X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=ac85aad051b2b49d9057496b10eb6fe67a48fb9f;hb=d1671a58c39dc5cd36e742fe7c2cff5aa7ac8fe7;hp=a3604d67c0b93dcc3ee618dde69e563f4584ceb2;hpb=1c6ddae580d69eb0fa5b4291ba84fd6ba9b83621;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index a3604d6..ac85aad 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; @@ -71,7 +72,7 @@ import jalview.schemabinding.version2.Viewport; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemeProperty; -import jalview.schemes.GraduatedColor; +import jalview.schemes.FeatureColour; import jalview.schemes.ResidueColourScheme; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; @@ -634,11 +635,15 @@ public class Jalview2XML object.setVersion(jalview.bin.Cache.getDefault("VERSION", "Development Build")); - jalview.datamodel.AlignmentI jal = av.getAlignment(); + /** + * rjal is full height alignment, jal is actual alignment with full metadata + * but excludes hidden sequences. + */ + jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal; if (av.hasHiddenRows()) { - jal = jal.getHiddenSequences().getFullAlignment(); + rjal = jal.getHiddenSequences().getFullAlignment(); } SequenceSet vamsasSet = new SequenceSet(); @@ -655,6 +660,7 @@ public class Jalview2XML { // switch jal and the dataset jal = jal.getDataset(); + rjal = jal; } } if (jal.getProperties() != null) @@ -674,9 +680,8 @@ public class Jalview2XML Set calcIdSet = new HashSet(); // SAVE SEQUENCES - for (int i = 0; i < jal.getHeight(); i++) + for (final SequenceI jds : rjal.getSequences()) { - final SequenceI jds = jal.getSequenceAt(i); final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds : jds.getDatasetSequence(); String id = seqHash(jds); @@ -715,26 +720,34 @@ public class Jalview2XML // Store any sequences this sequence represents if (av.hasHiddenRows()) { + // use rjal, contains the full height alignment jseq.setHidden(av.getAlignment().getHiddenSequences() .isHidden(jds)); - if (av.isHiddenRepSequence(jal.getSequenceAt(i))) + if (av.isHiddenRepSequence(jds)) { jalview.datamodel.SequenceI[] reps = av - .getRepresentedSequences(jal.getSequenceAt(i)) - .getSequencesInOrder(jal); + .getRepresentedSequences(jds) + .getSequencesInOrder(rjal); for (int h = 0; h < reps.length; h++) { - if (reps[h] != jal.getSequenceAt(i)) + if (reps[h] != jds) { - jseq.addHiddenSequences(jal.findIndex(reps[h])); + jseq.addHiddenSequences(rjal.findIndex(reps[h])); } } } } + // mark sequence as reference - if it is the reference for this view + if (jal.hasSeqrep()) + { + jseq.setViewreference(jds == jal.getSeqrep()); + } } + // TODO: omit sequence features from each alignment view's XML dump if we + // are storing dataset if (jds.getSequenceFeatures() != null) { jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures(); @@ -900,7 +913,7 @@ public class Jalview2XML alc.addAlcodMap(alcmap); } } - + // TODO: delete this ? dead code from 2.8.3->2.9 ? // { // AlcodonFrame alc = new AlcodonFrame(); // vamsasSet.addAlcodonFrame(alc); @@ -1196,31 +1209,31 @@ public class Jalview2XML .toArray(new String[0]); Vector settingsAdded = new Vector(); - Object gstyle = null; - GraduatedColor gcol = null; if (renderOrder != null) { for (String featureType : renderOrder) { - gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer() + FeatureColourI fcol = ap.getSeqPanel().seqCanvas + .getFeatureRenderer() .getFeatureStyle(featureType); Setting setting = new Setting(); setting.setType(featureType); - if (gstyle instanceof GraduatedColor) + if (!fcol.isSimpleColour()) { - gcol = (GraduatedColor) gstyle; - setting.setColour(gcol.getMaxColor().getRGB()); - setting.setMincolour(gcol.getMinColor().getRGB()); - setting.setMin(gcol.getMin()); - setting.setMax(gcol.getMax()); - setting.setColourByLabel(gcol.isColourByLabel()); - setting.setAutoScale(gcol.isAutoScale()); - setting.setThreshold(gcol.getThresh()); - setting.setThreshstate(gcol.getThreshType()); + setting.setColour(fcol.getMaxColour().getRGB()); + setting.setMincolour(fcol.getMinColour().getRGB()); + setting.setMin(fcol.getMin()); + setting.setMax(fcol.getMax()); + setting.setColourByLabel(fcol.isColourByLabel()); + setting.setAutoScale(fcol.isAutoScaled()); + setting.setThreshold(fcol.getThreshold()); + // -1 = No threshold, 0 = Below, 1 = Above + setting.setThreshstate(fcol.isAboveThreshold() ? 