X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=9a9c7b318b7e0456b095da884c3e81660fd7c5b1;hb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;hp=2434b0026cbff5521c68a8e3b4c857e8df9e0a34;hpb=c37b687de83b672fb6585db5fcd93189e3582139;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 2434b00..9a9c7b3 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import jalview.api.FeatureColourI; +import jalview.api.ViewStyleI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.AlignedCodonFrame; @@ -70,7 +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; @@ -89,6 +91,7 @@ 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; @@ -676,8 +679,7 @@ public class Jalview2XML { final SequenceI jds = jal.getSequenceAt(i); final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds - : jds - .getDatasetSequence(); + : jds.getDatasetSequence(); String id = seqHash(jds); if (seqRefIds.get(id) != null) @@ -736,8 +738,7 @@ public class Jalview2XML if (jds.getSequenceFeatures() != null) { - jalview.datamodel.SequenceFeature[] sf = jds - .getSequenceFeatures(); + jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures(); int index = 0; while (index < sf.length) { @@ -778,9 +779,9 @@ public class Jalview2XML } } - if (jdatasq.getPDBId() != null) + if (jdatasq.getAllPDBEntries() != null) { - Enumeration en = jdatasq.getPDBId().elements(); + Enumeration en = jdatasq.getAllPDBEntries().elements(); while (en.hasMoreElements()) { Pdbids pdb = new Pdbids(); @@ -900,36 +901,36 @@ public class Jalview2XML } } -// { -// AlcodonFrame alc = new AlcodonFrame(); -// vamsasSet.addAlcodonFrame(alc); -// for (int p = 0; p < acf.aaWidth; p++) -// { -// Alcodon cmap = new Alcodon(); -// if (acf.codons[p] != null) -// { -// // Null codons indicate a gapped column in the translated peptide -// // alignment. -// cmap.setPos1(acf.codons[p][0]); -// cmap.setPos2(acf.codons[p][1]); -// cmap.setPos3(acf.codons[p][2]); -// } -// alc.addAlcodon(cmap); -// } -// if (acf.getProtMappings() != null -// && acf.getProtMappings().length > 0) -// { -// SequenceI[] dnas = acf.getdnaSeqs(); -// jalview.datamodel.Mapping[] pmaps = acf.getProtMappings(); -// for (int m = 0; m < pmaps.length; m++) -// { -// AlcodMap alcmap = new AlcodMap(); -// alcmap.setDnasq(seqHash(dnas[m])); -// alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, -// false)); -// alc.addAlcodMap(alcmap); -// } -// } + // { + // AlcodonFrame alc = new AlcodonFrame(); + // vamsasSet.addAlcodonFrame(alc); + // for (int p = 0; p < acf.aaWidth; p++) + // { + // Alcodon cmap = new Alcodon(); + // if (acf.codons[p] != null) + // { + // // Null codons indicate a gapped column in the translated peptide + // // alignment. + // cmap.setPos1(acf.codons[p][0]); + // cmap.setPos2(acf.codons[p][1]); + // cmap.setPos3(acf.codons[p][2]); + // } + // alc.addAlcodon(cmap); + // } + // if (acf.getProtMappings() != null + // && acf.getProtMappings().length > 0) + // { + // SequenceI[] dnas = acf.getdnaSeqs(); + // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings(); + // for (int m = 0; m < pmaps.length; m++) + // { + // AlcodMap alcmap = new AlcodMap(); + // alcmap.setDnasq(seqHash(dnas[m])); + // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null, + // false)); + // alc.addAlcodMap(alcmap); + // } + // } } } @@ -1032,13 +1033,11 @@ public class Jalview2XML if (sg.cs instanceof jalview.schemes.UserColourScheme) { - jGroup.setColour(setUserColourScheme(sg.cs, userColours, - jms)); + jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); } else { - jGroup - .setColour(ColourSchemeProperty.getColourName(sg.cs)); + jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs)); } } else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient) @@ -1050,8 +1049,7 @@ public class Jalview2XML } else if (sg.cs instanceof jalview.schemes.UserColourScheme) { - jGroup - .setColour(setUserColourScheme(sg.cs, userColours, jms)); + jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); } else { @@ -1096,15 +1094,26 @@ 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); @@ -1154,6 +1163,7 @@ public class Jalview2XML view.setFontName(av.font.getName()); view.setFontSize(av.font.getSize()); view.setFontStyle(av.font.getStyle()); + view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna()); view.setRenderGaps(av.isRenderGaps()); view.setShowAnnotation(av.isShowAnnotation()); view.setShowBoxes(av.getShowBoxes()); @@ -1185,34 +1195,32 @@ 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++) { - gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer() + FeatureColourI gstyle = ap.getSeqPanel().seqCanvas + .getFeatureRenderer() .getFeatureStyle(renderOrder[ro]); Setting setting = new Setting(); setting.setType(renderOrder[ro]); - if (gstyle instanceof GraduatedColor) + if (!gstyle.