X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=09f167512d2062a6a7d0f13fc506e828c231f12c;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=194cbf24c4a269db0834739101def9992d792cb0;hpb=59d9dfb7b746fcc396af9b572b40636028df9fed;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 194cbf2..09f1675 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -20,17 +20,28 @@ */ package jalview.project; +import static jalview.math.RotatableMatrix.Axis.X; +import static jalview.math.RotatableMatrix.Axis.Y; +import static jalview.math.RotatableMatrix.Axis.Z; + import jalview.analysis.Conservation; +import jalview.analysis.PCA; +import jalview.analysis.scoremodels.ScoreModels; +import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; +import jalview.api.analysis.ScoreModelI; +import jalview.api.analysis.SimilarityParamsI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; import jalview.datamodel.GraphLine; import jalview.datamodel.PDBEntry; +import jalview.datamodel.Point; import jalview.datamodel.RnaViewerModel; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -49,18 +60,21 @@ import jalview.gui.AppVarna; import jalview.gui.ChimeraViewFrame; import jalview.gui.Desktop; import jalview.gui.FeatureRenderer; -import jalview.gui.Jalview2XML_V1; import jalview.gui.JvOptionPane; import jalview.gui.OOMWarning; +import jalview.gui.PCAPanel; import jalview.gui.PaintRefresher; import jalview.gui.SplitFrame; import jalview.gui.StructureViewer; import jalview.gui.StructureViewer.ViewerType; import jalview.gui.StructureViewerBase; import jalview.gui.TreePanel; +import jalview.io.BackupFiles; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.NewickFile; +import jalview.math.Matrix; +import jalview.math.MatrixI; import jalview.renderer.ResidueShaderI; import jalview.schemes.AnnotationColourGradient; import jalview.schemes.ColourSchemeI; @@ -77,6 +91,7 @@ import jalview.util.StringUtils; import jalview.util.jarInputStreamProvider; import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.PCAModel; import jalview.viewmodel.ViewportRanges; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; @@ -92,6 +107,8 @@ import jalview.xml.binding.jalview.Annotation; import jalview.xml.binding.jalview.Annotation.ThresholdLine; import jalview.xml.binding.jalview.AnnotationColourScheme; import jalview.xml.binding.jalview.AnnotationElement; +import jalview.xml.binding.jalview.DoubleMatrix; +import jalview.xml.binding.jalview.DoubleVector; import jalview.xml.binding.jalview.Feature; import jalview.xml.binding.jalview.Feature.OtherData; import jalview.xml.binding.jalview.FeatureMatcherSet.CompoundMatcher; @@ -106,6 +123,11 @@ import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids; import jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState; import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer; import jalview.xml.binding.jalview.JalviewModel.JSeq.RnaViewer.SecondaryStructure; +import jalview.xml.binding.jalview.JalviewModel.PcaViewer; +import jalview.xml.binding.jalview.JalviewModel.PcaViewer.Axis; +import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMax; +import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SeqPointMin; +import jalview.xml.binding.jalview.JalviewModel.PcaViewer.SequencePoint; import jalview.xml.binding.jalview.JalviewModel.Tree; import jalview.xml.binding.jalview.JalviewModel.UserColours; import jalview.xml.binding.jalview.JalviewModel.Viewport; @@ -118,6 +140,7 @@ import jalview.xml.binding.jalview.MapListType.MapListTo; import jalview.xml.binding.jalview.Mapping; import jalview.xml.binding.jalview.NoValueColour; import jalview.xml.binding.jalview.ObjectFactory; +import jalview.xml.binding.jalview.PcaDataType; import jalview.xml.binding.jalview.Pdbentry.Property; import