1 + : (fcol.isBelowThreshold() ? 0 : -1)); } else { - setting.setColour(((Color) gstyle).getRGB()); + setting.setColour(fcol.getColour().getRGB()); } setting.setDisplay(av.getFeaturesDisplayed().isVisible( @@ -1257,7 +1270,6 @@ public class Jalview2XML groupsAdded.addElement(grp); } jms.setFeatureSettings(fs); - } if (av.hasHiddenColumns()) @@ -2654,7 +2666,7 @@ public class Jalview2XML List tmpseqs = new ArrayList(); boolean multipleView = false; - + SequenceI referenceseqForView = null; JSeq[] jseqs = object.getJalviewModelSequence().getJSeq(); int vi = 0; // counter in vamsasSeq array for (int i = 0; i < jseqs.length; i++) @@ -2679,6 +2691,11 @@ public class Jalview2XML vi++; } + if (jseqs[i].hasViewreference() && jseqs[i].getViewreference()) + { + referenceseqForView = tmpseqs.get(tmpseqs.size() - 1); + } + if (jseqs[i].getHidden()) { if (hiddenSeqs == null) @@ -2688,7 +2705,6 @@ public class Jalview2XML hiddenSeqs.add(seqRefIds.get(seqId)); } - } // / @@ -2697,8 +2713,12 @@ public class Jalview2XML SequenceI[] orderedSeqs = tmpseqs .toArray(new SequenceI[tmpseqs.size()]); - Alignment al = new Alignment(orderedSeqs); + AlignmentI al = new Alignment(orderedSeqs); + if (referenceseqForView != null) + { + al.setSeqrep(referenceseqForView); + } // / Add the alignment properties for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++) { @@ -4076,7 +4096,7 @@ public class Jalview2XML } AlignFrame loadViewport(String file, JSeq[] JSEQ, - List hiddenSeqs, Alignment al, + List hiddenSeqs, AlignmentI al, JalviewModelSequence jms, Viewport view, String uniqueSeqSetId, String viewId, List autoAlan) { @@ -4092,6 +4112,12 @@ public class Jalview2XML .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour())); } + if (al.hasSeqrep()) + { + af.getViewport().setColourByReferenceSeq(true); + af.getViewport().setDisplayReferenceSeq(true); + } + af.viewport.setGatherViewsHere(view.getGatheredViews()); if (view.getSequenceSetId() != null) @@ -4118,25 +4144,25 @@ public class Jalview2XML { for (int s = 0; s < JSEQ.length; s++) { - jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup(); - + SequenceGroup hidden = new SequenceGroup(); + boolean isRepresentative = false; for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++) { - hidden.addSequence( - al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false); + isRepresentative = true; + SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s] + .getHiddenSequences(r)); + hidden.addSequence(sequenceToHide, false); + // remove from hiddenSeqs list so we don't try to hide it twice + hiddenSeqs.remove(sequenceToHide); + } + if (isRepresentative) + { + SequenceI representativeSequence = al.getSequenceAt(s); + hidden.addSequence(representativeSequence, false); + af.viewport.hideRepSequences(representativeSequence, hidden); } - af.viewport.hideRepSequences(al.getSequenceAt(s), hidden); } - // jalview.datamodel.SequenceI[] hseqs = new - // jalview.datamodel.SequenceI[hiddenSeqs - // .size()]; - // - // for (int s = 0; s < hiddenSeqs.size(); s++) - // { - // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s); - // } - SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs .size()]); af.viewport.hideSequence(hseqs); @@ -4295,25 +4321,33 @@ public class Jalview2XML af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; - Hashtable featureGroups = new Hashtable(); - Hashtable featureColours = new Hashtable(); - Hashtable featureOrder = new Hashtable(); + Map featureColours = new Hashtable(); + Map featureOrder = new