X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=2509f15ee2d7d3798c7ff592bfb0ca9507170fa9;hb=07c11f6db82ac33ec895aa82e603d4a659928a24;hp=da9c6a9ad46a69b6afd2b27bcf43ef4c4eafd459;hpb=d2ad79a5a6edf4c1dbbbc2f454579864dcf1e3b8;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index da9c6a9..2509f15 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -20,45 +20,7 @@ */ package jalview.gui; -import java.awt.Rectangle; -import java.io.BufferedReader; -import java.io.DataInputStream; -import java.io.DataOutputStream; -import java.io.File; -import java.io.FileInputStream; -import java.io.FileOutputStream; -import java.io.IOException; -import java.io.InputStreamReader; -import java.io.OutputStreamWriter; -import java.io.PrintWriter; -import java.lang.reflect.InvocationTargetException; -import java.net.MalformedURLException; -import java.net.URL; -import java.util.ArrayList; -import java.util.Enumeration; -import java.util.HashMap; -import java.util.HashSet; -import java.util.Hashtable; -import java.util.IdentityHashMap; -import java.util.Iterator; -import java.util.LinkedHashMap; -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; -import java.util.jar.JarOutputStream; - -import javax.swing.JInternalFrame; -import javax.swing.JOptionPane; -import javax.swing.SwingUtilities; - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - +import jalview.api.ViewStyleI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.AlignedCodonFrame; @@ -66,9 +28,12 @@ import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; +import jalview.datamodel.RnaViewerModel; +import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.datamodel.StructureViewerModel; import jalview.datamodel.StructureViewerModel.StructureData; +import jalview.ext.varna.RnaModel; import jalview.gui.StructureViewer.ViewerType; import jalview.schemabinding.version2.AlcodMap; import jalview.schemabinding.version2.AlcodonFrame; @@ -92,6 +57,8 @@ import jalview.schemabinding.version2.OtherData; import jalview.schemabinding.version2.PdbentryItem; import jalview.schemabinding.version2.Pdbids; import jalview.schemabinding.version2.Property; +import jalview.schemabinding.version2.RnaViewer; +import jalview.schemabinding.version2.SecondaryStructure; import jalview.schemabinding.version2.Sequence; import jalview.schemabinding.version2.SequenceSet; import jalview.schemabinding.version2.SequenceSetProperties; @@ -112,6 +79,7 @@ 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; @@ -123,6 +91,45 @@ 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; +import java.io.DataOutputStream; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStreamReader; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.lang.reflect.InvocationTargetException; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.Enumeration; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Hashtable; +import java.util.IdentityHashMap; +import java.util.Iterator; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.Set; +import java.util.Vector; +import java.util.jar.JarEntry; +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; +import org.exolab.castor.xml.Unmarshaller; + /** * Write out the current jalview desktop state as a Jalview XML stream. * @@ -135,8 +142,15 @@ import jalview.ws.params.WsParamSetI; */ public class Jalview2XML { + private static final String VIEWER_PREFIX = "viewer_"; + + private static final String RNA_PREFIX = "rna_"; + private static final String UTF_8 = "UTF-8"; + // use this with nextCounter() to make unique names for entities + private int counter = 0; + /* * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps * of sequence objects are created. @@ -150,7 +164,7 @@ public class Jalview2XML */ Map seqRefIds = null; - Vector frefedSequence = null; + Vector frefedSequence = null; boolean raiseGUI = true; // whether errors are raised in dialog boxes or not @@ -160,6 +174,12 @@ public class Jalview2XML */ private Map splitFrameCandidates = new HashMap(); + /* + * Map from displayed rna structure models to their saved session state jar + * entry names + */ + private Map rnaSessions = new HashMap(); + /** * create/return unique hash string for sq * @@ -239,7 +259,7 @@ 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]; @@ -369,7 +389,7 @@ public class Jalview2XML */ public void saveState(JarOutputStream jout) { - AlignFrame[] frames = Desktop.getAlignFrames(); // Desktop.desktop.getAllFrames(); + AlignFrame[] frames = Desktop.getAlignFrames(); if (frames == null) { @@ -378,6 +398,13 @@ public class Jalview2XML Hashtable dsses = new Hashtable(); + /* + * ensure cached data is clear before starting + */ + // todo tidy up seqRefIds, seqsToIds initialisation / reset + rnaSessions.clear(); + splitFrameCandidates.clear(); + try { @@ -385,6 +412,7 @@ public class Jalview2XML // ////////////////////////////////////////////////// List shortNames = new ArrayList(); + List viewIds = new ArrayList(); // REVERSE ORDER for (int i = frames.length - 1; i > -1; i--) @@ -411,7 +439,7 @@ public class Jalview2XML fileName = fileName + ".xml"; } - saveState(apanel, fileName, jout); + saveState(apanel, fileName, jout, viewIds); String dssid = getDatasetIdRef(af.getViewport().getAlignment() .getDataset()); @@ -497,6 +525,8 @@ public class Jalview2XML FileOutputStream fos = new FileOutputStream(jarFile); JarOutputStream jout = new JarOutputStream(fos); Hashtable dsses = new Hashtable(); + List viewIds = new ArrayList(); + for (AlignmentPanel apanel : af.alignPanels) { String jfileName = apSize == 1 ? fileName : fileName + ap; @@ -505,7 +535,7 @@ public class Jalview2XML { jfileName = jfileName + ".xml"; } - saveState(apanel, jfileName, jout); + saveState(apanel, jfileName, jout, viewIds); String dssid = getDatasetIdRef(af.getViewport().getAlignment() .getDataset()); if (!dsses.containsKey(dssid)) @@ -543,7 +573,7 @@ public class Jalview2XML { jfileName = jfileName + ".xml"; } - saveState(_af.alignPanel, jfileName, true, jout); + saveState(_af.alignPanel, jfileName, true, jout, null); } } @@ -557,13 +587,14 @@ public class Jalview2XML * name of alignment panel written to output stream * @param jout * jar output stream + * @param viewIds * @param out * jar entry name */ public JalviewModel