jalview.xml.binding.jalview.Sequence; import jalview.xml.binding.jalview.Sequence.DBRef; @@ -214,6 +237,12 @@ public class Jalview2XML private static final String UTF_8 = "UTF-8"; + /** + * prefix for recovering datasets for alignments with multiple views where + * non-existent dataset IDs were written for some views + */ + private static final String UNIQSEQSETID = "uniqueSeqSetId."; + // use this with nextCounter() to make unique names for entities private int counter = 0; @@ -545,24 +574,30 @@ public class Jalview2XML public void saveState(File statefile) { FileOutputStream fos = null; + try { + fos = new FileOutputStream(statefile); + JarOutputStream jout = new JarOutputStream(fos); saveState(jout); + fos.close(); } catch (Exception e) { + Cache.log.error("Couln't write Jalview state to " + statefile, e); // TODO: inform user of the problem - they need to know if their data was // not saved ! if (errorMessage == null) { - errorMessage = "Couldn't write Jalview Archive to output file '" + errorMessage = "Did't write Jalview Archive to output file '" + statefile + "' - See console error log for details"; } else { - errorMessage += "(output file was '" + statefile + "')"; + errorMessage += "(Didn't write Jalview Archive to output file '" + + statefile + ")"; } e.printStackTrace(); } finally @@ -732,7 +767,11 @@ public class Jalview2XML { try { - FileOutputStream fos = new FileOutputStream(jarFile); + // create backupfiles object and get new temp filename destination + BackupFiles backupfiles = new BackupFiles(jarFile); + FileOutputStream fos = new FileOutputStream( + backupfiles.getTempFilePath()); + JarOutputStream jout = new JarOutputStream(fos); List frames = new ArrayList<>(); @@ -754,7 +793,12 @@ public class Jalview2XML } ; jout.close(); - return true; + boolean success = true; + + backupfiles.setWriteSuccess(success); + success = backupfiles.rollBackupsAndRenameTempFile(); + + return success; } catch (Exception ex) { errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details"; @@ -1231,6 +1275,9 @@ public class Jalview2XML tree.setXpos(tp.getX()); tree.setYpos(tp.getY()); tree.setId(makeHashCode(tp, null)); + tree.setLinkToAllViews( + tp.getTreeCanvas().isApplyToAllViews()); + // jms.addTree(tree); object.getTree().add(tree); } @@ -1239,6 +1286,24 @@ public class Jalview2XML } } + /* + * save PCA viewers + */ + if (!storeDS && Desktop.desktop != null) + { + for (JInternalFrame frame : Desktop.desktop.getAllFrames()) + { + if (frame instanceof PCAPanel) + { + PCAPanel panel = (PCAPanel) frame; + if (panel.getAlignViewport().getAlignment() == jal) + { + savePCA(panel, object); + } + } + } + } + // SAVE ANNOTATIONS /** * store forward refs from an annotationRow to any groups @@ -1617,6 +1682,7 @@ public class Jalview2XML // using save and then load try { + fileName = fileName.replace('\\', '/'); System.out.println("Writing jar entry " + fileName); JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); @@ -1646,6 +1712,196 @@ public class Jalview2XML } /** + * Writes PCA viewer attributes and computed values to an XML model object and + * adds it to the JalviewModel. Any exceptions are reported by logging. + */ + protected void savePCA(PCAPanel panel, JalviewModel object) + { + try + { + PcaViewer viewer = new PcaViewer(); + viewer.setHeight(panel.getHeight()); + viewer.setWidth(panel.getWidth()); + viewer.setXpos(panel.getX()); + viewer.setYpos(panel.getY()); + viewer.setTitle(panel.getTitle()); + PCAModel pcaModel = panel.getPcaModel(); + viewer.setScoreModelName(pcaModel.getScoreModelName()); + viewer.setXDim(panel.getSelectedDimensionIndex(X)); + viewer.setYDim(panel.getSelectedDimensionIndex(Y)); + viewer.setZDim(panel.getSelectedDimensionIndex(Z)); + viewer.setBgColour( + panel.getRotatableCanvas().getBackgroundColour().getRGB()); + viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor()); + float[] spMin = panel.getRotatableCanvas().getSeqMin(); + SeqPointMin spmin = new SeqPointMin(); + spmin.setXPos(spMin[0]); + spmin.setYPos(spMin[1]); + spmin.setZPos(spMin[2]); + viewer.setSeqPointMin(spmin); + float[] spMax = panel.getRotatableCanvas().getSeqMax(); + SeqPointMax spmax = new SeqPointMax(); + spmax.setXPos(spMax[0]); + spmax.setYPos(spMax[1]); + spmax.setZPos(spMax[2]); + viewer.setSeqPointMax(spmax); + viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels()); + viewer.setLinkToAllViews( + panel.getRotatableCanvas().isApplyToAllViews()); + SimilarityParamsI sp = pcaModel.getSimilarityParameters(); + viewer.setIncludeGaps(sp.includeGaps()); + viewer.setMatchGaps(sp.matchGaps()); + viewer.setIncludeGappedColumns(sp.includeGappedColumns()); + viewer.setDenominateByShortestLength(sp.denominateByShortestLength()); + + /* + * sequence points on display + */ + for (jalview.datamodel.SequencePoint spt : pcaModel + .getSequencePoints()) + { + SequencePoint point = new SequencePoint(); + point.setSequenceRef(seqHash(spt.getSequence())); + point.setXPos(spt.coord.x); + point.setYPos(spt.coord.y); + point.setZPos(spt.coord.z); + viewer.getSequencePoint().add(point); + } + + /* + * (end points of) axes on display + */ + for (Point p : panel.getRotatableCanvas().getAxisEndPoints()) + { + + Axis axis = new Axis(); + axis.setXPos(p.x); + axis.setYPos(p.y); + axis.setZPos(p.z); + viewer.getAxis().add(axis); + } + + /* + * raw PCA data (note we are not restoring PCA inputs here - + * alignment view, score model, similarity parameters) + */ + PcaDataType data = new PcaDataType(); + viewer.setPcaData(data); + PCA pca = pcaModel.getPcaData(); + + DoubleMatrix pm = new DoubleMatrix(); + saveDoubleMatrix(pca.getPairwiseScores(), pm); + data.setPairwiseMatrix(pm); + + DoubleMatrix tm = new DoubleMatrix(); + saveDoubleMatrix(pca.getTridiagonal(), tm); + data.setTridiagonalMatrix(tm); + + DoubleMatrix eigenMatrix = new DoubleMatrix(); + data.setEigenMatrix(eigenMatrix); + saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix); + + object.getPcaViewer().add(viewer); + } catch (Throwable t) + { + Cache.log.error("Error saving PCA: " + t.getMessage()); + } + } + + /** + * Stores values from a matrix into an XML element, including (if present) the + * D or E vectors + * + * @param m + * @param xmlMatrix + * @see #loadDoubleMatrix(DoubleMatrix) + */ + protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix) + { + xmlMatrix.setRows(m.height()); + xmlMatrix.setColumns(m.width()); + for (int i = 0; i < m.height(); i++) + { + DoubleVector row = new DoubleVector(); + for (int j = 0; j < m.width(); j++) + { + row.getV().add(m.getValue(i, j)); + } + xmlMatrix.getRow().add(row); + } + if (m.getD() != null) + { + DoubleVector dVector = new DoubleVector(); + for (double d : m.getD()) + { + dVector.getV().add(d); + } + xmlMatrix.setD(dVector); + } + if (m.getE() != null) + { + DoubleVector eVector = new DoubleVector(); + for (double e : m.getE()) + { + eVector.getV().add(e); + } + xmlMatrix.setE(eVector); + } + } + + /** + * Loads XML matrix data into a new Matrix object, including the D and/or E + * vectors (if present) + * + * @param mData + * @return + * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix) + */ + protected MatrixI loadDoubleMatrix(DoubleMatrix mData) + { + int rows = mData.getRows(); + double[][] vals = new double[rows][]; + + for (int i = 0; i < rows; i++) + { + List dVector = mData.getRow().get(i).getV(); + vals[i] = new double[dVector.size()]; + int dvi = 0; + for (Double d : dVector) + { + vals[i][dvi++] = d; + } + } + + MatrixI m = new Matrix(vals); + + if (mData.getD() != null) + { + List dVector = mData.getD().getV(); + double[] vec = new double[dVector.size()]; + int dvi = 0; + for (Double d : dVector) + { + vec[dvi++] = d; + } + m.setD(vec); + } + if (mData.getE() != null) + { + List dVector = mData.getE().getV(); + double[] vec = new double[dVector.size()]; + int dvi = 0; + for (Double d : dVector) + { + vec[dvi++] = d; + } + m.setE(vec); + } + + return m; + } + + /** * Save any Varna viewers linked to this sequence. Writes an rnaViewer element * for each viewer, with *
