X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=aed73d6e6086b76c2e14a5a105ba2e31292bc262;hb=f37c3fd4fe12799de498de5f397252e9f457fee9;hp=9e319c1f38e2b6d581c4c4b5626b22bb0c73615b;hpb=bf8275c621048462bd0275e31bf490dca443b477;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 9e319c1..aed73d6 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -30,6 +30,7 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.GraphLine; +import jalview.datamodel.HiddenMarkovModel; import jalview.datamodel.PDBEntry; import jalview.datamodel.RnaViewerModel; import jalview.datamodel.SequenceFeature; @@ -37,10 +38,15 @@ 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.io.HMMFile; import jalview.renderer.ResidueShaderI; import jalview.schemabinding.version2.AlcodMap; import jalview.schemabinding.version2.AlcodonFrame; @@ -48,6 +54,7 @@ import jalview.schemabinding.version2.Annotation; import jalview.schemabinding.version2.AnnotationColours; import jalview.schemabinding.version2.AnnotationElement; import jalview.schemabinding.version2.CalcIdParam; +import jalview.schemabinding.version2.CompoundMatcher; import jalview.schemabinding.version2.DBRef; import jalview.schemabinding.version2.Features; import jalview.schemabinding.version2.Group; @@ -60,6 +67,8 @@ 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; @@ -75,6 +84,9 @@ 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; @@ -83,10 +95,12 @@ 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; @@ -115,6 +129,7 @@ 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; @@ -153,6 +168,8 @@ public class Jalview2XML private static final String RNA_PREFIX = "rna_"; + private static final String HMMER_PREFIX = "hmmer_"; + private static final String UTF_8 = "UTF-8"; // use this with nextCounter() to make unique names for entities @@ -216,34 +233,6 @@ 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) @@ -881,55 +870,28 @@ public class Jalview2XML } } - // TODO: omit sequence features from each alignment view's XML dump if we - // are storing dataset - List sfs = jds - .getSequenceFeatures(); + /* + * save sequence features + * TODO: omit sequence features from each alignment view's + * XML dump if we are storing dataset + */ + List sfs = jds.getSequenceFeatures(); for (SequenceFeature sf : sfs) { - Features features = new Features(); - - 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++) - { - OtherData keyValue = new OtherData(); - keyValue.setKey("LINK_" + l); - keyValue.setValue(sf.links.elementAt(l).toString()); - features.addOtherData(keyValue); - } - } - if (sf.otherDetails != null) - { - String key; - Iterator keys = sf.otherDetails.keySet().iterator(); - while (keys.hasNext()) - { - key = keys.next(); - OtherData keyValue = new OtherData(); - keyValue.setKey(key); - keyValue.setValue(sf.otherDetails.get(key).toString()); - features.addOtherData(keyValue); - } - } - + Features features = saveFeature(sf); jseq.addFeatures(features); } + /* + * save PDB entries for sequence + */ if (jdatasq.getAllPDBEntries() != null) { - Enumeration en = jdatasq.getAllPDBEntries().elements(); + Enumeration en = jdatasq.getAllPDBEntries().elements(); while (en.hasMoreElements()) { Pdbids pdb = new Pdbids(); - jalview.datamodel.PDBEntry entry = (jalview.datamodel.PDBEntry) en - .nextElement(); + PDBEntry entry = en.nextElement(); String pdbId = entry.getId(); pdb.setId(pdbId); @@ -1013,6 +975,11 @@ public class Jalview2XML saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS); + if (jds.hasHMMProfile()) + { + saveHmmerProfile(jout, jseq, jds); + } + jms.addJSeq(jseq); } @@ -1219,7 +1186,7 @@ public class Jalview2XML jGroup.setTextCol2(sg.textColour2.getRGB()); jGroup.setTextColThreshold(sg.thresholdTextColour); jGroup.setShowUnconserved(sg.getShowNonconserved()); - jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); + jGroup.setIgnoreGapsinConsensus(sg.isIgnoreGapsConsensus()); jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram()); jGroup.setShowSequenceLogo(sg.isShowSequenceLogo()); jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo()); @@ -1341,19 +1308,33 @@ 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<>(); 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()); @@ -1361,8 +1342,25 @@ 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)); @@ -1374,7 +1372,7 @@ public class Jalview2XML setting.setDisplay( av.getFeaturesDisplayed().isVisible(featureType)); - float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() + float rorder = fr .getOrder(featureType); if (rorder > -1) { @@ -1386,8 +1384,7 @@ public class Jalview2XML } // is groups actually supposed to be a map here ? - Iterator en = ap.getSeqPanel().seqCanvas - .getFeatureRenderer().getFeatureGroups().iterator(); + Iterator en = fr.getFeatureGroups().iterator(); Vector groupsAdded = new Vector<>(); while (en.hasNext()) { @@ -1398,8 +1395,7 @@ public class Jalview2XML } Group g = new Group(); g.setName(grp); - g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas - .getFeatureRenderer().checkGroupVisibility(grp, false)) + g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false)) .booleanValue()); fs.addGroup(g); groupsAdded.addElement(grp); @@ -1417,9 +1413,10 @@ public class Jalview2XML } else { - ArrayList hiddenRegions = hidden.getHiddenColumnsCopy(); - for (int[] region : hiddenRegions) + Iterator hiddenRegions = hidden.iterator(); + while (hiddenRegions.hasNext()) { + int[] region = hiddenRegions.next(); HiddenColumns hc = new HiddenColumns(); hc.setStart(region[0]); hc.setEnd(region[1]); @@ -1474,6 +1471,98 @@ public class Jalview2XML } /** + * Saves the HMMER profile associated with the sequence as a file in the jar, + * in HMMER format, and saves the name of the file as a child element of the + * XML sequence element + * + * @param jout + * @param xmlSeq + * @param seq + */ + protected void saveHmmerProfile(JarOutputStream jout, JSeq xmlSeq, + SequenceI seq) + { + HiddenMarkovModel profile = seq.getHMM(); + if (profile == null) + { + warn("Want to save HMM profile for " + seq.getName() + + " but none found"); + return; + } + HMMFile hmmFile = new HMMFile(profile); + String hmmAsString = hmmFile.print(); + String jarEntryName = HMMER_PREFIX + nextCounter(); + try + { + writeJarEntry(jout, jarEntryName, hmmAsString.getBytes()); + xmlSeq.setHmmerProfile(jarEntryName); + } catch (IOException e) + { + warn("Error saving HMM profile: " + e.getMessage()); + } + } + + /** + * Converts a Jalview SequenceFeature into the XML model of it to save + * + * @param sf + * @return + */ + protected Features saveFeature(SequenceFeature sf) + { + Features features = new Features(); + + 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++) + { + OtherData keyValue = new OtherData(); + keyValue.setKey("LINK_" + l); + keyValue.setValue(sf.links.elementAt(l).toString()); + features.addOtherData(keyValue); + } + } + 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 = 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 + { + OtherData otherData = new OtherData(); + otherData.setKey(key); + otherData.setValue(value.toString()); + features.addOtherData(otherData); + } + } + } + return features; + } + + /** * Save any Varna viewers linked to this sequence. Writes an rnaViewer element * for each viewer, with *
    @@ -1674,9 +1763,8 @@ 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): " - + pdbentry.getFile()); + warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): " + + pdbentry.getFile()); } // record the // file so we @@ -2160,12 +2248,12 @@ public class Jalview2XML mpc.setDseqFor(jmpid); if (!seqRefIds.containsKey(mpc.getDseqFor())) { - jalview.bin.Cache.log.debug("creatign new DseqFor ID"); + debug("creating new DseqFor ID"); seqRefIds.put(mpc.getDseqFor(), ps); } else { - jalview.bin.Cache.log.debug("reusing DseqFor ID"); + debug("reusing DseqFor ID"); } mp.setMappingChoice(mpc); @@ -2980,40 +3068,68 @@ public class Jalview2XML // for (int i = 0; i < vamsasSeq.length; i++) { + SequenceI alignmentSeq = al.getSequenceAt(i); if (jseqs[i].getFeaturesCount() > 0) { Features[] features = jseqs[i].getFeatures(); for (int f = 0; f < features.length; f++) { - SequenceFeature sf = new SequenceFeature(features[f].getType(), - features[f].getDescription(), features[f].getBegin(), - features[f].getEnd(), features[f].getScore(), - features[f].getFeatureGroup()); - sf.setStatus(features[f].getStatus()); - for (int od = 0; od < features[f].getOtherDataCount(); od++) + Features feature = features[f]; + SequenceFeature sf = new SequenceFeature(feature.getType(), + feature.getDescription(), feature.getBegin(), + feature.getEnd(), feature.getScore(), + feature.getFeatureGroup()); + sf.setStatus(feature.getStatus()); + + /* + * load any feature attributes - include map-valued attributes + */ + Map> mapAttributes = new HashMap<>(); + for (int od = 0; od < feature.getOtherDataCount(); od++) { - OtherData keyValue = features[f].getOtherData(od); - if (keyValue.getKey().startsWith("LINK")) + OtherData keyValue = feature.getOtherData(od); + 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()); + } + // adds feature to datasequence's feature set (since Jalview 2.10) - al.getSequenceAt(i).addSequenceFeature(sf); + alignmentSeq.addSequenceFeature(sf); } } if (vamsasSeq[i].getDBRefCount() > 0) { // adds dbrefs to datasequence's set (since Jalview 2.10) addDBRefs( - al.getSequenceAt(i).getDatasetSequence() == null - ? al.getSequenceAt(i) - : al.getSequenceAt(i).getDatasetSequence(), + alignmentSeq.getDatasetSequence() == null ? alignmentSeq + : alignmentSeq.getDatasetSequence(), vamsasSeq[i]); } if (jseqs[i].getPdbidsCount() > 0) @@ -3061,16 +3177,25 @@ public class Jalview2XML .getStructureSelectionManager(Desktop.instance) .registerPDBEntry(entry); // adds PDBEntry to datasequence's set (since Jalview 2.10) - if (al.getSequenceAt(i).getDatasetSequence() != null) + if (alignmentSeq.getDatasetSequence() != null) { - al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + alignmentSeq.getDatasetSequence().addPDBId(entry); } else { - al.getSequenceAt(i).addPDBId(entry); + alignmentSeq.addPDBId(entry); } } } + + /* + * load any HMMER profile + */ + String hmmJarFile = jseqs[i].getHmmerProfile(); + if (hmmJarFile != null) + { + loadHmmerProfile(jprovider, hmmJarFile, alignmentSeq); + } } } // end !multipleview @@ -3568,6 +3693,31 @@ public class Jalview2XML } /** + * Loads a HMMER profile from a file stored in the project, and associates it + * with the specified sequence + * + * @param jprovider + * @param hmmJarFile + * @param seq + */ + protected void loadHmmerProfile(jarInputStreamProvider jprovider, + String hmmJarFile, SequenceI seq) + { + try + { + String hmmFile = copyJarEntry(jprovider, hmmJarFile, "hmm", null); + HMMFile parser = new HMMFile(hmmFile, DataSourceType.FILE); + HiddenMarkovModel hmmModel = parser.getHMM(); + hmmModel = new HiddenMarkovModel(hmmModel, seq); + seq.setHMM(hmmModel); + } catch (IOException e) + { + warn("Error loading HMM profile for " + seq.getName() + ": " + + e.getMessage()); + } + } + + /** * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna * panel is restored from separate jar entries, two (gapped and trimmed) per * sequence and secondary structure. @@ -4500,7 +4650,7 @@ public class Jalview2XML af.viewport.getResidueShading().setThreshold(view.getPidThreshold(), view.getIgnoreGapsinConsensus()); af.viewport.getResidueShading() - .setConsensus(af.viewport.getSequenceConsensusHash()); + .setConsensus(af.viewport.getConsensusProfiles()); af.viewport.setColourAppliesToAllGroups(false); if (view.getConservationSelected() && cs != null) @@ -4578,9 +4728,11 @@ 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() @@ -4592,14 +4744,51 @@ public class Jalview2XML .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()); @@ -4624,26 +4813,26 @@ 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( + featureOrder.put(featureType, new Float( fs / jms.getFeatureSettings().getSettingCount())); } if (setting.getDisplay()) { - fdi.setVisible(setting.getType()); + fdi.setVisible(featureType); } } Map fgtable = new Hashtable<>(); @@ -4657,9 +4846,7 @@ public class Jalview2XML // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder); FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, fgtable, featureColours, 1.0f, featureOrder); - af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() - .transferSettings(frs); - + fr.transferSettings(frs); } if (view.getHiddenColumnsCount() > 0) @@ -4957,10 +5144,7 @@ public class Jalview2XML id = object.getJalviewModelSequence().getViewport()[0] .getSequenceSetId())) { - if (Cache.log != null && Cache.log.isDebugEnabled()) - { - Cache.log.debug("Skipping seuqence set id " + id); - } + debug("Skipping sequence set id " + id); return true; } return false; @@ -5334,7 +5518,7 @@ public class Jalview2XML seqRefIds.put(sqid, djs); } - jalview.bin.Cache.log.debug("about to recurse on addDBRefs."); + debug("about to recurse on addDBRefs."); addDBRefs(djs, ms); } @@ -5343,28 +5527,25 @@ 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(); @@ -5384,32 +5565,8 @@ 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); @@ -5539,7 +5696,7 @@ public class Jalview2XML } else { - Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id); + debug("Ignoring " + jvobj.getClass() + " (ID = " + id); } } } @@ -5640,4 +5797,292 @@ 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) + { + if (Cache.log != null) + { + 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; + } }