X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=b6295d9fde930ac4880ad23690d86f826f276ab1;hb=74e963518532e173a8b026bf0de00993ab678ad0;hp=8c3175fe10b0d38475da4bffbee79bc4255f95c5;hpb=2574bf4ab96840e3e064a0e4de521973fd299edc;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 8c3175f..b6295d9 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -20,17 +20,78 @@ */ 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 java.awt.Color; +import java.awt.Font; +import java.awt.Rectangle; +import java.io.BufferedReader; +import java.io.DataOutputStream; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileOutputStream; +import java.io.IOException; +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.OutputStream; +import java.io.OutputStreamWriter; +import java.io.PrintWriter; +import java.lang.reflect.InvocationTargetException; +import java.math.BigInteger; +import java.net.MalformedURLException; +import java.net.URL; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.Enumeration; +import java.util.GregorianCalendar; +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.SwingUtilities; +import javax.xml.bind.JAXBContext; +import javax.xml.bind.JAXBElement; +import javax.xml.bind.Marshaller; +import javax.xml.datatype.DatatypeConfigurationException; +import javax.xml.datatype.DatatypeFactory; +import javax.xml.datatype.XMLGregorianCalendar; +import javax.xml.stream.XMLInputFactory; +import javax.xml.stream.XMLStreamReader; + 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.GeneLocus; import jalview.datamodel.GraphLine; import jalview.datamodel.PDBEntry; +import jalview.datamodel.Point; import jalview.datamodel.RnaViewerModel; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -41,26 +102,32 @@ import jalview.datamodel.features.FeatureMatcher; import jalview.datamodel.features.FeatureMatcherI; import jalview.datamodel.features.FeatureMatcherSet; import jalview.datamodel.features.FeatureMatcherSetI; +import jalview.ext.rbvi.chimera.JalviewChimeraBinding; import jalview.ext.varna.RnaModel; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; import jalview.gui.AlignmentPanel; import jalview.gui.AppVarna; import jalview.gui.ChimeraViewFrame; +import jalview.gui.ChimeraXViewFrame; import jalview.gui.Desktop; -import jalview.gui.FeatureRenderer; -import jalview.gui.Jalview2XML_V1; +import jalview.gui.JalviewChimeraXBindingModel; import jalview.gui.JvOptionPane; import jalview.gui.OOMWarning; +import jalview.gui.PCAPanel; import jalview.gui.PaintRefresher; +import jalview.gui.PymolViewer; 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; @@ -77,7 +144,9 @@ 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.FeatureRendererModel; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import jalview.ws.jws2.Jws2Discoverer; @@ -92,6 +161,8 @@ 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 +177,11 @@ 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 +194,7 @@ 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; @@ -126,54 +203,6 @@ import jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties; import jalview.xml.binding.jalview.ThresholdType; import jalview.xml.binding.jalview.VAMSAS; -import java.awt.Color; -import java.awt.Font; -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.math.BigInteger; -import java.net.MalformedURLException; -import java.net.URL; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.Enumeration; -import java.util.GregorianCalendar; -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.SwingUtilities; -import javax.xml.bind.JAXBContext; -import javax.xml.bind.JAXBElement; -import javax.xml.bind.Marshaller; -import javax.xml.datatype.DatatypeConfigurationException; -import javax.xml.datatype.DatatypeFactory; -import javax.xml.datatype.XMLGregorianCalendar; -import javax.xml.stream.XMLInputFactory; -import javax.xml.stream.XMLStreamReader; - /** * Write out the current jalview desktop state as a Jalview XML stream. * @@ -529,24 +558,30 @@ 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 @@ -716,7 +751,11 @@ 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<>(); @@ -738,7 +777,12 @@ 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"; @@ -1048,15 +1092,17 @@ public class Jalview2XML if (!storeDS && !viewIds.contains(viewId)) { viewIds.add(viewId); - try + File viewerState = viewFrame.saveSession(); + if (viewerState != null) { - String viewerState = viewFrame.getStateInfo(); - writeJarEntry(jout, getViewerJarEntryName(viewId), - viewerState.getBytes()); - } catch (IOException e) + copyFileToJar(jout, viewerState.getPath(), + getViewerJarEntryName(viewId)); + } + else { - System.err.println( - "Error saving viewer state: " + e.getMessage()); + Cache.log.error("Failed to save viewer state for " + + + viewFrame.getViewerType().toString()); } } } @@ -1215,6 +1261,9 @@ 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); } @@ -1223,6 +1272,24 @@ 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 @@ -1441,11 +1508,14 @@ public class Jalview2XML view.setFollowHighlight(av.isFollowHighlight()); view.setFollowSelection(av.followSelection); view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus()); + view.setShowComplementFeatures(av.isShowComplementFeatures()); + view.setShowComplementFeaturesOnTop( + av.isShowComplementFeaturesOnTop()); if (av.getFeaturesDisplayed() != null) { FeatureSettings fs = new FeatureSettings(); - FeatureRenderer fr = ap.getSeqPanel().seqCanvas + FeatureRendererModel fr = ap.getSeqPanel().seqCanvas .getFeatureRenderer(); String[] renderOrder = fr.getRenderOrder().toArray(new String[0]); @@ -1630,6 +1700,196 @@ 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 *
    @@ -1739,32 +1999,23 @@ public class Jalview2XML protected void copyFileToJar(JarOutputStream jout, String infilePath, String jarEntryName) { - DataInputStream dis = null; - try + try (InputStream is = new FileInputStream(infilePath)) { File file = new File(infilePath); if (file.exists() && jout != null) { - dis = new DataInputStream(new FileInputStream(file)); - byte[] data = new byte[(int) file.length()]; - dis.readFully(data); - writeJarEntry(jout, jarEntryName, data); + System.out.println("Writing jar entry " + jarEntryName); + jout.putNextEntry(new JarEntry(jarEntryName)); + copyAll(is, jout); + jout.closeEntry(); + // dis = new DataInputStream(new FileInputStream(file)); + // byte[] data = new byte[(int) file.length()]; + // dis.readFully(data); + // writeJarEntry(jout, jarEntryName, data); } } catch (Exception ex) { ex.printStackTrace(); - } finally - { - if (dis != null) - { - try - { - dis.close(); - } catch (IOException e) - { - // ignore - } - } } } @@ -1791,6 +2042,24 @@ public class Jalview2XML } /** + * Copies input to output, in 4K buffers; handles any data (text or binary) + * + * @param in + * @param out + * @throws IOException + */ + protected void copyAll(InputStream in, OutputStream out) + throws IOException + { + byte[] buffer = new byte[4096]; + int bytesRead = 0; + while ((bytesRead = in.read(buffer)) != -1) + { + out.write(buffer, 0, bytesRead); + } + } + + /** * Save the state of a structure viewer * * @param ap @@ -1857,7 +2126,7 @@ public class Jalview2XML final String viewId = viewFrame.getViewId(); state.setViewId(viewId); state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap)); - state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap)); + state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap)); state.setColourByJmol(viewFrame.isColouredByViewer()); state.setType(viewFrame.getViewerType().toString()); // pdb.addStructureState(state); @@ -2257,21 +2526,29 @@ public class Jalview2XML parentseq = jds; } } + + /* + * save any dbrefs; special subclass GeneLocus is flagged as 'locus' + */ if (dbrefs != null) { for (int d = 0; d < dbrefs.length; 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 dbRefEntry = dbrefs[d]; + dbref.setSource(dbRefEntry.getSource()); + dbref.setVersion(dbRefEntry.getVersion()); + dbref.setAccessionId(dbRefEntry.getAccessionId()); + if (dbRefEntry instanceof GeneLocus) + { + dbref.setLocus(true); + } + if (dbRefEntry.hasMap()) { - Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq, + Mapping