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(gstyle.getMaxColour().getRGB()); + setting.setMincolour(gstyle.getMinColour().getRGB()); + setting.setMin(gstyle.getMin()); + setting.setMax(gstyle.getMax()); + setting.setColourByLabel(gstyle.isColourByLabel()); + setting.setAutoScale(gstyle.isAutoScaled()); + setting.setThreshold(gstyle.getThreshold()); + // -1 = No threshold, 0 = Below, 1 = Above + setting.setThreshstate(gstyle.isAboveThreshold() ? 1 + : (gstyle.isBelowThreshold() ? 0 : -1)); } else { - setting.setColour(ap.getSeqPanel().seqCanvas - .getFeatureRenderer() - .getColour(renderOrder[ro]).getRGB()); + setting.setColour(gstyle.getColour().getRGB()); } setting.setDisplay(av.getFeaturesDisplayed().isVisible( @@ -1228,36 +1236,11 @@ public class Jalview2XML } } - // 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(); @@ -1274,7 +1257,6 @@ public class Jalview2XML groupsAdded.addElement(grp); } jms.setFeatureSettings(fs); - } if (av.hasHiddenColumns()) @@ -1372,6 +1354,10 @@ public class Jalview2XML final SequenceI jds, List viewIds, AlignmentPanel ap, boolean storeDataset) { + if (Desktop.desktop == null) + { + return; + } JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int f = frames.length - 1; f > -1; f--) { @@ -1420,8 +1406,7 @@ public class Jalview2XML { String varnaStateFile = varna.getStateInfo(model.rna); - jarEntryName = RNA_PREFIX + viewId + "_" - + nextCounter(); + jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter(); copyFileToJar(jout, varnaStateFile, jarEntryName); rnaSessions.put(model, jarEntryName); } @@ -1604,8 +1589,8 @@ public class Jalview2XML private void storeAlignmentAnnotation(AlignmentAnnotation[] aa, IdentityHashMap groupRefs, - AlignmentViewport av, - Set calcIdSet, boolean storeDS, SequenceSet vamsasSet) + AlignmentViewport av, Set calcIdSet, boolean storeDS, + SequenceSet vamsasSet) { for (int i = 0; i < aa.length; i++) @@ -1635,9 +1620,11 @@ 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()); } @@ -1852,8 +1839,8 @@ public class Jalview2XML } } throw new Error(MessageManager.formatMessage( - "error.unsupported_version_calcIdparam", new Object[] - { calcIdParam.toString() })); + "error.unsupported_version_calcIdparam", + new Object[] { calcIdParam.toString() })); } /** @@ -1935,16 +1922,16 @@ 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) { @@ -2165,6 +2152,7 @@ public class Jalview2XML { SwingUtilities.invokeAndWait(new Runnable() { + @Override public void run() { setLoadingFinishedForNewStructureViewers(); @@ -2415,7 +2403,8 @@ public class Jalview2XML .entrySet()) { AlignFrame af = candidate.getValue(); - if (!addedToSplitFrames.contains(af)) { + if (!addedToSplitFrames.contains(af)) + { Viewport view = candidate.getKey(); Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view.getHeight()); @@ -2450,6 +2439,11 @@ 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); /* @@ -2836,8 +2830,8 @@ public class Jalview2XML else { // defer to later - frefedSequence.add(new Object[] - { maps[m].getDnasq(), cf, mapping }); + frefedSequence.add(new Object[] { maps[m].getDnasq(), cf, + mapping }); } } } @@ -2888,8 +2882,7 @@ public class Jalview2XML // set visiblity for other annotation in this view String annotationId = annotation.getId(); - if (annotationId != null - && annotationIds.containsKey(annotationId)) + if (annotationId != null && annotationIds.containsKey(annotationId)) { AlignmentAnnotation jda = annotationIds.get(annotationId); // in principle Visible should always be true for annotation displayed @@ -3123,8 +3116,7 @@ public class Jalview2XML SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs, jGroup.getDisplayBoxes(), jGroup.getDisplayText(), - jGroup.getColourText(), jGroup.getStart(), - jGroup.getEnd()); + jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd()); sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour())); @@ -3163,8 +3155,8 @@ 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) @@ -3192,8 +3184,8 @@ public class Jalview2XML if (addAnnotSchemeGroup) { // reconstruct the annotation colourscheme - sg.cs = constructAnnotationColour( - jGroup.getAnnotationColours(), null, al, jms, false); + sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(), + null, al, jms, false); } } } @@ -3249,8 +3241,8 @@ 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; @@ -3325,8 +3317,8 @@ 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++) { @@ -3344,9 +3336,8 @@ public class Jalview2XML String sessionState = ss.getViewerState(); String tempStateFile = copyJarEntry(jprovider, sessionState, "varna"); - RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped, - tempStateFile); - appVarna.addModel(rna, rnaTitle); + RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped); + appVarna.addModelSession(rna, rnaTitle, tempStateFile); } appVarna.setInitialSelection(viewer.getSelectedRna()); } @@ -3389,8 +3380,8 @@ public class Jalview2XML * viewer not found - make it */ RnaViewerModel model = new RnaViewerModel(postLoadId, - viewer.getTitle(), viewer.getXpos(), - viewer.getYpos(), viewer.getWidth(), viewer.getHeight(), + viewer.getTitle(), viewer.getXpos(), viewer.getYpos(), + viewer.getWidth(), viewer.getHeight(), viewer.getDividerLocation()); AppVarna varna = new AppVarna(model, ap); @@ -3675,12 +3666,12 @@ public class Jalview2XML * @param af * @param jprovider */ - protected void createChimeraViewer(Entry viewerData, - AlignFrame af, + protected void createChimeraViewer( + Entry viewerData, AlignFrame af, jarInputStreamProvider jprovider) { StructureViewerModel data = viewerData.getValue(); - String chimeraSessionFile = data.getStateData(); + String chimeraSessionFile = data.getStateData(); /* * Copy Chimera session from jar entry "viewer_"+viewId to a temporary file @@ -3717,8 +3708,8 @@ public class Jalview2XML String newViewId = viewerData.getKey(); ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile, - af.alignPanel, pdbArray, - seqsArray, colourByChimera, colourBySequence, newViewId); + af.alignPanel, pdbArray, seqsArray, colourByChimera, + colourBySequence, newViewId); cvf.setSize(data.getWidth(), data.getHeight()); cvf.setLocation(data.getX(), data.getY()); } @@ -3884,6 +3875,7 @@ public class Jalview2XML { // e.printStackTrace(); } + } /** @@ -4036,7 +4028,7 @@ public class Jalview2XML * @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]*) */ - protected boolean isVersionStringLaterThan(String supported, + public static boolean isVersionStringLaterThan(String supported, String version) { if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD") @@ -4059,11 +4051,18 @@ public class Jalview2XML String fileT = fileV.nextToken().toLowerCase().replace('b', '.'); try { - if (Float.valueOf(curT) > Float.valueOf(fileT)) + float supportedVersionToken = Float.parseFloat(curT); + float myVersiontoken = Float.parseFloat(fileT); + if (supportedVersionToken > myVersiontoken) { // current version is newer than the version that wrote the file return false; } + if (supportedVersionToken < myVersiontoken) + { + // current version is older than the version that wrote the file + return true; + } } catch (NumberFormatException nfe) { System.err @@ -4195,6 +4194,9 @@ public class Jalview2XML 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); // TODO: allow custom charWidth/Heights to be restored by updating them // after setting font - which means set above to false af.viewport.setRenderGaps(view.getRenderGaps()); @@ -4325,25 +4327,33 @@ 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()) @@ -4359,8 +4369,8 @@ 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()) @@ -4377,7 +4387,7 @@ 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); @@ -4420,7 +4430,7 @@ public class Jalview2XML } } af.setMenusFromViewport(af.viewport); - + // TODO: we don't need to do this if the viewport is aready visible. /* * Add the AlignFrame to the desktop (it may be 'gathered' later), unless it @@ -4579,8 +4589,8 @@ public class Jalview2XML /** * Kludge for magic autoannotation names (see JAL-811) */ - String[] magicNames = new String[] - { "Consensus", "Quality", "Conservation" }; + String[] magicNames = new String[] { "Consensus", "Quality", + "Conservation" }; JvAnnotRow nullAnnot = new JvAnnotRow(-1, null); Hashtable visan = new Hashtable(); for (String nm : magicNames) @@ -4990,8 +5000,7 @@ public class Jalview2XML } else { - frefedSequence.add(new Object[] - { dsfor, jmap }); + frefedSequence.add(new Object[] { dsfor, jmap }); } } else @@ -5325,7 +5334,7 @@ public class Jalview2XML } } } - + return result; }