saveState(AlignmentPanel ap, String fileName, - JarOutputStream jout) + JarOutputStream jout, List viewIds) { - return saveState(ap, fileName, false, jout); + return saveState(ap, fileName, false, jout, viewIds); } /** @@ -583,10 +614,15 @@ public class Jalview2XML * jar entry name */ public JalviewModel saveState(AlignmentPanel ap, String fileName, - boolean storeDS, JarOutputStream jout) + boolean storeDS, JarOutputStream jout, List viewIds) { + if (viewIds == null) + { + viewIds = new ArrayList(); + } + initSeqRefs(); - List viewIds = new ArrayList(); + List userColours = new ArrayList(); AlignViewport av = ap.av; @@ -598,11 +634,15 @@ 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(); @@ -619,6 +659,7 @@ public class Jalview2XML { // switch jal and the dataset jal = jal.getDataset(); + rjal = jal; } } if (jal.getProperties() != null) @@ -638,14 +679,12 @@ public class Jalview2XML Set calcIdSet = new HashSet(); // SAVE SEQUENCES - String id = ""; - jalview.datamodel.SequenceI jds, jdatasq; - for (int i = 0; i < jal.getHeight(); i++) + for (int i = 0; i < rjal.getHeight(); i++) { - jds = jal.getSequenceAt(i); - jdatasq = jds.getDatasetSequence() == null ? jds : jds - .getDatasetSequence(); - id = seqHash(jds); + final SequenceI jds = rjal.getSequenceAt(i); + final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds + : jds.getDatasetSequence(); + String id = seqHash(jds); if (seqRefIds.get(id) != null) { @@ -681,30 +720,37 @@ 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(rjal.getSequenceAt(i))) { jalview.datamodel.SequenceI[] reps = av - .getRepresentedSequences(jal.getSequenceAt(i)) - .getSequencesInOrder(jal); + .getRepresentedSequences(rjal.getSequenceAt(i)) + .getSequencesInOrder(rjal); for (int h = 0; h < reps.length; h++) { - if (reps[h] != jal.getSequenceAt(i)) + if (reps[h] != rjal.getSequenceAt(i)) { - 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(rjal.getSequenceAt(i) == 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(); + jalview.datamodel.SequenceFeature[] sf = jds.getSequenceFeatures(); int index = 0; while (index < sf.length) { @@ -729,10 +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()); @@ -745,9 +792,9 @@ 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(); @@ -774,8 +821,8 @@ public class Jalview2XML matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds, matchedFile, viewFrame); /* - * Only store each structure viewer's state once in each XML - * document. First time through only (storeDS==false) + * Only store each structure viewer's state once in the project + * jar. First time through only (storeDS==false) */ String viewId = viewFrame.getViewId(); if (!storeDS && !viewIds.contains(viewId)) @@ -783,8 +830,9 @@ public class Jalview2XML viewIds.add(viewId); try { + String viewerState = viewFrame.getStateInfo(); writeJarEntry(jout, getViewerJarEntryName(viewId), - viewFrame.getStateInfo().getBytes()); + viewerState.getBytes()); } catch (IOException e) { System.err.println("Error saving viewer state: " @@ -834,6 +882,8 @@ public class Jalview2XML } } + saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS); + jms.addJSeq(jseq); } @@ -844,7 +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(); @@ -863,37 +913,37 @@ public class Jalview2XML 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); -// } -// } + // TODO: delete this ? dead code from 2.8.3->2.9 ? + // { + // 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); + // } + // } } } @@ -942,35 +992,17 @@ public class Jalview2XML } } - /* - * Save associated Varna panels - */ - if (Desktop.desktop != null) - { - for (JInternalFrame frame : Desktop.desktop.getAllFrames()) - { - if (frame instanceof AppVarna) - { - AppVarna vp = (AppVarna) frame; - if (vp.ap == ap) - { - // save Varna state - } - } - } - } - // SAVE ANNOTATIONS /** * store forward refs from an annotationRow to any groups */ - IdentityHashMap groupRefs = new IdentityHashMap(); + IdentityHashMap groupRefs = new IdentityHashMap(); if (storeDS) { for (SequenceI sq : jal.getSequences()) { // Store annotation on dataset sequences only - jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation(); + AlignmentAnnotation[] aa = sq.getAnnotation(); if (aa != null && aa.length > 0) { storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS, @@ -983,8 +1015,7 @@ public class Jalview2XML if (jal.getAlignmentAnnotation() != null) { // Store the annotation shown on the alignment. - jalview.datamodel.AlignmentAnnotation[] aa = jal - .getAlignmentAnnotation(); + AlignmentAnnotation[] aa = jal.getAlignmentAnnotation(); storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS, vamsasSet); } @@ -996,70 +1027,66 @@ public class Jalview2XML int i = -1; for (jalview.datamodel.SequenceGroup sg : jal.getGroups()) { - groups[++i] = new JGroup(); + JGroup jGroup = new JGroup(); + groups[++i] = jGroup; - groups[i].setStart(sg.getStartRes()); - groups[i].setEnd(sg.getEndRes()); - groups[i].setName(sg.getName()); + jGroup.setStart(sg.getStartRes()); + jGroup.setEnd(sg.getEndRes()); + jGroup.setName(sg.getName()); if (groupRefs.containsKey(sg)) { - // group has references so set it's ID field - groups[i].setId(groupRefs.get(sg).toString()); + // group has references so set its ID field + jGroup.setId(groupRefs.get(sg)); } if (sg.cs != null) { if (sg.cs.conservationApplied()) { - groups[i].setConsThreshold(sg.cs.getConservationInc()); + jGroup.setConsThreshold(sg.cs.getConservationInc()); if (sg.cs instanceof jalview.schemes.UserColourScheme) { - groups[i].setColour(setUserColourScheme(sg.cs, userColours, - jms)); + jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); } else { - groups[i] - .setColour(ColourSchemeProperty.getColourName(sg.cs)); + jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs)); } } else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient) { - groups[i].setColour("AnnotationColourGradient"); - groups[i].setAnnotationColours(constructAnnotationColours( + jGroup.setColour("AnnotationColourGradient"); + jGroup.setAnnotationColours(constructAnnotationColours( (jalview.schemes.AnnotationColourGradient) sg.cs, userColours, jms)); } else if (sg.cs instanceof