mp = createVamsasMapping(dbRefEntry.getMap(), parentseq, jds, recurse); dbref.setMapping(mp); } - // vamsasSeq.addDBRef(dbref); vamsasSeq.getDBRef().add(dbref); } } @@ -2649,16 +2926,7 @@ public class Jalview2XML 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) { @@ -2911,53 +3179,42 @@ public class Jalview2XML * @param prefix * a prefix for the temporary file name, must be at least three * characters long - * @param origFile + * @param suffixModel * null or original file - so new file can be given the same suffix * as the old one * @return */ protected String copyJarEntry(jarInputStreamProvider jprovider, - String jarEntryName, String prefix, String origFile) + String jarEntryName, String prefix, String suffixModel) { - BufferedReader in = null; - PrintWriter out = null; String suffix = ".tmp"; - if (origFile == null) + if (suffixModel == null) { - origFile = jarEntryName; + suffixModel = jarEntryName; } - int sfpos = origFile.lastIndexOf("."); - if (sfpos > -1 && sfpos < (origFile.length() - 3)) + int sfpos = suffixModel.lastIndexOf("."); + if (sfpos > -1 && sfpos < (suffixModel.length() - 1)) { - suffix = "." + origFile.substring(sfpos + 1); + suffix = "." + suffixModel.substring(sfpos + 1); } - try - { - JarInputStream jin = jprovider.getJarInputStream(); - /* - * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new - * URL(jprovider).openStream()); } else { jin = new JarInputStream(new - * FileInputStream(jprovider)); } - */ + try (JarInputStream jin = jprovider.getJarInputStream()) + { JarEntry entry = null; do { entry = jin.getNextJarEntry(); } while (entry != null && !entry.getName().equals(jarEntryName)); + if (entry != null) { - in = new BufferedReader(new InputStreamReader(jin, UTF_8)); + // in = new BufferedReader(new InputStreamReader(jin, UTF_8)); File outFile = File.createTempFile(prefix, suffix); outFile.deleteOnExit(); - out = new PrintWriter(new FileOutputStream(outFile)); - String data; - - while ((data = in.readLine()) != null) + try (OutputStream os = new FileOutputStream(outFile)) { - out.println(data); + copyAll(jin, os); } - out.flush(); String t = outFile.getAbsolutePath(); return t; } @@ -2968,22 +3225,6 @@ public class Jalview2XML } catch (Exception ex) { ex.printStackTrace(); - } finally - { - if (in != null) - { - try - { - in.close(); - } catch (IOException e) - { - // ignore - } - } - if (out != null) - { - out.close(); - } } return null; @@ -3084,8 +3325,10 @@ public class Jalview2XML || tmpSeq.getEnd() != jseq.getEnd()) { System.err.println( - "Warning JAL-2154 regression: updating start/end for sequence " - + tmpSeq.toString() + " to " + jseq); + String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d", + tmpSeq.getName(), tmpSeq.getStart(), + tmpSeq.getEnd(), jseq.getStart(), + jseq.getEnd())); } } else @@ -3620,7 +3863,7 @@ public class Jalview2XML } else { - cs = ColourSchemeProperty.getColourScheme(al, + cs = ColourSchemeProperty.getColourScheme(null, al, jGroup.getColour()); } } @@ -3799,6 +4042,7 @@ public class Jalview2XML if (loadTreesAndStructures) { loadTrees(jalviewModel, view, af, av, ap); + loadPCAViewers(jalviewModel, ap); loadPDBStructures(jprovider, jseqs, af, ap); loadRnaViewers(jprovider, jseqs, ap); } @@ -3947,8 +4191,8 @@ public class Jalview2XML // TODO: verify 'associate with all views' works still tp.getTreeCanvas().setViewport(av); // af.viewport; tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel; - } + tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews()); if (tp == null) { warn("There was a problem recovering stored Newick tree: \n" @@ -4159,29 +4403,41 @@ public class Jalview2XML * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry * "viewer_"+stateData.viewId */ - if (ViewerType.CHIMERA.toString().equals(stateData.getType())) + ViewerType viewerType = ViewerType.valueOf(stateData.getType()); + try { - createChimeraViewer(viewerData, af, jprovider); - } - else + switch (viewerType) + { + case CHIMERA: + createChimeraViewer(viewerData, af, jprovider, false); + break; + case CHIMERAX: + createChimeraViewer(viewerData, af, jprovider, true); + break; + case PYMOL: + createPymolViewer(viewerData, af, jprovider); + break; + case JMOL: + createJmolViewer(viewerData, af, jprovider); + } + } catch (IllegalArgumentException | NullPointerException e) { - /* - * else Jmol (if pre-2.9, stateData contains JMOL state string) - */ - createJmolViewer(viewerData, af, jprovider); + Cache.log.error( + "Invalid structure viewer type: " + stateData.getType()); } } /** - * Create a new Chimera viewer. + * Create a new Chimera or ChimeraX viewer * * @param data * @param af * @param jprovider + * @param isChimeraX */ protected void createChimeraViewer( Entry viewerData, AlignFrame af, - jarInputStreamProvider jprovider) + jarInputStreamProvider jprovider, boolean isChimeraX) { StructureViewerModel data = viewerData.getValue(); String chimeraSessionFile = data.getStateData(); @@ -4193,8 +4449,11 @@ public class Jalview2XML * 'uniquified' sviewid used to reconstruct the viewer here */ String viewerJarEntryName = getViewerJarEntryName(data.getViewId()); + String extension = isChimeraX + ? JalviewChimeraXBindingModel.CHIMERAX_SESSION_EXTENSION + : JalviewChimeraBinding.CHIMERA_SESSION_EXTENSION; chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName, - "chimera", null); + "chimera", extension); Set> fileData = data.getFileData() .entrySet(); @@ -4220,9 +4479,13 @@ public class Jalview2XML .toArray(new SequenceI[allseqs.size()][]); String newViewId = viewerData.getKey(); - ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile, - af.alignPanel, pdbArray, seqsArray, colourByChimera, - colourBySequence, newViewId); + ChimeraViewFrame cvf = isChimeraX + ? new ChimeraXViewFrame(chimeraSessionFile, af.alignPanel, + pdbArray, seqsArray, colourByChimera, colourBySequence, + newViewId) + : new ChimeraViewFrame(chimeraSessionFile, af.alignPanel, + pdbArray, seqsArray, colourByChimera, colourBySequence, + newViewId); cvf.setSize(data.getWidth(), data.getHeight()); cvf.setLocation(data.getX(), data.getY()); } @@ -4280,7 +4543,7 @@ public class Jalview2XML String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\"); filedat = oldFiles.get(new File(reformatedOldFilename)); } - newFileLoc.append(Platform.escapeString(filedat.getFilePath())); + newFileLoc.append(Platform.escapeBackslashes(filedat.getFilePath())); pdbfilenames.add(filedat.getFilePath()); pdbids.add(filedat.getPdbId()); seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0])); @@ -4731,25 +4994,27 @@ public class Jalview2XML } 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 @@ -4767,11 +5032,14 @@ public class Jalview2XML viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip())); viewport.setShowGroupConsensus(view.isShowGroupConsensus()); viewport.setShowGroupConservation(view.isShowGroupConservation()); + viewport.setShowComplementFeatures(view.isShowComplementFeatures()); + viewport.setShowComplementFeaturesOnTop( + view.isShowComplementFeaturesOnTop()); // recover feature settings if (jm.getFeatureSettings() != null) { - FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas + FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas .getFeatureRenderer(); FeaturesDisplayed fdi; viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); @@ -4825,7 +5093,8 @@ public class Jalview2XML 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) { @@ -4870,7 +5139,7 @@ public class Jalview2XML } else { - featureOrder.put(featureType, new Float( + featureOrder.put(featureType, Float.valueOf( fs / jm.getFeatureSettings().getSetting().size())); } if (safeBoolean(setting.isDisplay())) @@ -4882,7 +5151,7 @@ public class Jalview2XML for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++) { Group grp = jm.getFeatureSettings().getGroup().get(gs); - fgtable.put(grp.getName(), new Boolean(grp.isDisplay())); + fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay())); } // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ? @@ -5027,7 +5296,7 @@ public class Jalview2XML else { cs = new