X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=cadc25316bf76411604cf6976b3a4f7d474bd0ea;hb=595a9e25db7f4f24c17de84656d7d5391a3d104d;hp=5106e45652eb37f6342ef9408e688d9c9acfb60f;hpb=e4168062ee12d66e4632df214a06fc9a575615c7;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 5106e45..cadc253 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -20,17 +20,29 @@ */ 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.AlignmentViewPanel; 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; @@ -49,17 +61,21 @@ 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; @@ -67,7 +83,6 @@ import jalview.schemes.ColourSchemeProperty; import jalview.schemes.FeatureColour; import jalview.schemes.ResidueProperties; import jalview.schemes.UserColourScheme; -import jalview.structure.StructureSelectionManager; import jalview.structures.models.AAStructureBindingModel; import jalview.util.Format; import jalview.util.MessageManager; @@ -76,6 +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; @@ -91,6 +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; @@ -105,6 +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; @@ -117,6 +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; @@ -129,6 +153,7 @@ import java.awt.Color; import java.awt.Font; import java.awt.Rectangle; import java.io.BufferedReader; +import java.io.ByteArrayInputStream; import java.io.DataInputStream; import java.io.DataOutputStream; import java.io.File; @@ -138,7 +163,6 @@ 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; @@ -185,12 +209,27 @@ import javax.xml.stream.XMLStreamReader; */ public class Jalview2XML { + + // BH 2018 we add the .jvp binary extension to J2S so that + // it will declare that binary when we do the file save from the browser + + static + { + Platform.addJ2SBinaryType(".jvp?"); + } + private static final String VIEWER_PREFIX = "viewer_"; private static final String RNA_PREFIX = "rna_"; 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; @@ -226,6 +265,45 @@ public class Jalview2XML private Map rnaSessions = new HashMap<>(); /** + * A helper method for safely using the value of an optional attribute that + * may be null if not present in the XML. Answers the boolean value, or false + * if null. + * + * @param b + * @return + */ + public static boolean safeBoolean(Boolean b) + { + return b == null ? false : b.booleanValue(); + } + + /** + * A helper method for safely using the value of an optional attribute that + * may be null if not present in the XML. Answers the integer value, or zero + * if null. + * + * @param i + * @return + */ + public static int safeInt(Integer i) + { + return i == null ? 0 : i.intValue(); + } + + /** + * A helper method for safely using the value of an optional attribute that + * may be null if not present in the XML. Answers the float value, or zero if + * null. + * + * @param f + * @return + */ + public static float safeFloat(Float f) + { + return f == null ? 0f : f.floatValue(); + } + + /** * create/return unique hash string for sq * * @param sq @@ -383,7 +461,7 @@ public class Jalview2XML public boolean isResolvable() { return super.isResolvable() && mp.getTo() != null; - }; + } @Override boolean resolve() @@ -483,24 +561,30 @@ 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 @@ -539,13 +623,14 @@ public class Jalview2XML * core method for storing state for a set of AlignFrames. * * @param frames - * - frames involving all data to be exported (including containing - * splitframes) + * - frames involving all data to be exported (including those + * contained in splitframes, though not the split frames themselves) * @param jout * - project output stream */ private void saveAllFrames(List frames, JarOutputStream jout) { + Hashtable dsses = new Hashtable<>(); /* @@ -568,21 +653,22 @@ public class Jalview2XML for (int i = frames.size() - 1; i > -1; i--) { AlignFrame af = frames.get(i); + AlignViewport vp = af.getViewport(); // skip ? if (skipList != null && skipList - .containsKey(af.getViewport().getSequenceSetId())) + .containsKey(vp.getSequenceSetId())) { continue; } String shortName = makeFilename(af, shortNames); - int apSize = af.getAlignPanels().size(); - + AlignmentI alignment = vp.getAlignment(); + List panels = af.getAlignPanels(); + int apSize = panels.size(); for (int ap = 0; ap < apSize; ap++) - { - AlignmentPanel apanel = (AlignmentPanel) af.getAlignPanels() - .get(ap); + { + AlignmentPanel apanel = (AlignmentPanel) panels.get(ap); String fileName = apSize == 1 ? shortName : ap + shortName; if (!fileName.endsWith(".xml")) { @@ -590,11 +676,17 @@ public class Jalview2XML } saveState(apanel, fileName, jout, viewIds); - - String dssid = getDatasetIdRef( - af.getViewport().getAlignment().getDataset()); + } + if (apSize > 0) + { + // BH moved next bit out of inner loop, not that it really matters. + // so we are testing to make sure we actually have an alignment, + // apparently. + String dssid = getDatasetIdRef(alignment.getDataset()); if (!dsses.containsKey(dssid)) { + // We have not already covered this data by reference from another + // frame. dsses.put(dssid, af); } } @@ -609,7 +701,6 @@ public class Jalview2XML } catch (Exception foo) { } - ; jout.close(); } catch (Exception ex) { @@ -670,7 +761,12 @@ public class Jalview2XML { try { - FileOutputStream fos = new FileOutputStream(jarFile); + // create backupfiles object and get new temp filename destination + boolean doBackup = BackupFiles.getEnabled(); + BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null; + FileOutputStream fos = new FileOutputStream(doBackup ? + backupfiles.getTempFilePath() : jarFile); + JarOutputStream jout = new JarOutputStream(fos); List frames = new ArrayList<>(); @@ -690,9 +786,16 @@ public class Jalview2XML } catch (Exception foo) { } - ; jout.close(); - return true; + boolean success = true; + + if (doBackup) + { + 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"; @@ -701,10 +804,22 @@ public class Jalview2XML } } + /** + * Each AlignFrame has a single data set associated with it. Note that none of + * these frames are split frames, because Desktop.getAlignFrames() collects + * top and bottom separately here. + * + * @param dsses + * @param fileName + * @param jout + */ private void writeDatasetFor(Hashtable dsses, String fileName, JarOutputStream jout) { + // Note that in saveAllFrames we have associated each specific dataset to + // ONE of its associated frames. + for (String dssids : dsses.keySet()) { AlignFrame _af = dsses.get(dssids); @@ -985,7 +1100,7 @@ public class Jalview2XML * only view *should* be coped with sensibly. */ // This must have been loaded, is it still visible? - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); String matchedFile = null; for (int f = frames.length - 1; f > -1; f--) { @@ -1137,9 +1252,9 @@ public class Jalview2XML { // FIND ANY ASSOCIATED TREES // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT - if (Desktop.desktop != null) + if (Desktop.getDesktopPane() != null) { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); for (int t = 0; t < frames.length; t++) { @@ -1169,6 +1284,9 @@ 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); } @@ -1177,6 +1295,24 @@ public class Jalview2XML } } + /* + * save PCA viewers + */ + if (!storeDS && Desktop.getDesktopPane() != null) + { + for (JInternalFrame frame : Desktop.getDesktopPane().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 @@ -1555,6 +1691,7 @@ 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); @@ -1584,6 +1721,196 @@ 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 *
    @@ -1611,11 +1938,11 @@ public class Jalview2XML final SequenceI jds, List viewIds, AlignmentPanel ap, boolean storeDataset) { - if (Desktop.desktop == null) + if (Desktop.getDesktopPane() == null) { return; } - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); for (int f = frames.length - 1; f > -1; f--) { if (frames[f] instanceof AppVarna) @@ -1735,6 +2062,7 @@ 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); @@ -2070,7 +2398,7 @@ public class Jalview2XML if (calcIdParam.getVersion().equals("1.0")) { final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]); - Jws2Instance service = Jws2Discoverer.getDiscoverer() + Jws2Instance service = Jws2Discoverer.getInstance() .getPreferredServiceFor(calcIds); if (service != null) { @@ -2195,7 +2523,7 @@ 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())); @@ -2213,15 +2541,16 @@ 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); } @@ -2417,7 +2746,7 @@ public class Jalview2XML * @param file * - HTTP URL or filename */ - public AlignFrame loadJalviewAlign(final String file) + public AlignFrame loadJalviewAlign(final Object file) { jalview.gui.AlignFrame af = null; @@ -2445,13 +2774,14 @@ public class Jalview2XML { try { - SwingUtilities.invokeAndWait(new Runnable() + // BH 2019 -- can't wait + SwingUtilities.invokeLater(new Runnable() { @Override public void run() { setLoadingFinishedForNewStructureViewers(); - }; + } }); } catch (Exception x) { @@ -2461,44 +2791,52 @@ public class Jalview2XML return af; } - private jarInputStreamProvider createjarInputStreamProvider( - final String file) throws MalformedURLException - { - 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; - } - }; - } + @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 = Platform.isJS() ? Platform.getFileBytes((File) ofile) + : 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; + } + } /** * Recover jalview session from a jalview project archive. Caller may @@ -2524,12 +2862,19 @@ public class Jalview2XML IdentityHashMap importedDatasets = new IdentityHashMap<>(); Map gatherToThisFrame = new HashMap<>(); final String file = jprovider.getFilename(); + + List alignFrames = new ArrayList<>(); + try { JarInputStream jin = null; JarEntry jarentry = null; int entryCount = 1; + + // Look for all the entry names ending with ".xml" + // This includes all panels and at least one frame. +// Platform.timeCheck(null, Platform.TIME_MARK); do { jin = jprovider.getJarInputStream(); @@ -2537,12 +2882,27 @@ public class Jalview2XML { jarentry = jin.getNextJarEntry(); } + String name = (jarentry == null ? null : jarentry.getName()); - if (jarentry != null && jarentry.getName().endsWith(".xml")) +// System.out.println("Jalview2XML opening " + name); + if (name != null && name.endsWith(".xml")) { - InputStreamReader in = new InputStreamReader(jin, UTF_8); - // JalviewModel object = new JalviewModel(); + // DataSet for.... is read last. + + + // The question here is what to do with the two + // .xml files in the jvp file. + // Some number of them, "...Dataset for...", will be the + // Only AlignPanels and will have Viewport. + // One or more will be the source data, with the DBRefs. + // + // JVP file writing (above) ensures tha the AlignPanels are written + // first, then all relevant datasets (which are + // Jalview.datamodel.Alignment). + // + +// Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK); JAXBContext jc = JAXBContext .newInstance("jalview.xml.binding.jalview"); XMLStreamReader streamReader = XMLInputFactory.newInstance() @@ -2550,19 +2910,25 @@ public class Jalview2XML javax.xml.bind.Unmarshaller um = jc.createUnmarshaller(); JAXBElement jbe = um .unmarshal(streamReader, JalviewModel.class); - JalviewModel object = jbe.getValue(); + JalviewModel model = 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); - if (_af != null && object.getViewport().size() > 0) - // getJalviewModelSequence().getViewportCount() > 0) + // Q: Do we have to load from the model, even if it + // does not have a viewport, could we discover that early on? + // Q: Do we need to load this object? + _af = loadFromObject(model, file, true, jprovider); +// Platform.timeCheck("Jalview2XML.loadFromObject", + // Platform.TIME_MARK); + + if (_af != null) + { + alignFrames.add(_af); + } + if (_af != null && model.getViewport().size() > 0) { + + // That is, this is one of the AlignmentPanel models if (af == null) { // store a reference to the first view @@ -2582,6 +2948,7 @@ public class Jalview2XML af.getViewport().getAlignment().getDataset()); } } +// Platform.timeCheck("JAXB " + name, Platform.TIME_MARK); entryCount++; } else if (jarentry != null) @@ -2590,7 +2957,10 @@ public class Jalview2XML entryCount++; } } while (jarentry != null); +// Platform.timeCheck("JAXB loop exit", Platform.TIME_MARK); resolveFrefedSequences(); +// Platform.timeCheck("JAXB resolveFrefed", Platform.TIME_MARK); + } catch (IOException ex) { ex.printStackTrace(); @@ -2603,20 +2973,11 @@ 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) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } if (af != null) { @@ -2633,6 +2994,13 @@ public