061,7 +5298,7 @@ public class Jalview2XML { if (datasetIds == null) { - datasetIds = new Hashtable(); + datasetIds = new Hashtable<>(); } datasetIds.put(datasetId, dataset); } @@ -5084,7 +5321,7 @@ public class Jalview2XML // make a new datasetId and record it if (dataset2Ids == null) { - dataset2Ids = new IdentityHashMap(); + dataset2Ids = new IdentityHashMap<>(); } else { @@ -5105,8 +5342,9 @@ public class Jalview2XML { DBRef dr = sequence.getDBRef(d); jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry( - sequence.getDBRef(d).getSource(), sequence.getDBRef(d) - .getVersion(), sequence.getDBRef(d).getAccessionId()); + sequence.getDBRef(d).getSource(), + sequence.getDBRef(d).getVersion(), + sequence.getDBRef(d).getAccessionId()); if (dr.getMapping() != null) { entry.setMap(addMapping(dr.getMapping())); @@ -5135,8 +5373,8 @@ public class Jalview2XML fto[_i] = mf.getStart(); fto[_i + 1] = mf.getEnd(); } - jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, - fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit()); + jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr, + fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit()); if (m.getMappingChoice() != null) { MappingChoice mc = m.getMappingChoice(); @@ -5172,8 +5410,8 @@ public class Jalview2XML } else { - System.err - .println("Warning - making up dataset sequence id for DbRef sequence map reference"); + System.err.println( + "Warning - making up dataset sequence id for DbRef sequence map reference"); sqid = ((Object) ms).toString(); // make up a new hascode for // undefined dataset sequence hash // (unlikely to happen) @@ -5203,28 +5441,25 @@ public class Jalview2XML } - public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, - boolean keepSeqRefs) + /** + * Provides a 'copy' of an alignment view (on action New View) by 'saving' the + * view as XML (but not to file), and then reloading it + * + * @param ap + * @return + */ + public AlignmentPanel copyAlignPanel(AlignmentPanel ap) { initSeqRefs(); JalviewModel jm = saveState(ap, null, null, null); - if (!keepSeqRefs) - { - clearSeqRefs(); - jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null); - } - else - { - uniqueSetSuffix = ""; - jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't - // overwrite the - // view we just - // copied - } + uniqueSetSuffix = ""; + jm.getJalviewModelSequence().getViewport(0).setId(null); + // we don't overwrite the view we just copied + if (this.frefedSequence == null) { - frefedSequence = new Vector(); + frefedSequence = new Vector<>(); } viewportsAdded.clear(); @@ -5244,32 +5479,8 @@ public class Jalview2XML return af.alignPanel; } - /** - * flag indicating if hashtables should be cleared on finalization TODO this - * flag may not be necessary - */ - private final boolean _cleartables = true; - private Hashtable jvids2vobj; - /* - * (non-Javadoc) - * - * @see java.lang.Object#finalize() - */ - @Override - protected void finalize() throws Throwable - { - // really make sure we have no buried refs left. - if (_cleartables) - { - clearSeqRefs(); - } - this.seqRefIds = null; - this.seqsToIds = null; - super.finalize(); - } - private void warn(String msg) { warn(msg, null); @@ -5363,11 +5574,11 @@ public class Jalview2XML // register sequence object so the XML parser can recover it. if (seqRefIds == null) { - seqRefIds = new HashMap(); + seqRefIds = new HashMap<>(); } if (seqsToIds == null) { - seqsToIds = new IdentityHashMap(); + seqsToIds = new IdentityHashMap<>(); } seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj); seqsToIds.put((SequenceI) jvobj, id); @@ -5500,4 +5711,289 @@ public class Jalview2XML { return counter++; } + + /** + * Populates an XML model of the feature colour scheme for one feature type + * + * @param featureType + * @param fcol + * @return + */ + protected static jalview.schemabinding.version2.Colour marshalColour( + String featureType, FeatureColourI fcol) + { + jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); + if (fcol.isSimpleColour()) + { + col.setRGB(Format.getHexString(fcol.getColour())); + } + else + { + col.setRGB(Format.getHexString(fcol.getMaxColour())); + col.setMin(fcol.getMin()); + col.setMax(fcol.getMax()); + col.setMinRGB(jalview.util.Format.getHexString(fcol.getMinColour())); + col.setAutoScale(fcol.isAutoScaled()); + col.setThreshold(fcol.getThreshold()); + col.setColourByLabel(fcol.isColourByLabel()); + col.setThreshType(fcol.isAboveThreshold() ? ColourThreshTypeType.ABOVE + : (fcol.isBelowThreshold() ? ColourThreshTypeType.BELOW + : ColourThreshTypeType.NONE)); + if (fcol.isColourByAttribute()) + { + col.setAttributeName(fcol.getAttributeName()); + } + Color noColour = fcol.getNoColour(); + if (noColour == null) + { + col.setNoValueColour(NoValueColour.NONE); + } + else if (noColour == fcol.getMaxColour()) + { + col.setNoValueColour(NoValueColour.MAX); + } + else + { + col.setNoValueColour(NoValueColour.MIN); + } + } + col.setName(featureType); + return col; + } + + /** + * Populates an XML model of the feature filter(s) for one feature type + * + * @param firstMatcher + * the first (or only) match condition) + * @param filter + * remaining match conditions (if any) + * @param and + * if true, conditions are and-ed, else or-ed + */ + protected static MatcherSet marshalFilter(FeatureMatcherI firstMatcher, + Iterator filters, boolean and) + { + MatcherSet result = new MatcherSet(); + + if (filters.hasNext()) + { + /* + * compound matcher + */ + CompoundMatcher compound = new CompoundMatcher(); + compound.setAnd(and); + MatcherSet matcher1 = marshalFilter(firstMatcher, + Collections.emptyIterator(), and); + compound.addMatcherSet(matcher1); + FeatureMatcherI nextMatcher = filters.next(); + MatcherSet matcher2 = marshalFilter(nextMatcher, filters, and); + compound.addMatcherSet(matcher2); + result.setCompoundMatcher(compound); + } + else + { + /* + * single condition matcher + */ + MatchCondition matcherModel = new MatchCondition(); + matcherModel.setCondition( + firstMatcher.getMatcher().getCondition().getStableName()); + matcherModel.setValue(firstMatcher.getMatcher().getPattern()); + if (firstMatcher.isByAttribute()) + { + matcherModel.setBy(FeatureMatcherByType.BYATTRIBUTE); + matcherModel.setAttributeName(firstMatcher.getAttribute()); + } + else if (firstMatcher.isByLabel()) + { + matcherModel.setBy(FeatureMatcherByType.BYLABEL); + } + else if (firstMatcher.isByScore()) + { + matcherModel.setBy(FeatureMatcherByType.BYSCORE); + } + result.setMatchCondition(matcherModel); + } + + return result; + } + + /** + * Loads one XML model of a feature filter to a Jalview object + * + * @param featureType + * @param matcherSetModel + * @return + */ + protected static FeatureMatcherSetI unmarshalFilter( + String featureType, MatcherSet matcherSetModel) + { + FeatureMatcherSetI result = new FeatureMatcherSet(); + try + { + unmarshalFilterConditions(result, matcherSetModel, true); + } catch (IllegalStateException e) + { + // mixing AND and OR conditions perhaps + System.err.println( + String.format("Error reading filter conditions for '%s': %s", + featureType, e.getMessage())); + // return as much as was parsed up to the error + } + + return result; + } + + /** + * Adds feature match conditions to matcherSet as unmarshalled from XML + * (possibly recursively for compound conditions) + * + * @param matcherSet + * @param matcherSetModel + * @param and + * if true, multiple conditions are AND-ed, else they are OR-ed + * @throws IllegalStateException + * if AND and OR conditions are mixed + */ + protected static void unmarshalFilterConditions( + FeatureMatcherSetI matcherSet, MatcherSet matcherSetModel, + boolean and) + { + MatchCondition mc = matcherSetModel.getMatchCondition(); + if (mc != null) + { + /* + * single condition + */ + FeatureMatcherByType filterBy = mc.getBy(); + Condition cond = Condition.fromString(mc.getCondition()); + String pattern = mc.getValue(); + FeatureMatcherI matchCondition = null; + if (filterBy == FeatureMatcherByType.BYLABEL) + { + matchCondition = FeatureMatcher.byLabel(cond, pattern); + } + else if (filterBy == FeatureMatcherByType.BYSCORE) + { + matchCondition = FeatureMatcher.byScore(cond, pattern); + + } + else if (filterBy == FeatureMatcherByType.BYATTRIBUTE) + { + String[] attNames = mc.getAttributeName(); + matchCondition = FeatureMatcher.byAttribute(cond, pattern, + attNames); + } + + /* + * note this throws IllegalStateException if AND-ing to a + * previously OR-ed compound condition, or vice versa + */ + if (and) + { + matcherSet.and(matchCondition); + } + else + { + matcherSet.or(matchCondition); + } + } + else + { + /* + * compound condition + */ + MatcherSet[] matchers = matcherSetModel.getCompoundMatcher() + .getMatcherSet(); + boolean anded = matcherSetModel.getCompoundMatcher().getAnd(); + if (matchers.length == 2) + { + unmarshalFilterConditions(matcherSet, matchers[0], anded); + unmarshalFilterConditions(matcherSet, matchers[1], anded); + } + else + { + System.err.println("Malformed compound filter condition"); + } + } + } + + /** + * Loads one XML model of a feature colour to a Jalview object + * + * @param colourModel + * @return + */ + protected static FeatureColourI unmarshalColour( + jalview.schemabinding.version2.Colour colourModel) + { + FeatureColourI colour = null; + + if (colourModel.hasMax()) + { + Color mincol = null; + Color maxcol = null; + Color noValueColour = null; + + try + { + mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16)); + maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16)); + } catch (Exception e) + { + Cache.log.warn("Couldn't parse out graduated feature color.", e); + } + + NoValueColour noCol = colourModel.getNoValueColour(); + if (noCol == NoValueColour.MIN) + { + noValueColour = mincol; + } + else if (noCol == NoValueColour.MAX) + { + noValueColour = maxcol; + } + + colour = new FeatureColour(mincol, maxcol, noValueColour, + colourModel.getMin(), + colourModel.getMax()); + String[] attributes = colourModel.getAttributeName(); + if (attributes != null && attributes.length > 0) + { + colour.setAttributeName(attributes); + } + if (colourModel.hasAutoScale()) + { + colour.setAutoScaled(colourModel.getAutoScale()); + } + if (colourModel.hasColourByLabel()) + { + colour.setColourByLabel(colourModel.getColourByLabel()); + } + if (colourModel.hasThreshold()) + { + colour.setThreshold(colourModel.getThreshold()); + } + ColourThreshTypeType ttyp = colourModel.getThreshType(); + if (ttyp != null) + { + if (ttyp == ColourThreshTypeType.ABOVE) + { + colour.setAboveThreshold(true); + } + else if (ttyp == ColourThreshTypeType.BELOW) + { + colour.setBelowThreshold(true); + } + } + } + else + { + Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16)); + colour = new FeatureColour(color); + } + + return colour; + } }