    @@ -1797,6 +2053,7 @@ public class Jalview2XML { if (jout != null) { + jarEntryName = jarEntryName.replace('\\','/'); System.out.println("Writing jar entry " + jarEntryName); jout.putNextEntry(new JarEntry(jarEntryName)); DataOutputStream dout = new DataOutputStream(jout); @@ -2257,7 +2514,7 @@ public class Jalview2XML vamsasSeq.setName(jds.getName()); vamsasSeq.setSequence(jds.getSequenceAsString()); vamsasSeq.setDescription(jds.getDescription()); - jalview.datamodel.DBRefEntry[] dbrefs = null; + List dbrefs = null; if (jds.getDatasetSequence() != null) { vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence())); @@ -2275,15 +2532,16 @@ public class Jalview2XML } if (dbrefs != null) { - for (int d = 0; d < dbrefs.length; d++) + for (int d = 0, nd = dbrefs.size(); d < nd; d++) { DBRef dbref = new DBRef(); - dbref.setSource(dbrefs[d].getSource()); - dbref.setVersion(dbrefs[d].getVersion()); - dbref.setAccessionId(dbrefs[d].getAccessionId()); - if (dbrefs[d].hasMap()) + DBRefEntry ref = dbrefs.get(d); + dbref.setSource(ref.getSource()); + dbref.setVersion(ref.getVersion()); + dbref.setAccessionId(ref.getAccessionId()); + if (ref.hasMap()) { - Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq, + Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds, recurse); dbref.setMapping(mp); } @@ -2523,68 +2781,52 @@ public class Jalview2XML return af; } - @SuppressWarnings("unused") -private jarInputStreamProvider createjarInputStreamProvider( - final Object ofile) throws MalformedURLException - { - - // BH 2018 allow for bytes already attached to File object - final String file = ofile.toString(); - byte[] bytes = /** @j2sNative ofile._bytes ||*/null; - if (bytes != null) { - - return new jarInputStreamProvider() - { - - @Override - public JarInputStream getJarInputStream() throws IOException - { - return new JarInputStream(new ByteArrayInputStream(bytes)); - } - - @Override - public String getFilename() - { - return file; - } - }; - + @SuppressWarnings("unused") + private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException { + + // BH 2018 allow for bytes already attached to File object + try { + String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString()); + byte[] bytes = /** @j2sNative ofile._bytes || */ + null; + URL url = null; + errorMessage = null; + uniqueSetSuffix = null; + seqRefIds = null; + viewportsAdded.clear(); + frefedSequence = null; + + if (file.startsWith("http://")) { + url = new URL(file); + } + final URL _url = url; + return new jarInputStreamProvider() { + + @Override + public JarInputStream getJarInputStream() throws IOException { + if (bytes != null) { +// System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length); + return new JarInputStream(new ByteArrayInputStream(bytes)); + } + if (_url != null) { +// System.out.println("Jalview2XML: opening url jarInputStream for " + _url); + return new JarInputStream(_url.openStream()); + } else { +// System.out.println("Jalview2XML: opening file jarInputStream for " + file); + return new JarInputStream(new FileInputStream(file)); + } + } + + @Override + public String getFilename() { + return file; + } + }; + } catch (IOException e) { + e.printStackTrace(); + return null; + } } - URL url = null; - errorMessage = null; - uniqueSetSuffix = null; - seqRefIds = null; - viewportsAdded.clear(); - frefedSequence = null; - - if (file.startsWith("http://")) - { - url = new URL(file); - } - final URL _url = url; - return new jarInputStreamProvider() - { - - @Override - public JarInputStream getJarInputStream() throws IOException - { - if (_url != null) - { - return new JarInputStream(_url.openStream()); - } - else - { - return new JarInputStream(new FileInputStream(file)); - } - } - - @Override - public String getFilename() - { - return file; - } - }; - } /** * Recover jalview session from a jalview project archive. Caller may @@ -2626,9 +2868,6 @@ private jarInputStreamProvider createjarInputStreamProvider( if (jarentry != null && jarentry.getName().endsWith(".xml")) { - InputStreamReader in = new InputStreamReader(jin, UTF_8); - // JalviewModel object = new JalviewModel(); - JAXBContext jc = JAXBContext .newInstance("jalview.xml.binding.jalview"); XMLStreamReader streamReader = XMLInputFactory.newInstance() @@ -2638,11 +2877,6 @@ private jarInputStreamProvider createjarInputStreamProvider( .unmarshal(streamReader, JalviewModel.class); JalviewModel object = jbe.getValue(); - /* - Unmarshaller unmar = new Unmarshaller(object); - unmar.setValidation(false); - object = (JalviewModel) unmar.unmarshal(in); - */ if (true) // !skipViewport(object)) { _af = loadFromObject(object, file, true, jprovider); @@ -2689,16 +2923,7 @@ private jarInputStreamProvider createjarInputStreamProvider( ex.printStackTrace(System.err); if (attemptversion1parse) { - // Is Version 1 Jar file? - try - { - af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider); - } catch (Exception ex2) - { - System.err.println("Exception whilst loading as jalviewXMLV1:"); - ex2.printStackTrace(); - af = null; - } + // used to attempt to parse as V1 castor-generated xml } if (Desktop.instance != null) { @@ -3076,6 +3301,28 @@ private jarInputStreamProvider createjarInputStreamProvider( : null; // //////////////////////////////// + // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID + // + // + // If we just load in the same jar file again, the sequenceSetId + // will be the same, and we end up with multiple references + // to the same sequenceSet. We must modify this id on load + // so that each load of the file gives a unique id + + /** + * used to resolve correct alignment dataset for alignments with multiple + * views + */ + String uniqueSeqSetId = null; + String viewId = null; + if (view != null) + { + uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; + viewId = (view.getId() == null ? null + : view.getId() + uniqueSetSuffix); + } + + // //////////////////////////////// // LOAD SEQUENCES List hiddenSeqs = null; @@ -3196,7 +3443,7 @@ private jarInputStreamProvider createjarInputStreamProvider( // finally, verify all data in vamsasSet is actually present in al // passing on flag indicating if it is actually a stored dataset - recoverDatasetFor(vamsasSet, al, isdsal); + recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId); } if (referenceseqForView != null) @@ -3638,7 +3885,7 @@ private jarInputStreamProvider createjarInputStreamProvider( } else { - cs = ColourSchemeProperty.getColourScheme(al, + cs = ColourSchemeProperty.getColourScheme(null, al, jGroup.getColour()); } } @@ -3736,13 +3983,6 @@ private jarInputStreamProvider createjarInputStreamProvider( // /////////////////////////////// // LOAD VIEWPORT - // If we just load in the same jar file again, the sequenceSetId - // will be the same, and we end up with multiple references - // to the same sequenceSet. We must modify this id on load - // so that each load of the file gives a unique id - String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix; - String viewId = (view.getId() == null ? null - : view.getId() + uniqueSetSuffix); AlignFrame af = null; AlignViewport av = null; // now check to see if we really need to create a new viewport. @@ -3824,6 +4064,7 @@ private jarInputStreamProvider createjarInputStreamProvider( if (loadTreesAndStructures) { loadTrees(jalviewModel, view, af, av, ap); + loadPCAViewers(jalviewModel, ap); loadPDBStructures(jprovider, jseqs, af, ap); loadRnaViewers(jprovider, jseqs, ap); } @@ -3972,6 +4213,8 @@ private jarInputStreamProvider createjarInputStreamProvider( // TODO: verify 'associate with all views' works still tp.getTreeCanvas().setViewport(av); // af.viewport; tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel; + // FIXME: should we use safeBoolean here ? + tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews()); } if (tp == null) @@ -4624,7 +4867,18 @@ private jarInputStreamProvider createjarInputStreamProvider( { AlignFrame af = null; af = new AlignFrame(al, safeInt(view.getWidth()), - safeInt(view.getHeight()), uniqueSeqSetId, viewId); + safeInt(view.getHeight()), uniqueSeqSetId, viewId) +// { +// +// @Override +// protected void processKeyEvent(java.awt.event.KeyEvent e) { +// System.out.println("Jalview2XML AF " + e); +// super.processKeyEvent(e); +// +// } +// +// } + ; af.setFileName(file, FileFormat.Jalview); @@ -4756,25 +5010,27 @@ private jarInputStreamProvider createjarInputStreamProvider( } else { - cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour()); + cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al, + view.getBgColour()); } } + /* + * turn off 'alignment colour applies to all groups' + * while restoring global colour scheme + */ + viewport.setColourAppliesToAllGroups(false); viewport.setGlobalColourScheme(cs); viewport.getResidueShading().setThreshold(pidThreshold, view.isIgnoreGapsinConsensus()); viewport.getResidueShading() .setConsensus(viewport.getSequenceConsensusHash()); - viewport.setColourAppliesToAllGroups(false); - if (safeBoolean(view.isConservationSelected()) && cs != null) { viewport.getResidueShading() .setConservationInc(safeInt(view.getConsThreshold())); } - af.changeColour(cs); - viewport.setColourAppliesToAllGroups(true); viewport @@ -4850,7 +5106,8 @@ private jarInputStreamProvider createjarInputStreamProvider( float min = safeFloat(safeFloat(setting.getMin())); float max = setting.getMax() == null ? 1f : setting.getMax().floatValue(); - FeatureColourI gc = new FeatureColour(minColour, maxColour, + FeatureColourI gc = new FeatureColour(maxColour, minColour, + maxColour, noValueColour, min, max); if (setting.getAttributeName().size() > 0) { @@ -5052,7 +5309,7 @@ private jarInputStreamProvider createjarInputStreamProvider( else { cs = new AnnotationColourGradient(matchedAnnotation, - ColourSchemeProperty.getColourScheme(al, + ColourSchemeProperty.getColourScheme(af.getViewport(), al, viewAnnColour.getColourScheme()), safeInt(viewAnnColour.getAboveThreshold())); } @@ -5241,13 +5498,51 @@ private jarInputStreamProvider createjarInputStreamProvider( } private void recoverDatasetFor(SequenceSet vamsasSet, AlignmentI al, - boolean ignoreUnrefed) + boolean ignoreUnrefed, String uniqueSeqSetId) { jalview.datamodel.AlignmentI ds = getDatasetFor( vamsasSet.getDatasetId()); + AlignmentI xtant_ds = ds; + if (xtant_ds == null) + { + // good chance we are about to create a new dataset, but check if we've + // seen some of the dataset sequence IDs before. + // TODO: skip this check if we are working with project generated by + // version 2.11 or later + xtant_ds = checkIfHasDataset(vamsasSet.getSequence()); + if (xtant_ds != null) + { + ds = xtant_ds; + addDatasetRef(vamsasSet.getDatasetId(), ds); + } + } Vector dseqs = null; + if (!ignoreUnrefed) + { + // recovering an alignment View + AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId); + if (seqSetDS != null) + { + if (ds != null && ds != seqSetDS) + { + warn("JAL-3171 regression: Overwriting a dataset reference for an alignment" + + " - CDS/Protein crossreference data may be lost"); + if (xtant_ds != null) + { + // This can only happen if the unique sequence set ID was bound to a + // dataset that did not contain any of the sequences in the view + // currently being restored. + warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed."); + } + } + ds = seqSetDS; + addDatasetRef(vamsasSet.getDatasetId(), ds); + } + } if (ds == null) { + // try even harder to restore dataset + AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence()); // create a list of new dataset sequences dseqs = new Vector(); } @@ -5270,10 +5565,58 @@ private jarInputStreamProvider createjarInputStreamProvider( if (al.getDataset() == null && !ignoreUnrefed) { al.setDataset(ds); + // register dataset for the alignment's uniqueSeqSetId for legacy projects + addDatasetRef(UNIQSEQSETID + uniqueSeqSetId, ds); } + updateSeqDatasetBinding(vamsasSet.getSequence(), ds); } /** + * XML dataset sequence ID to materialised dataset reference + */ + HashMap seqToDataset = new HashMap<>(); + + /** + * @return the first materialised dataset reference containing a dataset + * sequence referenced in the given view + * @param list + * - sequences from the view + */ + AlignmentI checkIfHasDataset(List list) + { + for (Sequence restoredSeq : list) + { + AlignmentI datasetFor = seqToDataset.get(restoredSeq.getDsseqid()); + if (datasetFor != null) + { + return datasetFor; + } + } + return null; + } + + /** + * Register ds as the containing dataset for the dataset sequences referenced + * by sequences in list + * + * @param list + * - sequences in a view + * @param ds + */ + void updateSeqDatasetBinding(List list, AlignmentI ds) + { + for (Sequence restoredSeq : list) + { + AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds); + if (prevDS != null && prevDS != ds) + { + warn("Dataset sequence appears in many datasets: " + + restoredSeq.getDsseqid()); + // TODO: try to merge! + } + } + } + /** * * @param vamsasSeq * sequence definition to create/merge dataset sequence for @@ -5532,15 +5875,16 @@ private jarInputStreamProvider createjarInputStreamProvider( jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr, fto, m.getMapFromUnit().intValue(), m.getMapToUnit().intValue()); - // if (m.getMappingChoice() != null) - // { - // MappingChoice mc = m.getMappingChoice(); + + /* + * (optional) choice of dseqFor or Sequence + */ if (m.getDseqFor() != null) { String dsfor = m.getDseqFor(); if (seqRefIds.containsKey(dsfor)) { - /** + /* * recover from hash */ jmap.setTo(seqRefIds.get(dsfor)); @@ -5550,9 +5894,9 @@ private jarInputStreamProvider createjarInputStreamProvider( frefedSequence.add(newMappingRef(dsfor, jmap)); } } - else + else if (m.getSequence() != null) { - /** + /* * local sequence definition */ Sequence ms = m.getSequence(); @@ -5609,6 +5953,10 @@ private jarInputStreamProvider createjarInputStreamProvider( initSeqRefs(); JalviewModel jm = saveState(ap, null, null, null); + addDatasetRef( + jm.getVamsasModel().getSequenceSet().get(0).getDatasetId(), + ap.getAlignment().getDataset()); + uniqueSetSuffix = ""; // jm.getJalviewModelSequence().getViewport(0).setId(null); jm.getViewport().get(0).setId(null); @@ -5870,6 +6218,128 @@ private jarInputStreamProvider createjarInputStreamProvider( } /** + * Loads any saved PCA viewers + * + * @param jms + * @param ap + */ + protected void loadPCAViewers(JalviewModel model, AlignmentPanel ap) + { + try + { + List pcaviewers = model.getPcaViewer(); + for (PcaViewer viewer : pcaviewers) + { + String modelName = viewer.getScoreModelName(); + SimilarityParamsI