class Jalview2XML errorMessage = "Out of memory loading jalview XML file"; System.err.println("Out of memory whilst loading jalview XML file"); e.printStackTrace(); + } finally + { + for (AlignFrame alf : alignFrames) + { + alf.alignPanel.setHoldRepaint(false); + } + } /* @@ -2644,7 +3012,7 @@ public class Jalview2XML */ for (AlignFrame fr : gatherToThisFrame.values()) { - Desktop.instance.gatherViews(fr); + Desktop.getInstance().gatherViews(fr); } restoreSplitFrames(); @@ -2652,8 +3020,7 @@ public class Jalview2XML { if (ds.getCodonFrames() != null) { - StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + Desktop.getStructureSelectionManager() .registerMappings(ds.getCodonFrames()); } } @@ -2662,9 +3029,9 @@ public class Jalview2XML reportErrors(); } - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } return af; @@ -2732,8 +3099,8 @@ public class Jalview2XML if (!addedToSplitFrames.contains(af)) { Viewport view = candidate.getKey(); - Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), - view.getHeight()); + Desktop.addInternalFrame(af, view.getTitle(), + safeInt(view.getWidth()), safeInt(view.getHeight())); af.setMenusForViewport(); System.err.println("Failed to restore view " + view.getTitle() + " to split frame"); @@ -2745,7 +3112,7 @@ public class Jalview2XML */ for (SplitFrame sf : gatherTo) { - Desktop.instance.gatherViews(sf); + Desktop.getInstance().gatherViews(sf); } splitFrameCandidates.clear(); @@ -2804,7 +3171,7 @@ public class Jalview2XML @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), finalErrorMessage, "Error " + (saving ? "saving" : "loading") + " Jalview file", @@ -2963,7 +3330,9 @@ public class Jalview2XML } /** - * Load alignment frame from jalview XML DOM object + * Load alignment frame from jalview XML DOM object. For a DOM object that + * includes one or more Viewport elements (one with a title that does NOT + * contain "Dataset for"), create the frame. * * @param jalviewModel * DOM @@ -2978,9 +3347,13 @@ public class Jalview2XML AlignFrame loadFromObject(JalviewModel jalviewModel, String file, boolean loadTreesAndStructures, jarInputStreamProvider jprovider) { + +// Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK); + SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0); List vamsasSeqs = vamsasSet.getSequence(); + // JalviewModelSequence jms = object.getJalviewModelSequence(); // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0) @@ -2990,6 +3363,29 @@ public class Jalview2XML : 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); + } + +// Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK); + // //////////////////////////////// // LOAD SEQUENCES List hiddenSeqs = null; @@ -3009,6 +3405,7 @@ public class Jalview2XML SequenceI tmpSeq = seqRefIds.get(seqId); if (tmpSeq != null) { + // if (!incompleteSeqs.containsKey(seqId)) { // may not need this check, but keep it for at least 2.9,1 release @@ -3057,8 +3454,7 @@ public class Jalview2XML vi++; } - if (jseq.isViewreference() != null - && jseq.isViewreference().booleanValue()) + if (safeBoolean(jseq.isViewreference())) { referenceseqForView = tmpseqs.get(tmpseqs.size() - 1); } @@ -3074,6 +3470,8 @@ public class Jalview2XML } } +// Platform.timeCheck("Jalview2XML.loadFromObject-seq", +// Platform.TIME_MARK); // / // Create the alignment object from the sequence set // /////////////////////////////// @@ -3111,9 +3509,11 @@ public class Jalview2XML // 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); } +// Platform.timeCheck("Jalview2XML.loadFromObject-align", +// Platform.TIME_MARK); if (referenceseqForView != null) { al.setSeqrep(referenceseqForView); @@ -3126,6 +3526,8 @@ public class Jalview2XML al.setProperty(ssp.getKey(), ssp.getValue()); } +// Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop", +// Platform.TIME_MARK); // /////////////////////////////// Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this?? @@ -3139,6 +3541,7 @@ public class Jalview2XML // now, for 2.10 projects, this is also done if the xml doc includes // dataset sequences not actually present in any particular view. // +// Platform.timeCheck("J2XML features0", Platform.TIME_RESET); for (int i = 0; i < vamsasSeqs.size(); i++) { JSeq jseq = jseqs.get(i); @@ -3150,7 +3553,7 @@ public class Jalview2XML Feature feat = features.get(f); SequenceFeature sf = new SequenceFeature(feat.getType(), feat.getDescription(), feat.getBegin(), feat.getEnd(), - feat.getScore(), feat.getFeatureGroup()); + safeFloat(feat.getScore()), feat.getFeatureGroup()); sf.setStatus(feat.getStatus()); /* @@ -3193,7 +3596,9 @@ public class Jalview2XML } // adds feature to datasequence's feature set (since Jalview 2.10) +// Platform.timeCheck(null, Platform.TIME_SET); al.getSequenceAt(i).addSequenceFeature(sf); +// Platform.timeCheck(null, Platform.TIME_MARK); } } if (vamsasSeqs.get(i).getDBRef().size() > 0) @@ -3253,8 +3658,7 @@ public class Jalview2XML { entry.setProperty(prop.getName(), prop.getValue()); } - StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + Desktop.getStructureSelectionManager() .registerPDBEntry(entry); // adds PDBEntry to datasequence's set (since Jalview 2.10) if (al.getSequenceAt(i).getDatasetSequence() != null) @@ -3267,7 +3671,12 @@ public class Jalview2XML } } } + } + +// Platform.timeCheck("features done", Platform.TIME_GET); +// Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview", +// Platform.TIME_MARK); } // end !multipleview // /////////////////////////////// @@ -3309,6 +3718,8 @@ public class Jalview2XML al.addCodonFrame(cf); } } +// Platform.timeCheck("Jalview2XML.loadFromObject-seqmap", +// Platform.TIME_MARK); } // //////////////////////////////// @@ -3344,22 +3755,21 @@ public class Jalview2XML // annotation.setAutoCalculated(true); // } } - if (autoForView || // (annotation.hasAutoCalculated() && - annotation.isAutoCalculated()) + if (autoForView || annotation.isAutoCalculated()) { // remove ID - we don't recover annotation from other views for // view-specific annotation annotation.setId(null); } - // set visiblity for other annotation in this view + // set visibility for other annotation in this view String annotationId = annotation.getId(); if (annotationId != null && annotationIds.containsKey(annotationId)) { AlignmentAnnotation jda = annotationIds.get(annotationId); // in principle Visible should always be true for annotation displayed // in multiple views - if (annotation.isVisible() != null) // annotation.hasVisible()) + if (annotation.isVisible() != null) { jda.visible = annotation.isVisible(); } @@ -3370,6 +3780,9 @@ public class Jalview2XML } // Construct new annotation from model. List ae = annotation.getAnnotationElement(); +// System.err.println( +// "Jalview2XML processing " + ae.size() + " annotations"); + jalview.datamodel.Annotation[] anot = null; java.awt.Color firstColour = null; int anpos; @@ -3386,8 +3799,7 @@ public class Jalview2XML continue; } - float value = annElement.getValue() == null ? 0f - : annElement.getValue().floatValue(); + float value = safeFloat(annElement.getValue()); anot[anpos] = new jalview.datamodel.Annotation( annElement.getDisplayCharacter(), annElement.getDescription(), @@ -3399,22 +3811,14 @@ public class Jalview2XML .getSecondaryStructure() .charAt(0), value); - // JBPNote: Consider verifying dataflow for IO of secondary - // structure annotation read from Stockholm files - // this was added to try to ensure that - // if (anot[ annElement.getPosition()].secondaryStructure>' ') - // { - // anot[ annElement.getPosition()].displayCharacter = ""; - // } - final int colourValue = annElement.getColour() == null ? 0 - : annElement.getColour().intValue(); - anot[anpos].colour = new java.awt.Color(colourValue); + anot[anpos].colour = new Color(safeInt(annElement.getColour())); if (firstColour == null) { firstColour = anot[anpos].colour; } } } + // create the new AlignmentAnnotation jalview.datamodel.AlignmentAnnotation jaa = null; if (annotation.isGraph()) @@ -3425,18 +3829,17 @@ public class Jalview2XML // } jaa = new jalview.datamodel.AlignmentAnnotation( annotation.getLabel(), annotation.getDescription(), anot, - llim, hlim, annotation.getGraphType()); + llim, hlim, safeInt(annotation.getGraphType())); - jaa.graphGroup = annotation.getGraphGroup(); + jaa.graphGroup = safeInt(annotation.getGraphGroup()); jaa._linecolour = firstColour; if (annotation.getThresholdLine() != null) { jaa.setThreshold(new