AnnotationColourGradient(matchedAnnotation, - ColourSchemeProperty.getColourScheme(al, + ColourSchemeProperty.getColourScheme(af.getViewport(), al, viewAnnColour.getColourScheme()), safeInt(viewAnnColour.getAboveThreshold())); } @@ -5220,21 +5489,47 @@ public class Jalview2XML { 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 (ds == null) + if (!ignoreUnrefed) { - if (!ignoreUnrefed) + // recovering an alignment View + AlignmentI seqSetDS = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId); + if (seqSetDS != null) { - // try to resolve the dataset via uniqueSeqSetId - ds = getDatasetFor(UNIQSEQSETID + uniqueSeqSetId); - if (ds != null) + if (ds != null && ds != seqSetDS) { - addDatasetRef(vamsasSet.getDatasetId(), ds); + 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(); } @@ -5260,9 +5555,55 @@ public class Jalview2XML // 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 @@ -5483,13 +5824,29 @@ public class Jalview2XML return datasetId; } + /** + * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is + * constructed as a special subclass GeneLocus. + * + * @param datasetSequence + * @param sequence + */ private void addDBRefs(SequenceI datasetSequence, Sequence sequence) { for (int d = 0; d < sequence.getDBRef().size(); d++) { DBRef dr = sequence.getDBRef().get(d); - jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry( - dr.getSource(), dr.getVersion(), dr.getAccessionId()); + DBRefEntry entry; + if (dr.isLocus()) + { + entry = new GeneLocus(dr.getSource(), dr.getVersion(), + dr.getAccessionId()); + } + else + { + entry = new DBRefEntry(dr.getSource(), dr.getVersion(), + dr.getAccessionId()); + } if (dr.getMapping() != null) { entry.setMap(addMapping(dr.getMapping())); @@ -5521,15 +5878,16 @@ public class Jalview2XML 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)); @@ -5539,9 +5897,9 @@ public class Jalview2XML frefedSequence.add(newMappingRef(dsfor, jmap)); } } - else + else if (m.getSequence() != null) { - /** + /* * local sequence definition */ Sequence ms = m.getSequence(); @@ -5863,6 +6221,183 @@ public class Jalview2XML } /** + * 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()); + } + } + + /** + * Create a new PyMol viewer + * + * @param data + * @param af + * @param jprovider + */ + protected void createPymolViewer( + Entry viewerData, AlignFrame af, + jarInputStreamProvider jprovider) + { + StructureViewerModel data = viewerData.getValue(); + String pymolSessionFile = data.getStateData(); + + /* + * Copy PyMol session from jar entry "viewer_"+viewId to a temporary file + * + * NB this is the 'saved' viewId as in the project file XML, _not_ the + * 'uniquified' sviewid used to reconstruct the viewer here + */ + String viewerJarEntryName = getViewerJarEntryName(data.getViewId()); + pymolSessionFile = copyJarEntry(jprovider, viewerJarEntryName, + "pymol", ".pse"); + + Set> fileData = data.getFileData() + .entrySet(); + List pdbs = new ArrayList<>(); + List allseqs = new ArrayList<>(); + for (Entry pdb : fileData) + { + String filePath = pdb.getValue().getFilePath(); + String pdbId = pdb.getValue().getPdbId(); + // pdbs.add(new PDBEntry(filePath, pdbId)); + pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath)); + final List seqList = pdb.getValue().getSeqList(); + SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]); + allseqs.add(seqs); + } + + boolean colourByPymol = data.isColourByViewer(); + boolean colourBySequence = data.isColourWithAlignPanel(); + + // TODO use StructureViewer as a factory here, see JAL-1761 + final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]); + final SequenceI[][] seqsArray = allseqs + .toArray(new SequenceI[allseqs.size()][]); + String newViewId = viewerData.getKey(); + + PymolViewer pv = new PymolViewer(pymolSessionFile, + af.alignPanel, pdbArray, seqsArray, colourByPymol, + colourBySequence, newViewId); + pv.setSize(data.getWidth(), data.getHeight()); + pv.setLocation(data.getX(), data.getY()); + } + + /** * Populates an XML model of the feature colour scheme for one feature type * * @param featureType @@ -6125,7 +6660,7 @@ public class Jalview2XML 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();