X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=945651b9dcefd8ec123d90d1a3acb23a1293bb57;hb=8dfdafee89d06dd397c392619b4b285f0dc35430;hp=f87fbe5dc0c92da821debd3cd346ff6277fa108f;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index f87fbe5..945651b 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; @@ -79,6 +80,7 @@ import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.util.StringUtils; import jalview.util.jarInputStreamProvider; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; @@ -90,6 +92,7 @@ import jalview.ws.params.ArgumentI; import jalview.ws.params.AutoCalcSetting; import jalview.ws.params.WsParamSetI; +import java.awt.Color; import java.awt.Rectangle; import java.io.BufferedReader; import java.io.DataInputStream; @@ -116,7 +119,6 @@ import java.util.List; import java.util.Map; import java.util.Map.Entry; import java.util.Set; -import java.util.StringTokenizer; import java.util.Vector; import java.util.jar.JarEntry; import java.util.jar.JarInputStream; @@ -163,7 +165,7 @@ public class Jalview2XML */ Map seqRefIds = null; - Vector frefedSequence = null; + Vector frefedSequence = null; boolean raiseGUI = true; // whether errors are raised in dialog boxes or not @@ -258,7 +260,7 @@ public class Jalview2XML int r = 0, rSize = frefedSequence.size(); while (r < rSize) { - Object[] ref = (Object[]) frefedSequence.elementAt(r); + Object[] ref = frefedSequence.elementAt(r); if (ref != null) { String sref = (String) ref[0]; @@ -633,11 +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(); @@ -654,6 +660,7 @@ public class Jalview2XML { // switch jal and the dataset jal = jal.getDataset(); + rjal = jal; } } if (jal.getProperties() != null) @@ -673,9 +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); @@ -714,26 +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(); @@ -761,10 +775,11 @@ public class Jalview2XML if (sf[index].otherDetails != null) { String key; - Enumeration keys = sf[index].otherDetails.keys(); - while (keys.hasMoreElements()) + Iterator keys = sf[index].otherDetails.keySet() + .iterator(); + while (keys.hasNext()) { - key = keys.nextElement().toString(); + key = keys.next(); OtherData keyValue = new OtherData(); keyValue.setKey(key); keyValue.setValue(sf[index].otherDetails.get(key).toString()); @@ -879,7 +894,7 @@ public class Jalview2XML // SAVE MAPPINGS if (jal.getCodonFrames() != null) { - Set jac = jal.getCodonFrames(); + List jac = jal.getCodonFrames(); for (AlignedCodonFrame acf : jac) { AlcodonFrame alc = new AlcodonFrame(); @@ -898,7 +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); @@ -1092,15 +1107,26 @@ public class Jalview2XML view.setViewName(av.viewName); view.setGatheredViews(av.isGatherViewsHere()); - Rectangle position = ap.av.getExplodedGeometry(); - if (position == null) + Rectangle size = ap.av.getExplodedGeometry(); + Rectangle position = size; + if (size == null) { - position = ap.alignFrame.getBounds(); + size = ap.alignFrame.getBounds(); + if (av.getCodingComplement() != null) + { + position = ((SplitFrame) ap.alignFrame.getSplitViewContainer()) + .getBounds(); + } + else + { + position = size; + } } view.setXpos(position.x); view.setYpos(position.y); - view.setWidth(position.width); - view.setHeight(position.height); + + view.setWidth(size.width); + view.setHeight(size.height); view.setStartRes(av.startRes); view.setStartSeq(av.startSeq); @@ -1182,82 +1208,55 @@ public class Jalview2XML .getFeatureRenderer().getRenderOrder() .toArray(new String[0]); - Vector settingsAdded = new Vector(); - Object gstyle = null; - GraduatedColor gcol = null; + Vector settingsAdded = new Vector(); if (renderOrder != null) { - for (int ro = 0; ro < renderOrder.length; ro++) + for (String featureType : renderOrder) { - gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getFeatureStyle(renderOrder[ro]); + FeatureColourI fcol = ap.getSeqPanel().seqCanvas + .getFeatureRenderer() + .getFeatureStyle(featureType); Setting setting = new Setting(); - setting.setType(renderOrder[ro]); - if (gstyle instanceof GraduatedColor) + setting.setType(featureType); + 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(ap.getSeqPanel().seqCanvas - .getFeatureRenderer().getColour(renderOrder[ro]) - .getRGB()); + setting.setColour(fcol.getColour().getRGB()); } setting.setDisplay(av.getFeaturesDisplayed().isVisible( - renderOrder[ro])); + featureType)); float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getOrder(renderOrder[ro]); + .getOrder(featureType); if (rorder > -1) { setting.setOrder(rorder); } fs.addSetting(setting); - settingsAdded.addElement(renderOrder[ro]); + settingsAdded.addElement(featureType); } } - // Make sure we save none displayed feature settings - Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getFeatureColours().keySet().iterator(); - while (en.hasNext()) - { - String key = en.next().toString(); - if (settingsAdded.contains(key)) - { - continue; - } - - Setting setting = new Setting(); - setting.setType(key); - setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getColour(key).getRGB()); - - setting.setDisplay(false); - float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getOrder(key); - if (rorder > -1) - { - setting.setOrder(rorder); - } - fs.addSetting(setting); - settingsAdded.addElement(key); - } // is