Hashtable(); for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); if (setting.hasMincolour()) { - GraduatedColor gc = setting.hasMin() ? new GraduatedColor( - new java.awt.Color(setting.getMincolour()), - new java.awt.Color(setting.getColour()), - setting.getMin(), setting.getMax()) : new GraduatedColor( - new java.awt.Color(setting.getMincolour()), - new java.awt.Color(setting.getColour()), 0, 1); + FeatureColourI gc = setting.hasMin() ? new FeatureColour( + new Color(setting.getMincolour()), new Color( + setting.getColour()), setting.getMin(), + setting.getMax()) : new FeatureColour(new Color( + setting.getMincolour()), new Color(setting.getColour()), + 0, 1); if (setting.hasThreshold()) { - gc.setThresh(setting.getThreshold()); - gc.setThreshType(setting.getThreshstate()); + gc.setThreshold(setting.getThreshold()); + int threshstate = setting.getThreshstate(); + // -1 = None, 0 = Below, 1 = Above threshold + if (threshstate == 0) + { + gc.setBelowThreshold(true); + } + else if (threshstate == 1) + { + gc.setAboveThreshold(true); + } } gc.setAutoScaled(true); // default if (setting.hasAutoScale()) @@ -4329,8 +4363,8 @@ public class Jalview2XML } else { - featureColours.put(setting.getType(), - new java.awt.Color(setting.getColour())); + featureColours.put(setting.getType(), new FeatureColour( + new Color(setting.getColour()))); } renderOrder[fs] = setting.getType(); if (setting.hasOrder()) @@ -4347,7 +4381,7 @@ public class Jalview2XML fdi.setVisible(setting.getType()); } } - Hashtable fgtable = new Hashtable(); + Map fgtable = new Hashtable(); for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) { Group grp = jms.getFeatureSettings().getGroup(gs); @@ -4415,7 +4449,7 @@ public class Jalview2XML } private ColourSchemeI constructAnnotationColour( - AnnotationColours viewAnnColour, AlignFrame af, Alignment al, + AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al, JalviewModelSequence jms, boolean checkGroupAnnColour) { boolean propagateAnnColour = false; @@ -4539,7 +4573,7 @@ public class Jalview2XML return cs; } - private void reorderAutoannotation(AlignFrame af, Alignment al, + private void reorderAutoannotation(AlignFrame af, AlignmentI al, List autoAlan) { // copy over visualization settings for autocalculated annotation in the @@ -4694,10 +4728,11 @@ public class Jalview2XML } } - private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al, + private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al, boolean ignoreUnrefed) { - jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId()); + jalview.datamodel.AlignmentI ds = getDatasetFor(vamsasSet + .getDatasetId()); Vector dseqs = null; if (ds == null) { @@ -4847,15 +4882,15 @@ public class Jalview2XML * TODO use AlignmentI here and in related methods - needs * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment */ - Hashtable datasetIds = null; + Hashtable datasetIds = null; - IdentityHashMap dataset2Ids = null; + IdentityHashMap dataset2Ids = null; - private Alignment getDatasetFor(String datasetId) + private AlignmentI getDatasetFor(String datasetId) { if (datasetIds == null) { - datasetIds = new Hashtable(); + datasetIds = new Hashtable(); return null; } if (datasetIds.containsKey(datasetId)) @@ -4865,11 +4900,11 @@ public class Jalview2XML return null; } - private void addDatasetRef(String datasetId, Alignment dataset) + private void addDatasetRef(String datasetId, AlignmentI dataset) { if (datasetIds == null) { - datasetIds = new Hashtable(); + datasetIds = new Hashtable(); } datasetIds.put(datasetId, dataset); } @@ -4880,7 +4915,7 @@ public class Jalview2XML * @param dataset * @return */ - private String getDatasetIdRef(Alignment dataset) + private String getDatasetIdRef(AlignmentI dataset) { if (dataset.getDataset() != null) { @@ -4892,7 +4927,7 @@ public class Jalview2XML // make a new datasetId and record it if (dataset2Ids == null) { - dataset2Ids = new IdentityHashMap(); + dataset2Ids = new IdentityHashMap(); } else {