jalview.schemes.UserColourScheme) { - groups[i] - .setColour(setUserColourScheme(sg.cs, userColours, jms)); + jGroup.setColour(setUserColourScheme(sg.cs, userColours, jms)); } else { - groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs)); + jGroup.setColour(ColourSchemeProperty.getColourName(sg.cs)); } - groups[i].setPidThreshold(sg.cs.getThreshold()); + jGroup.setPidThreshold(sg.cs.getThreshold()); } - groups[i].setOutlineColour(sg.getOutlineColour().getRGB()); - groups[i].setDisplayBoxes(sg.getDisplayBoxes()); - groups[i].setDisplayText(sg.getDisplayText()); - groups[i].setColourText(sg.getColourText()); - groups[i].setTextCol1(sg.textColour.getRGB()); - groups[i].setTextCol2(sg.textColour2.getRGB()); - groups[i].setTextColThreshold(sg.thresholdTextColour); - groups[i].setShowUnconserved(sg.getShowNonconserved()); - groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); - groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram()); - groups[i].setShowSequenceLogo(sg.isShowSequenceLogo()); - groups[i].setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo()); - for (int s = 0; s < sg.getSize(); s++) - { - jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg - .getSequenceAt(s); - groups[i].addSeq(seqHash(seq)); + jGroup.setOutlineColour(sg.getOutlineColour().getRGB()); + jGroup.setDisplayBoxes(sg.getDisplayBoxes()); + jGroup.setDisplayText(sg.getDisplayText()); + jGroup.setColourText(sg.getColourText()); + jGroup.setTextCol1(sg.textColour.getRGB()); + jGroup.setTextCol2(sg.textColour2.getRGB()); + jGroup.setTextColThreshold(sg.thresholdTextColour); + jGroup.setShowUnconserved(sg.getShowNonconserved()); + jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus()); + jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram()); + jGroup.setShowSequenceLogo(sg.isShowSequenceLogo()); + jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo()); + for (SequenceI seq : sg.getSequences()) + { + jGroup.addSeq(seqHash(seq)); } } @@ -1080,15 +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); @@ -1138,6 +1176,7 @@ 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()); @@ -1169,17 +1208,17 @@ public class Jalview2XML .getFeatureRenderer().getRenderOrder() .toArray(new String[0]); - Vector settingsAdded = new Vector(); + Vector settingsAdded = new Vector(); Object gstyle = null; GraduatedColor gcol = null; if (renderOrder != null) { - for (int ro = 0; ro < renderOrder.length; ro++) + for (String featureType : renderOrder) { gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .getFeatureStyle(renderOrder[ro]); + .getFeatureStyle(featureType); Setting setting = new Setting(); - setting.setType(renderOrder[ro]); + setting.setType(featureType); if (gstyle instanceof GraduatedColor) { gcol = (GraduatedColor) gstyle; @@ -1194,57 +1233,30 @@ public class Jalview2XML } else { - setting.setColour(ap.getSeqPanel().seqCanvas - .getFeatureRenderer() - .getColour(renderOrder[ro]).getRGB()); + setting.setColour(((Color) gstyle).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; @@ -1310,6 +1322,7 @@ public class Jalview2XML // using save and then load try { + System.out.println("Writing jar entry " + fileName); JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout, @@ -1328,14 +1341,112 @@ public class Jalview2XML } /** - * Copy the contents of a file to a new file added to the output jar + * Save any Varna viewers linked to this sequence. Writes an rnaViewer element + * for each viewer, with + *
    + *
  • viewer geometry (position, size, split pane divider location)
    • + *
  • index of the selected structure in the viewer (currently shows gapped + * or ungapped)
    • + *
  • the id of the annotation holding RNA secondary structure
    • + *
  • (currently only one SS is shown per viewer, may be more in future)
    • + *
+ * Varna viewer state is also written out (in native Varna XML) to separate + * project jar entries. A separate entry is written for each RNA structure + * displayed, with the naming convention + *
    + *
  • rna_viewId_sequenceId_annotationId_[gapped|trimmed]
    • + *
+ * + * @param jout + * @param jseq + * @param jds + * @param viewIds + * @param ap + * @param storeDataset + */ + protected void saveRnaViewers(JarOutputStream jout, JSeq jseq, + 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--) + { + if (frames[f] instanceof AppVarna) + { + AppVarna varna = (AppVarna) frames[f]; + /* + * link the sequence to every viewer that is showing it and is linked to + * its alignment panel + */ + if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel()) + { + String viewId = varna.getViewId(); + RnaViewer rna = new RnaViewer(); + rna.setViewId(viewId); + rna.setTitle(varna.getTitle()); + rna.setXpos(varna.getX()); + rna.setYpos(varna.getY()); + rna.setWidth(varna.getWidth()); + rna.setHeight(varna.getHeight()); + rna.setDividerLocation(varna.getDividerLocation()); + rna.setSelectedRna(varna.getSelectedIndex()); + jseq.addRnaViewer(rna); + + /* + * Store each Varna panel's state once in the project per sequence. + * First time through only (storeDataset==false) + */ + // boolean storeSessions = false; + // String sequenceViewId = viewId + seqsToIds.get(jds); + // if (!storeDataset && !viewIds.contains(sequenceViewId)) + // { + // viewIds.add(sequenceViewId); + // storeSessions = true; + // } + for (RnaModel model : varna.getModels()) + { + if (model.seq == jds) + { + /* + * VARNA saves each view (sequence or alignment secondary + * structure, gapped or trimmed) as a separate XML file + */ + String jarEntryName = rnaSessions.get(model); + if (jarEntryName == null) + { + + String varnaStateFile = varna.getStateInfo(model.rna); + jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter(); + copyFileToJar(jout, varnaStateFile, jarEntryName); + rnaSessions.put(model, jarEntryName); + } + SecondaryStructure ss = new SecondaryStructure(); + String annotationId = varna.getAnnotation(jds).annotationId; + ss.setAnnotationId(annotationId); + ss.setViewerState(jarEntryName); + ss.setGapped(model.gapped); + ss.setTitle(model.title); + rna.addSecondaryStructure(ss); + } + } + } + } + } + } + + /** + * Copy the contents of a file to a new entry added to the output jar * * @param jout * @param infilePath - * @param jarfileName + * @param jarEntryName */ protected void copyFileToJar(JarOutputStream jout, String infilePath, - String jarfileName) + String jarEntryName) { DataInputStream dis = null; try @@ -1346,7 +1457,7 @@ public class Jalview2XML dis = new DataInputStream(new FileInputStream(file)); byte[] data = new byte[(int) file.length()]; dis.readFully(data); - writeJarEntry(jout, jarfileName, data); + writeJarEntry(jout, jarEntryName, data); } } catch (Exception ex) { @@ -1370,16 +1481,17 @@ public class Jalview2XML * Write the data to a new entry of given name in the output jar file * * @param jout - * @param jarfileName + * @param jarEntryName * @param data * @throws IOException */ - protected void writeJarEntry(JarOutputStream jout, String jarfileName, + protected void writeJarEntry(JarOutputStream jout, String jarEntryName, byte[] data) throws IOException { if (jout != null) { - jout.putNextEntry(new JarEntry(jarfileName)); + System.out.println("Writing jar entry " + jarEntryName); + jout.putNextEntry(new JarEntry(jarEntryName)); DataOutputStream dout = new DataOutputStream(jout); dout.write(data, 0, data.length); dout.flush(); @@ -1490,61 +1602,65 @@ public class Jalview2XML } private void storeAlignmentAnnotation(AlignmentAnnotation[] aa, - IdentityHashMap groupRefs, AlignmentViewport av, - Set calcIdSet, boolean storeDS, SequenceSet vamsasSet) + IdentityHashMap groupRefs, + AlignmentViewport av, Set calcIdSet, boolean storeDS, + SequenceSet vamsasSet) { for (int i = 0; i < aa.length; i++) { Annotation an = new Annotation(); - if (aa[i].annotationId != null) + AlignmentAnnotation annotation = aa[i]; + if (annotation.annotationId != null) { - annotationIds.put(aa[i].annotationId, aa[i]); + annotationIds.put(annotation.annotationId, annotation); } - an.setId(aa[i].annotationId); + an.setId(annotation.annotationId); - an.setVisible(aa[i].visible); + an.setVisible(annotation.visible); - an.setDescription(aa[i].description); + an.setDescription(annotation.description); - if (aa[i].sequenceRef != null) + if (annotation.sequenceRef != null) { // 2.9 JAL-1781 xref on sequence id rather than name - an.setSequenceRef(seqsToIds.get(aa[i].sequenceRef)); + an.setSequenceRef(seqsToIds.get(annotation.sequenceRef)); } - if (aa[i].groupRef != null) + if (annotation.groupRef != null) { - Object groupIdr = groupRefs.get(aa[i].groupRef); + String groupIdr = groupRefs.get(annotation.groupRef); if (groupIdr == null) { // make a locally unique String - groupRefs.put(aa[i].groupRef, + groupRefs.put( + annotation.groupRef, groupIdr = ("" + System.currentTimeMillis() - + aa[i].groupRef.getName() + groupRefs.size())); + + annotation.groupRef.getName() + groupRefs + .size())); } an.setGroupRef(groupIdr.toString()); } // store all visualization attributes for annotation - an.setGraphHeight(aa[i].graphHeight); - an.setCentreColLabels(aa[i].centreColLabels); - an.setScaleColLabels(aa[i].scaleColLabel); - an.setShowAllColLabels(aa[i].showAllColLabels); - an.setBelowAlignment(aa[i].belowAlignment); + an.setGraphHeight(annotation.graphHeight); + an.setCentreColLabels(annotation.centreColLabels); + an.setScaleColLabels(annotation.scaleColLabel); + an.setShowAllColLabels(annotation.showAllColLabels); + an.setBelowAlignment(annotation.belowAlignment); - if (aa[i].graph > 0) + if (annotation.graph > 0) { an.setGraph(true); - an.setGraphType(aa[i].graph); - an.setGraphGroup(aa[i].graphGroup); - if (aa[i].getThreshold() != null) + an.setGraphType(annotation.graph); + an.setGraphGroup(annotation.graphGroup); + if (annotation.getThreshold() != null) { ThresholdLine line = new ThresholdLine(); - line.setLabel(aa[i].getThreshold().label); - line.setValue(aa[i].getThreshold().value); - line.setColour(aa[i].getThreshold().colour.getRGB()); + line.setLabel(annotation.getThreshold().label); + line.setValue(annotation.getThreshold().value); + line.setColour(annotation.getThreshold().colour.getRGB()); an.setThresholdLine(line); } } @@ -1553,78 +1669,78 @@ public class Jalview2XML an.setGraph(false); } - an.setLabel(aa[i].label); + an.setLabel(annotation.label); - if (aa[i] == av.getAlignmentQualityAnnot() - || aa[i] == av.getAlignmentConservationAnnotation() - || aa[i] == av.getAlignmentConsensusAnnotation() - || aa[i].autoCalculated) + if (annotation == av.getAlignmentQualityAnnot() + || annotation == av.getAlignmentConservationAnnotation() + || annotation == av.getAlignmentConsensusAnnotation() + || annotation.autoCalculated) { // new way of indicating autocalculated annotation - - an.setAutoCalculated(aa[i].autoCalculated); + an.setAutoCalculated(annotation.autoCalculated); } - if (aa[i].hasScore()) + if (annotation.hasScore()) { - an.setScore(aa[i].getScore()); + an.setScore(annotation.getScore()); } - if (aa[i].getCalcId() != null) + if (annotation.getCalcId() != null) { - calcIdSet.add(aa[i].getCalcId()); - an.setCalcId(aa[i].getCalcId()); + calcIdSet.add(annotation.getCalcId()); + an.setCalcId(annotation.getCalcId()); } - if (aa[i].hasProperties()) + if (annotation.hasProperties()) { - for (String pr : aa[i].getProperties()) + for (String pr : annotation.getProperties()) { Property prop = new Property(); prop.setName(pr); - prop.setValue(aa[i].getProperty(pr)); + prop.setValue(annotation.getProperty(pr)); an.addProperty(prop); } } AnnotationElement ae; - if (aa[i].annotations != null) + if (annotation.annotations != null) { an.setScoreOnly(false); - for (int a = 0; a < aa[i].annotations.length; a++) + for (int a = 0; a < annotation.annotations.length; a++) { - if ((aa[i] == null) || (aa[i].annotations[a] == null)) + if ((annotation == null) || (annotation.annotations[a] == null)) { continue; } ae = new AnnotationElement(); - if (aa[i].annotations[a].description != null) + if (annotation.annotations[a].description != null) { - ae.setDescription(aa[i].annotations[a].description); + ae.setDescription(annotation.annotations[a].description); } - if (aa[i].annotations[a].displayCharacter != null) + if (annotation.annotations[a].displayCharacter != null) { - ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter); + ae.setDisplayCharacter(annotation.annotations[a].displayCharacter); } - if (!Float.isNaN(aa[i].annotations[a].value)) + if (!Float.isNaN(annotation.annotations[a].value)) { - ae.setValue(aa[i].annotations[a].value); + ae.setValue(annotation.annotations[a].value); } ae.setPosition(a); - if (aa[i].annotations[a].secondaryStructure > ' ') + if (annotation.annotations[a].secondaryStructure > ' ') { - ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure + ae.setSecondaryStructure(annotation.annotations[a].secondaryStructure + ""); } - if (aa[i].annotations[a].colour != null - && aa[i].annotations[a].colour != java.awt.Color.black) + if (annotation.annotations[a].colour != null + && annotation.annotations[a].colour != java.awt.Color.black) { - ae.setColour(aa[i].annotations[a].colour.getRGB()); + ae.setColour(annotation.annotations[a].colour.getRGB()); } an.addAnnotationElement(ae); - if (aa[i].autoCalculated) + if (annotation.autoCalculated) { // only write one non-null entry into the annotation row - // sufficient to get the visualization attributes necessary to @@ -1637,7 +1753,7 @@ public class Jalview2XML { an.setScoreOnly(true); } - if (!storeDS || (storeDS && !aa[i].autoCalculated)) + if (!storeDS || (storeDS && !annotation.autoCalculated)) { // skip autocalculated annotation - these are only provided for // alignments @@ -1737,8 +1853,8 @@ public class Jalview2XML } } throw new Error(MessageManager.formatMessage( - "error.unsupported_version_calcIdparam", new Object[] - { calcIdParam.toString() })); + "error.unsupported_version_calcIdparam", + new Object[] { calcIdParam.toString() })); } /** @@ -1820,16 +1936,16 @@ 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) { @@ -2050,6 +2166,7 @@ public class Jalview2XML { SwingUtilities.invokeAndWait(new Runnable() { + @Override public void run() { setLoadingFinishedForNewStructureViewers(); @@ -2057,7 +2174,7 @@ public class Jalview2XML }); } catch (Exception x) { - + System.err.println("Error loading alignment: " + x.getMessage()); } } return af; @@ -2124,7 +2241,7 @@ public class Jalview2XML } if (frefedSequence == null) { - frefedSequence = new Vector(); + frefedSequence = new Vector(); } AlignFrame af = null, _af = null; @@ -2173,13 +2290,7 @@ public class Jalview2XML } } while (jarentry != null); resolveFrefedSequences(); - } catch (java.io.FileNotFoundException ex) - { - ex.printStackTrace(); - errorMessage = "Couldn't locate Jalview XML file : " + file; - System.err.println("Exception whilst loading jalview XML file : " - + ex + "\n"); - } catch (java.net.UnknownHostException ex) + } catch (IOException ex) { ex.printStackTrace(); errorMessage = "Couldn't locate Jalview XML file : " + file; @@ -2306,7 +2417,8 @@ 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()); @@ -2341,6 +2453,11 @@ 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); /* @@ -2550,7 +2667,7 @@ 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++) @@ -2575,6 +2692,11 @@ public class Jalview2XML vi++; } + if (jseqs[i].hasViewreference() && jseqs[i].getViewreference()) + { + referenceseqForView = tmpseqs.get(tmpseqs.size() - 1); + } + if (jseqs[i].getHidden()) { if (hiddenSeqs == null) @@ -2584,7 +2706,6 @@ public class Jalview2XML hiddenSeqs.add(seqRefIds.get(seqId)); } - } // / @@ -2595,6 +2716,10 @@ 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++) { @@ -2720,15 +2845,15 @@ public class Jalview2XML { mapping = addMapping(maps[m].getMapping()); } - if (dnaseq != null) + if (dnaseq != null && mapping.getTo() != null) { cf.addMap(dnaseq, mapping.getTo(), mapping.getMap()); } else { // defer to later - frefedSequence.add(new Object[] - { maps[m].getDnasq(), cf, mapping }); + frefedSequence.add(new Object[] { maps[m].getDnasq(), cf, + mapping }); } } } @@ -2739,10 +2864,11 @@ public class Jalview2XML // //////////////////////////////// // LOAD ANNOTATIONS List autoAlan = new ArrayList(); - /** + + /* * store any annotations which forward reference a group's ID */ - Hashtable> groupAnnotRefs = new Hashtable>(); + Map> groupAnnotRefs = new Hashtable>(); if (vamsasSet.getAnnotationCount() > 0) { @@ -2750,39 +2876,42 @@ public class Jalview2XML for (int i = 0; i < an.length; i++) { + Annotation annotation = an[i]; + /** * test if annotation is automatically calculated for this view only */ boolean autoForView = false; - if (an[i].getLabel().equals("Quality") - || an[i].getLabel().equals("Conservation") - || an[i].getLabel().equals("Consensus")) + if (annotation.getLabel().equals("Quality") + || annotation.getLabel().equals("Conservation") + || annotation.getLabel().equals("Consensus")) { // Kludge for pre 2.5 projects which lacked the autocalculated flag autoForView = true; - if (!an[i].hasAutoCalculated()) + if (!annotation.hasAutoCalculated()) { - an[i].setAutoCalculated(true); + annotation.setAutoCalculated(true); } } if (autoForView - || (an[i].hasAutoCalculated() && an[i].isAutoCalculated())) + || (annotation.hasAutoCalculated() && annotation + .isAutoCalculated())) { // remove ID - we don't recover annotation from other views for // view-specific annotation - an[i].setId(null); + annotation.setId(null); } // set visiblity for other annotation in this view - if (an[i].getId() != null - && annotationIds.containsKey(an[i].getId())) + String annotationId = annotation.getId(); + if (annotationId != null && annotationIds.containsKey(annotationId)) { - AlignmentAnnotation jda = annotationIds.get(an[i].getId()); + AlignmentAnnotation jda = annotationIds.get(annotationId); // in principle Visible should always be true for annotation displayed // in multiple views - if (an[i].hasVisible()) + if (annotation.hasVisible()) { - jda.visible = an[i].getVisible(); + jda.visible = annotation.getVisible(); } al.addAnnotation(jda); @@ -2790,11 +2919,11 @@ public class Jalview2XML continue; } // Construct new annotation from model. - AnnotationElement[] ae = an[i].getAnnotationElement(); + AnnotationElement[] ae = annotation.getAnnotationElement(); jalview.datamodel.Annotation[] anot = null; java.awt.Color firstColour = null; int anpos; - if (!an[i].getScoreOnly()) + if (!annotation.getScoreOnly()) { anot = new jalview.datamodel.Annotation[al.getWidth()]; for (int aa = 0; aa < ae.length && aa < anot.length; aa++) @@ -2831,27 +2960,27 @@ public class Jalview2XML } jalview.datamodel.AlignmentAnnotation jaa = null; - if (an[i].getGraph()) + if (annotation.getGraph()) { float llim = 0, hlim = 0; // if (autoForView || an[i].isAutoCalculated()) { // hlim=11f; // } - jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot, llim, hlim, - an[i].getGraphType()); + jaa = new jalview.datamodel.AlignmentAnnotation( + annotation.getLabel(), annotation.getDescription(), anot, + llim, hlim, annotation.getGraphType()); - jaa.graphGroup = an[i].getGraphGroup(); + jaa.graphGroup = annotation.getGraphGroup(); jaa._linecolour = firstColour; - if (an[i].getThresholdLine() != null) + if (annotation.getThresholdLine() != null) { - jaa.setThreshold(new jalview.datamodel.GraphLine(an[i] - .getThresholdLine().getValue(), an[i] + jaa.setThreshold(new jalview.datamodel.GraphLine(annotation + .getThresholdLine().getValue(), annotation .getThresholdLine().getLabel(), new java.awt.Color( - an[i].getThresholdLine().getColour()))); + annotation.getThresholdLine().getColour()))); } - if (autoForView || an[i].isAutoCalculated()) + if (autoForView || annotation.isAutoCalculated()) { // Hardwire the symbol display line to ensure that labels for // histograms are displayed @@ -2890,7 +3019,7 @@ public class Jalview2XML // and make a note of any group association if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0) { - ArrayList aal = groupAnnotRefs + List aal = groupAnnotRefs .get(an[i].getGroupRef()); if (aal == null) { @@ -2964,37 +3093,37 @@ public class Jalview2XML boolean addAnnotSchemeGroup = false; for (int i = 0; i < groups.length; i++) { + JGroup jGroup = groups[i]; ColourSchemeI cs = null; - - if (groups[i].getColour() != null) + if (jGroup.getColour() != null) { - if (groups[i].getColour().startsWith("ucs")) + if (jGroup.getColour().startsWith("ucs")) { - cs = getUserColourScheme(jms, groups[i].getColour()); + cs = getUserColourScheme(jms, jGroup.getColour()); } - else if (groups[i].getColour().equals("AnnotationColourGradient") - && groups[i].getAnnotationColours() != null) + else if (jGroup.getColour().equals("AnnotationColourGradient") + && jGroup.getAnnotationColours() != null) { addAnnotSchemeGroup = true; cs = null; } else { - cs = ColourSchemeProperty.getColour(al, groups[i].getColour()); + cs = ColourSchemeProperty.getColour(al, jGroup.getColour()); } if (cs != null) { - cs.setThreshold(groups[i].getPidThreshold(), true); + cs.setThreshold(jGroup.getPidThreshold(), true); } } - Vector seqs = new Vector(); + Vector seqs = new Vector(); - for (int s = 0; s < groups[i].getSeqCount(); s++) + for (int s = 0; s < jGroup.getSeqCount(); s++) { - String seqId = groups[i].getSeq(s) + ""; - jalview.datamodel.SequenceI ts = seqRefIds.get(seqId); + String seqId = jGroup.getSeq(s) + ""; + SequenceI ts = seqRefIds.get(seqId); if (ts != null) { @@ -3007,36 +3136,35 @@ public class Jalview2XML continue; } - jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup( - seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(), - groups[i].getDisplayText(), groups[i].getColourText(), - groups[i].getStart(), groups[i].getEnd()); + SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs, + jGroup.getDisplayBoxes(), jGroup.getDisplayText(), + jGroup.getColourText(), jGroup.getStart(), jGroup.getEnd()); - sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour())); + sg.setOutlineColour(new java.awt.Color(jGroup.getOutlineColour())); - sg.textColour = new java.awt.Color(groups[i].getTextCol1()); - sg.textColour2 = new java.awt.Color(groups[i].getTextCol2()); - sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i] + sg.textColour = new java.awt.Color(jGroup.getTextCol1()); + sg.textColour2 = new java.awt.Color(jGroup.getTextCol2()); + sg.setShowNonconserved(jGroup.hasShowUnconserved() ? jGroup .isShowUnconserved() : false); - sg.thresholdTextColour = groups[i].getTextColThreshold(); - if (groups[i].hasShowConsensusHistogram()) + sg.thresholdTextColour = jGroup.getTextColThreshold(); + if (jGroup.hasShowConsensusHistogram()) { - sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram()); + sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram()); } ; - if (groups[i].hasShowSequenceLogo()) + if (jGroup.hasShowSequenceLogo()) { - sg.setshowSequenceLogo(groups[i].isShowSequenceLogo()); + sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); } - if (groups[i].hasNormaliseSequenceLogo()) + if (jGroup.hasNormaliseSequenceLogo()) { - sg.setNormaliseSequenceLogo(groups[i].isNormaliseSequenceLogo()); + sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); } - if (groups[i].hasIgnoreGapsinConsensus()) + if (jGroup.hasIgnoreGapsinConsensus()) { - sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus()); + sg.setIgnoreGapsConsensus(jGroup.getIgnoreGapsinConsensus()); } - if (groups[i].getConsThreshold() != 0) + if (jGroup.getConsThreshold() != 0) { jalview.analysis.Conservation c = new jalview.analysis.Conservation( "All", ResidueProperties.propHash, 3, @@ -3046,14 +3174,14 @@ public class Jalview2XML sg.cs.setConservation(c); } - if (groups[i].getId() != null && groupAnnotRefs.size() > 0) + if (jGroup.getId() != null && groupAnnotRefs.size() > 0) { // re-instate unique group/annotation row reference - ArrayList jaal = groupAnnotRefs - .get(groups[i].getId()); + List jaal = groupAnnotRefs.get(jGroup + .getId()); if (jaal != null) { - for (jalview.datamodel.AlignmentAnnotation jaa : jaal) + for (AlignmentAnnotation jaa : jaal) { jaa.groupRef = sg; if (jaa.autoCalculated) @@ -3078,8 +3206,8 @@ public class Jalview2XML if (addAnnotSchemeGroup) { // reconstruct the annotation colourscheme - sg.cs = constructAnnotationColour( - groups[i].getAnnotationColours(), null, al, jms, false); + sg.cs = constructAnnotationColour(jGroup.getAnnotationColours(), + null, al, jms, false); } } } @@ -3135,8 +3263,8 @@ 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; @@ -3170,90 +3298,202 @@ public class Jalview2XML av = af.viewport; ap = af.alignPanel; } - // LOAD TREES - // ///////////////////////////////////// - if (loadTreesAndStructures && jms.getTreeCount() > 0) + + /* + * Load any trees, PDB structures and viewers + * + * Not done if flag is false (when this method is used for New View) + */ + if (loadTreesAndStructures) { - try + loadTrees(jms, view, af, av, ap); + loadPDBStructures(jprovider, jseqs, af, ap); + loadRnaViewers(jprovider, jseqs, ap); + } + // and finally return. + return af; + } + + /** + * 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. + * + * Currently each viewer shows just one sequence and structure (gapped and + * trimmed), however this method is designed to support multiple sequences or + * structures in viewers if wanted in future. + * + * @param jprovider + * @param jseqs + * @param ap + */ + private void loadRnaViewers(jarInputStreamProvider jprovider, + JSeq[] jseqs, AlignmentPanel ap) + { + /* + * scan the sequences for references to viewers; create each one the first + * time it is referenced, add Rna models to existing viewers + */ + for (JSeq jseq : jseqs) + { + for (int i = 0; i < jseq.getRnaViewerCount(); i++) { - for (int t = 0; t < jms.getTreeCount(); t++) + RnaViewer viewer = jseq.getRnaViewer(i); + 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()); - Tree tree = jms.getTree(t); + /* + * add the structure to the Varna display (with session state copied + * from the jar to a temporary file) + */ + boolean gapped = ss.isGapped(); + String rnaTitle = ss.getTitle(); + String sessionState = ss.getViewerState(); + String tempStateFile = copyJarEntry(jprovider, sessionState, + "varna"); + RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped); + appVarna.addModelSession(rna, rnaTitle, tempStateFile); + } + appVarna.setInitialSelection(viewer.getSelectedRna()); + } + } + } - TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); - if (tp == null) - { - tp = af.ShowNewickTree( - new jalview.io.NewickFile(tree.getNewick()), - tree.getTitle(), tree.getWidth(), tree.getHeight(), - tree.getXpos(), tree.getYpos()); - if (tree.getId() != null) - { - // perhaps bind the tree id to something ? - } - } - else - { - // update local tree attributes ? - // 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 - // views' - // works still - tp.treeCanvas.av = av; // af.viewport; - tp.treeCanvas.ap = ap; // af.alignPanel; + /** + * Locate and return an already instantiated matching AppVarna, or create one + * if not found + * + * @param viewer + * @param viewIdSuffix + * @param ap + * @return + */ + protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer, + String viewIdSuffix, AlignmentPanel ap) + { + /* + * on each load a suffix is appended to the saved viewId, to avoid conflicts + * if load is repeated + */ + String postLoadId = viewer.getViewId() + viewIdSuffix; + for (JInternalFrame frame : getAllFrames()) + { + if (frame instanceof AppVarna) + { + AppVarna varna = (AppVarna) frame; + if (postLoadId.equals(varna.getViewId())) + { + // this viewer is already instantiated + // could in future here add ap as another 'parent' of the + // AppVarna window; currently just 1-to-many + return varna; + } + } + } - } - if (tp == null) - { - warn("There was a problem recovering stored Newick tree: \n" - + tree.getNewick()); - continue; - } + /* + * viewer not found - make it + */ + RnaViewerModel model = new RnaViewerModel(postLoadId, + viewer.getTitle(), viewer.getXpos(), viewer.getYpos(), + viewer.getWidth(), viewer.getHeight(), + viewer.getDividerLocation()); + AppVarna varna = new AppVarna(model, ap); - tp.fitToWindow.setState(tree.getFitToWindow()); - tp.fitToWindow_actionPerformed(null); + return varna; + } - if (tree.getFontName() != null) - { - tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree - .getFontStyle(), tree.getFontSize())); - } - else + /** + * Load any saved trees + * + * @param jms + * @param view + * @param af + * @param av + * @param ap + */ + protected void loadTrees(JalviewModelSequence jms, Viewport view, + AlignFrame af, AlignViewport av, AlignmentPanel ap) + { + // TODO result of automated refactoring - are all these parameters needed? + try + { + for (int t = 0; t < jms.getTreeCount(); t++) + { + + Tree tree = jms.getTree(t); + + TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); + if (tp == null) + { + tp = af.ShowNewickTree( + new jalview.io.NewickFile(tree.getNewick()), + tree.getTitle(), tree.getWidth(), tree.getHeight(), + tree.getXpos(), tree.getYpos()); + if (tree.getId() != null) { - tp.setTreeFont(new java.awt.Font(view.getFontName(), view - .getFontStyle(), tree.getFontSize())); + // perhaps bind the tree id to something ? } + } + else + { + // update local tree attributes ? + // 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 + // views' + // works still + tp.treeCanvas.av = av; // af.viewport; + tp.treeCanvas.ap = ap; // af.alignPanel; - tp.showPlaceholders(tree.getMarkUnlinked()); - tp.showBootstrap(tree.getShowBootstrap()); - tp.showDistances(tree.getShowDistances()); + } + if (tp == null) + { + warn("There was a problem recovering stored Newick tree: \n" + + tree.getNewick()); + continue; + } - tp.treeCanvas.threshold = tree.getThreshold(); + tp.fitToWindow.setState(tree.getFitToWindow()); + tp.fitToWindow_actionPerformed(null); - if (tree.getCurrentTree()) - { - af.viewport.setCurrentTree(tp.getTree()); - } + if (tree.getFontName() != null) + { + 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())); } - } catch (Exception ex) - { - ex.printStackTrace(); + tp.showPlaceholders(tree.getMarkUnlinked()); + tp.showBootstrap(tree.getShowBootstrap()); + tp.showDistances(tree.getShowDistances()); + + tp.treeCanvas.threshold = tree.getThreshold(); + + if (tree.getCurrentTree()) + { + af.viewport.setCurrentTree(tp.getTree()); + } } - } - // //LOAD STRUCTURES - if (loadTreesAndStructures) + } catch (Exception ex) { - loadStructures(jprovider, jseqs, af, ap); + ex.printStackTrace(); } - // and finally return. - return af; } /** @@ -3264,7 +3504,7 @@ public class Jalview2XML * @param af * @param ap */ - protected void loadStructures(jarInputStreamProvider jprovider, + protected void loadPDBStructures(jarInputStreamProvider jprovider, JSeq[] jseqs, AlignFrame af, AlignmentPanel ap) { /* @@ -3448,21 +3688,22 @@ 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 * - * Note this is the 'saved' viewId as in the project file XML, _not_ the + * NB this is the 'saved' viewId as in the project file XML, _not_ the * 'uniquified' sviewid used to reconstruct the viewer here */ - chimeraSessionFile = copyJarEntry(jprovider, - getViewerJarEntryName(data.getViewId()), "chimera"); + String viewerJarEntryName = getViewerJarEntryName(data.getViewId()); + chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName, + "chimera"); Set> fileData = data.getFileData() .entrySet(); @@ -3487,9 +3728,10 @@ public class Jalview2XML final SequenceI[][] seqsArray = allseqs.toArray(new SequenceI[allseqs .size()][]); 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()); } @@ -3578,16 +3820,23 @@ public class Jalview2XML newFileLoc.append(";"); } - if (newFileLoc.length() > 0) + if (newFileLoc.length() == 0) { - int histbug = newFileLoc.indexOf("history = "); + return; + } + int histbug = newFileLoc.indexOf("history = "); + if (histbug > -1) + { + /* + * change "history = [true|false];" to "history = [1|0];" + */ histbug += 10; int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug); String val = (diff == -1) ? null : newFileLoc .substring(histbug, diff); if (val != null && val.length() >= 4) { - if (val.contains("e")) + if (val.contains("e")) // eh? what can it be? { if (val.trim().equals("true")) { @@ -3600,54 +3849,55 @@ public class Jalview2XML newFileLoc.replace(histbug, diff, val); } } + } - 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()][]); - final String fileloc = newFileLoc.toString(); - final String sviewid = viewerData.getKey(); - final AlignFrame alf = af; - final Rectangle rect = new Rectangle(svattrib.getX(), - svattrib.getY(), svattrib.getWidth(), svattrib.getHeight()); - try + 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()][]); + final String fileloc = newFileLoc.toString(); + final String sviewid = viewerData.getKey(); + final AlignFrame alf = af; + final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(), + svattrib.getWidth(), svattrib.getHeight()); + try + { + javax.swing.SwingUtilities.invokeAndWait(new Runnable() { - javax.swing.SwingUtilities.invokeAndWait(new Runnable() + @Override + public void run() { - @Override - public void run() + JalviewStructureDisplayI sview = null; + try { - JalviewStructureDisplayI sview = null; - try - { - sview = new StructureViewer(alf.alignPanel - .getStructureSelectionManager()).createView( - StructureViewer.ViewerType.JMOL, pdbf, id, sq, - alf.alignPanel, svattrib, fileloc, rect, sviewid); - addNewStructureViewer(sview); - } catch (OutOfMemoryError ex) + sview = new StructureViewer(alf.alignPanel + .getStructureSelectionManager()).createView( + StructureViewer.ViewerType.JMOL, pdbf, id, sq, + alf.alignPanel, svattrib, fileloc, rect, sviewid); + addNewStructureViewer(sview); + } catch (OutOfMemoryError ex) + { + new OOMWarning("restoring structure view for PDB id " + id, + (OutOfMemoryError) ex.getCause()); + if (sview != null && sview.isVisible()) { - new OOMWarning("restoring structure view for PDB id " + id, - (OutOfMemoryError) ex.getCause()); - if (sview != null && sview.isVisible()) - { - sview.closeViewer(false); - sview.setVisible(false); - sview.dispose(); - } + sview.closeViewer(false); + sview.setVisible(false); + sview.dispose(); } } - }); - } catch (InvocationTargetException ex) - { - warn("Unexpected error when opening Jmol view.", ex); + } + }); + } catch (InvocationTargetException ex) + { + warn("Unexpected error when opening Jmol view.", ex); - } catch (InterruptedException e) - { - // e.printStackTrace(); - } + } catch (InterruptedException e) + { + // e.printStackTrace(); } + } /** @@ -3659,7 +3909,7 @@ public class Jalview2XML */ protected String getViewerJarEntryName(String viewId) { - return "viewer_" + viewId; + return VIEWER_PREFIX + viewId; } /** @@ -3792,17 +4042,22 @@ 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 */ - private boolean isVersionStringLaterThan(String supported, String version) + 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")) { @@ -3813,38 +4068,8 @@ 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; @@ -3888,6 +4113,12 @@ 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) @@ -3958,6 +4189,9 @@ 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()); @@ -4183,7 +4417,7 @@ 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 @@ -4342,8 +4576,8 @@ 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) @@ -4636,20 +4870,24 @@ public class Jalview2XML } } - java.util.Hashtable datasetIds = null; + /* + * TODO use AlignmentI here and in related methods - needs + * AlignmentI.getDataset() changed to return AlignmentI instead of Alignment + */ + Hashtable datasetIds = null; - java.util.IdentityHashMap dataset2Ids = null; + IdentityHashMap dataset2Ids = null; private Alignment getDatasetFor(String datasetId) { if (datasetIds == null) { - datasetIds = new Hashtable(); + datasetIds = new Hashtable(); return null; } if (datasetIds.containsKey(datasetId)) { - return (Alignment) datasetIds.get(datasetId); + return datasetIds.get(datasetId); } return null; } @@ -4658,7 +4896,7 @@ public class Jalview2XML { if (datasetIds == null) { - datasetIds = new Hashtable(); + datasetIds = new Hashtable(); } datasetIds.put(datasetId, dataset); } @@ -4669,7 +4907,7 @@ public class Jalview2XML * @param dataset * @return */ - private String getDatasetIdRef(jalview.datamodel.Alignment dataset) + private String getDatasetIdRef(Alignment dataset) { if (dataset.getDataset() != null) { @@ -4681,11 +4919,11 @@ public class Jalview2XML // make a new datasetId and record it if (dataset2Ids == null) { - dataset2Ids = new IdentityHashMap(); + dataset2Ids = new IdentityHashMap(); } else { - datasetId = (String) dataset2Ids.get(dataset); + datasetId = dataset2Ids.get(dataset); } if (datasetId == null) { @@ -4749,8 +4987,7 @@ public class Jalview2XML } else { - frefedSequence.add(new Object[] - { dsfor, jmap }); + frefedSequence.add(new Object[] { dsfor, jmap }); } } else @@ -4804,8 +5041,7 @@ public class Jalview2XML boolean keepSeqRefs) { initSeqRefs(); - jalview.schemabinding.version2.JalviewModel jm = saveState(ap, null, - null); + JalviewModel jm = saveState(ap, null, null, null); if (!keepSeqRefs) { @@ -5085,7 +5321,17 @@ public class Jalview2XML } } } - + return result; } + + /** + * Returns an incrementing counter (0, 1, 2...) + * + * @return + */ + private synchronized int nextCounter() + { + return counter++; + } }