params = new SimilarityParams( + viewer.isIncludeGappedColumns(), viewer.isMatchGaps(), + viewer.isIncludeGaps(), + viewer.isDenominateByShortestLength()); + + /* + * create the panel (without computing the PCA) + */ + PCAPanel panel = new PCAPanel(ap, modelName, params); + + panel.setTitle(viewer.getTitle()); + panel.setBounds(new Rectangle(viewer.getXpos(), viewer.getYpos(), + viewer.getWidth(), viewer.getHeight())); + + boolean showLabels = viewer.isShowLabels(); + panel.setShowLabels(showLabels); + panel.getRotatableCanvas().setShowLabels(showLabels); + panel.getRotatableCanvas() + .setBgColour(new Color(viewer.getBgColour())); + panel.getRotatableCanvas() + .setApplyToAllViews(viewer.isLinkToAllViews()); + + /* + * load PCA output data + */ + ScoreModelI scoreModel = ScoreModels.getInstance() + .getScoreModel(modelName, ap); + PCA pca = new PCA(null, scoreModel, params); + PcaDataType pcaData = viewer.getPcaData(); + + MatrixI pairwise = loadDoubleMatrix(pcaData.getPairwiseMatrix()); + pca.setPairwiseScores(pairwise); + + MatrixI triDiag = loadDoubleMatrix(pcaData.getTridiagonalMatrix()); + pca.setTridiagonal(triDiag); + + MatrixI result = loadDoubleMatrix(pcaData.getEigenMatrix()); + pca.setEigenmatrix(result); + + panel.getPcaModel().setPCA(pca); + + /* + * we haven't saved the input data! (JAL-2647 to do) + */ + panel.setInputData(null); + + /* + * add the sequence points for the PCA display + */ + List seqPoints = new ArrayList<>(); + for (SequencePoint sp : viewer.getSequencePoint()) + { + String seqId = sp.getSequenceRef(); + SequenceI seq = seqRefIds.get(seqId); + if (seq == null) + { + throw new IllegalStateException( + "Unmatched seqref for PCA: " + seqId); + } + Point pt = new Point(sp.getXPos(), sp.getYPos(), sp.getZPos()); + jalview.datamodel.SequencePoint seqPoint = new jalview.datamodel.SequencePoint( + seq, pt); + seqPoints.add(seqPoint); + } + panel.getRotatableCanvas().setPoints(seqPoints, seqPoints.size()); + + /* + * set min-max ranges and scale after setPoints (which recomputes them) + */ + panel.getRotatableCanvas().setScaleFactor(viewer.getScaleFactor()); + SeqPointMin spMin = viewer.getSeqPointMin(); + float[] min = new float[] { spMin.getXPos(), spMin.getYPos(), + spMin.getZPos() }; + SeqPointMax spMax = viewer.getSeqPointMax(); + float[] max = new float[] { spMax.getXPos(), spMax.getYPos(), + spMax.getZPos() }; + panel.getRotatableCanvas().setSeqMinMax(min, max); + + // todo: hold points list in PCAModel only + panel.getPcaModel().setSequencePoints(seqPoints); + + panel.setSelectedDimensionIndex(viewer.getXDim(), X); + panel.setSelectedDimensionIndex(viewer.getYDim(), Y); + panel.setSelectedDimensionIndex(viewer.getZDim(), Z); + + // is this duplication needed? + panel.setTop(seqPoints.size() - 1); + panel.getPcaModel().setTop(seqPoints.size() - 1); + + /* + * add the axes' end points for the display + */ + for (int i = 0; i < 3; i++) + { + Axis axis = viewer.getAxis().get(i); + panel.getRotatableCanvas().getAxisEndPoints()[i] = new Point( + axis.getXPos(), axis.getYPos(), axis.getZPos()); + } + + Desktop.addInternalFrame(panel, MessageManager.formatMessage( + "label.calc_title", "PCA", modelName), 475, 450); + } + } catch (Exception ex) + { + Cache.log.error("Error loading PCA: " + ex.toString()); + } + } + + /** * Populates an XML model of the feature colour scheme for one feature type * * @param featureType @@ -6132,7 +6602,7 @@ private jarInputStreamProvider createjarInputStreamProvider( noValueColour = maxcol; } - colour = new FeatureColour(mincol, maxcol, noValueColour, + colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour, safeFloat(colourModel.getMin()), safeFloat(colourModel.getMax())); final List attributeName = colourModel.getAttributeName();