groups actually supposed to be a map here ? - en = ap.getSeqPanel().seqCanvas.getFeatureRenderer() + Iterator en = ap.getSeqPanel().seqCanvas + .getFeatureRenderer() .getFeatureGroups().iterator(); - Vector groupsAdded = new Vector(); + Vector groupsAdded = new Vector(); while (en.hasNext()) { - String grp = en.next().toString(); + String grp = en.next(); if (groupsAdded.contains(grp)) { continue; @@ -1271,7 +1270,6 @@ public class Jalview2XML groupsAdded.addElement(grp); } jms.setFeatureSettings(fs); - } if (av.hasHiddenColumns()) @@ -1937,16 +1935,16 @@ public class Jalview2XML if (jds.getDatasetSequence() != null) { vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); - if (jds.getDatasetSequence().getDBRef() != null) + if (jds.getDatasetSequence().getDBRefs() != null) { - dbrefs = jds.getDatasetSequence().getDBRef(); + dbrefs = jds.getDatasetSequence().getDBRefs(); } } else { vamsasSeq.setDsseqid(id); // so we can tell which sequences really are // dataset sequences only - dbrefs = jds.getDBRef(); + dbrefs = jds.getDBRefs(); } if (dbrefs != null) { @@ -2167,6 +2165,7 @@ public class Jalview2XML { SwingUtilities.invokeAndWait(new Runnable() { + @Override public void run() { setLoadingFinishedForNewStructureViewers(); @@ -2241,7 +2240,7 @@ public class Jalview2XML } if (frefedSequence == null) { - frefedSequence = new Vector(); + frefedSequence = new Vector(); } AlignFrame af = null, _af = null; @@ -2453,6 +2452,11 @@ public class Jalview2XML int width = (int) dnaFrame.getBounds().getWidth(); int height = (int) (dnaFrame.getBounds().getHeight() + proteinFrame.getBounds().getHeight() + 50); + + /* + * SplitFrame location is saved to both enclosed frames + */ + splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY()); Desktop.addInternalFrame(splitFrame, title, width, height); /* @@ -2662,7 +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++) @@ -2687,6 +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) @@ -2696,7 +2705,6 @@ public class Jalview2XML hiddenSeqs.add(seqRefIds.get(seqId)); } - } // / @@ -2707,6 +2715,10 @@ public class Jalview2XML Alignment al = new Alignment(orderedSeqs); + if (referenceseqForView != null) + { + al.setSeqrep(referenceseqForView); + } // / Add the alignment properties for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++) { @@ -2832,7 +2844,7 @@ public class Jalview2XML { mapping = addMapping(maps[m].getMapping()); } - if (dnaseq != null) + if (dnaseq != null && mapping.getTo() != null) { cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); } @@ -3250,8 +3262,8 @@ public class Jalview2XML * indicate that annotation colours are applied across all groups (pre * Jalview 2.8.1 behaviour) */ - boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1", - object.getVersion()); + boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan( + "2.8.1", object.getVersion()); AlignmentPanel ap = null; boolean isnewview = true; @@ -4029,18 +4041,22 @@ public class Jalview2XML } /** + * Answers true if 'version' is equal to or later than 'supported', where each + * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix + * changes. Development and test values for 'version' are leniently treated + * i.e. answer true. * * @param supported * - minimum version we are comparing against * @param version - * - version of data being processsed. - * @return true if version is development/null or evaluates to the same or - * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*) + * - version of data being processsed + * @return */ - protected boolean isVersionStringLaterThan(String supported, + public static boolean isVersionStringLaterThan(String supported, String version) { - if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD") + if (supported == null || version == null + || version.equalsIgnoreCase("DEVELOPMENT BUILD") || version.equalsIgnoreCase("Test") || version.equalsIgnoreCase("AUTOMATED BUILD")) { @@ -4051,38 +4067,8 @@ public class Jalview2XML } else { - StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer( - version, "."); - while (currentV.hasMoreTokens() && fileV.hasMoreTokens()) - { - // convert b to decimal to catch bugfix releases within a series - String curT = currentV.nextToken().toLowerCase().replace('b', '.'); - String fileT = fileV.nextToken().toLowerCase().replace('b', '.'); - try - { - if (Float.valueOf(curT) > Float.valueOf(fileT)) - { - // current version is newer than the version that wrote the file - return false; - } - } catch (NumberFormatException nfe) - { - System.err - .println("** WARNING: Version comparison failed for tokens (" - + curT - + ") and (" - + fileT - + ")\n** Current: '" - + supported + "' and Version: '" + version + "'"); - } - } - if (currentV.hasMoreElements()) - { - // fileV has no minor version but identical series to current - return false; - } + return StringUtils.compareVersions(version, supported, "b") >= 0; } - return true; } Vector newStructureViewers = null; @@ -4126,6 +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) @@ -4152,25 +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); @@ -4329,25 +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()) @@ -4363,8 +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()) @@ -4381,7 +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);