jalview.datamodel.GraphLine( - annotation.getThresholdLine().getValue(), + safeFloat(annotation.getThresholdLine().getValue()), annotation.getThresholdLine().getLabel(), - new java.awt.Color( - annotation.getThresholdLine().getColour()))); - + new java.awt.Color(safeInt( + annotation.getThresholdLine().getColour())))); } if (autoForView || annotation.isAutoCalculated()) { @@ -3452,6 +3855,7 @@ public class Jalview2XML jaa._linecolour = firstColour; } // register new annotation + // Annotation graphs such as Conservation will not have id. if (annotation.getId() != null) { annotationIds.put(annotation.getId(), jaa); @@ -3490,7 +3894,7 @@ public class Jalview2XML if (annotation.getScore() != null) { - jaa.setScore(annotation.getScore()); + jaa.setScore(annotation.getScore().doubleValue()); } if (annotation.isVisible() != null) { @@ -3507,8 +3911,7 @@ public class Jalview2XML { jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue(); } - if (/*annotation.hasAutoCalculated() && */annotation - .isAutoCalculated()) + if (annotation.isAutoCalculated()) { // newer files have an 'autoCalculated' flag and store calculation // state in viewport properties @@ -3519,11 +3922,7 @@ public class Jalview2XML { jaa.graphHeight = annotation.getGraphHeight().intValue(); } - // if (annotation.hasBelowAlignment()) - // { - // schema specifies default for optional attribute - jaa.belowAlignment = annotation.isBelowAlignment(); - // } + jaa.belowAlignment = annotation.isBelowAlignment(); jaa.setCalcId(annotation.getCalcId()); if (annotation.getProperty().size() > 0) { @@ -3545,6 +3944,8 @@ public class Jalview2XML al.addAnnotation(jaa); } } +// Platform.timeCheck("Jalview2XML.loadFromObject-annot", +// Platform.TIME_MARK); } // /////////////////////// // LOAD GROUPS @@ -3570,12 +3971,11 @@ public class Jalview2XML } else { - cs = ColourSchemeProperty.getColourScheme(al, + cs = ColourSchemeProperty.getColourScheme(null, al, jGroup.getColour()); } } - int pidThreshold = jGroup.getPidThreshold() == null ? 0 - : jGroup.getPidThreshold().intValue(); + int pidThreshold = safeInt(jGroup.getPidThreshold()); Vector seqs = new Vector<>(); @@ -3596,40 +3996,24 @@ public class Jalview2XML } SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs, - jGroup.isDisplayBoxes(), jGroup.isDisplayText(), - jGroup.isColourText(), jGroup.getStart(), jGroup.getEnd()); + safeBoolean(jGroup.isDisplayBoxes()), + safeBoolean(jGroup.isDisplayText()), + safeBoolean(jGroup.isColourText()), + safeInt(jGroup.getStart()), safeInt(jGroup.getEnd())); sg.getGroupColourScheme().setThreshold(pidThreshold, true); sg.getGroupColourScheme() - .setConservationInc(jGroup.getConsThreshold() == null ? 0 - : jGroup.getConsThreshold().intValue()); - sg.setOutlineColour( - new java.awt.Color(jGroup.getOutlineColour() == null ? 0 - : jGroup.getOutlineColour().intValue())); - - sg.textColour = new java.awt.Color(jGroup.getTextCol1()); - sg.textColour2 = new java.awt.Color(jGroup.getTextCol2()); - sg.setShowNonconserved( - jGroup.isShowUnconserved() != null - ? jGroup.isShowUnconserved().booleanValue() - : false); - sg.thresholdTextColour = jGroup.getTextColThreshold(); + .setConservationInc(safeInt(jGroup.getConsThreshold())); + sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour()))); + + sg.textColour = new Color(safeInt(jGroup.getTextCol1())); + sg.textColour2 = new Color(safeInt(jGroup.getTextCol2())); + sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved())); + sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold()); // attributes with a default in the schema are never null - // if (jGroup.hasShowConsensusHistogram()) - // { sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram()); - // } - // if (jGroup.hasShowSequenceLogo()) - // { sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); - // } - // if (jGroup.hasNormaliseSequenceLogo()) - // { sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); - // } - // if (jGroup.hasIgnoreGapsinConsensus()) - // { sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus()); - // } if (jGroup.getConsThreshold() != null && jGroup.getConsThreshold().intValue() != 0) { @@ -3676,6 +4060,8 @@ public class Jalview2XML jGroup.getAnnotationColours(), null, al, jalviewModel, false)); } } +// Platform.timeCheck("Jalview2XML.loadFromObject-groups", +// Platform.TIME_MARK); } if (view == null) { @@ -3685,15 +4071,6 @@ public class Jalview2XML // /////////////////////////////// // 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. if (multipleView && viewportsAdded.size() == 0) { @@ -3724,6 +4101,8 @@ public class Jalview2XML } } +// Platform.timeCheck("Jalview2XML.loadFromObject-viewport", +// Platform.TIME_MARK); } /** * indicate that annotation colours are applied across all groups (pre @@ -3732,8 +4111,9 @@ public class Jalview2XML boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1", jalviewModel.getVersion()); + AlignFrame af = null; AlignmentPanel ap = null; - boolean isnewview = true; + AlignViewport av = null; if (viewId != null) { // Check to see if this alignment already has a view id == viewId @@ -3743,25 +4123,27 @@ public class Jalview2XML { for (int v = 0; v < views.length; v++) { - if (views[v].av.getViewId().equalsIgnoreCase(viewId)) + ap = views[v]; + av = ap.av; + if (av.getViewId().equalsIgnoreCase(viewId)) { // recover the existing alignpanel, alignframe, viewport - af = views[v].alignFrame; - av = views[v].av; - ap = views[v]; + af = ap.alignFrame; + break; // TODO: could even skip resetting view settings if we don't want to // change the local settings from other jalview processes - isnewview = false; } } } } - if (isnewview) + if (af == null) { af = loadViewport(file, jseqs, hiddenSeqs, al, jalviewModel, view, uniqueSeqSetId, viewId, autoAlan); av = af.getViewport(); + // note that this only retrieves the most recently accessed + // tab of an AlignFrame. ap = af.alignPanel; } @@ -3770,13 +4152,61 @@ public class Jalview2XML * * Not done if flag is false (when this method is used for New View) */ + final AlignFrame af0 = af; + final AlignViewport av0 = av; + final AlignmentPanel ap0 = ap; +// Platform.timeCheck("Jalview2XML.loadFromObject-beforetree", +// Platform.TIME_MARK); if (loadTreesAndStructures) { - loadTrees(jalviewModel, view, af, av, ap); - loadPDBStructures(jprovider, jseqs, af, ap); - loadRnaViewers(jprovider, jseqs, ap); + if (!jalviewModel.getTree().isEmpty()) + { + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { +// Platform.timeCheck(null, Platform.TIME_MARK); + loadTrees(jalviewModel, view, af0, av0, ap0); +// Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK); + } + }); + } + if (!jalviewModel.getPcaViewer().isEmpty()) + { + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { +// Platform.timeCheck(null, Platform.TIME_MARK); + loadPCAViewers(jalviewModel, ap0); +// Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK); + } + }); + } + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { +// Platform.timeCheck(null, Platform.TIME_MARK); + loadPDBStructures(jprovider, jseqs, af0, ap0); +// Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK); + } + }); + SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + loadRnaViewers(jprovider, jseqs, ap0); + } + }); } // and finally return. + // but do not set holdRepaint true just yet, because this could be the + // initial frame with just its dataset. return af; } @@ -3793,7 +4223,7 @@ public class Jalview2XML * @param jseqs * @param ap */ - private void loadRnaViewers(jarInputStreamProvider jprovider, + protected void loadRnaViewers(jarInputStreamProvider jprovider, List jseqs, AlignmentPanel ap) { /* @@ -3819,7 +4249,7 @@ public class Jalview2XML * add the structure to the Varna display (with session state copied * from the jar to a temporary file) */ - boolean gapped = ss.isGapped(); + boolean gapped = safeBoolean(ss.isGapped()); String rnaTitle = ss.getTitle(); String sessionState = ss.getViewerState(); String tempStateFile = copyJarEntry(jprovider, sessionState, @@ -3827,7 +4257,7 @@ public class Jalview2XML RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped); appVarna.addModelSession(rna, rnaTitle, tempStateFile); } - appVarna.setInitialSelection(viewer.getSelectedRna()); + appVarna.setInitialSelection(safeInt(viewer.getSelectedRna())); } } } @@ -3868,8 +4298,9 @@ public class Jalview2XML * viewer not found - make it */ RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(), - viewer.getXpos(), viewer.getYpos(), viewer.getWidth(), - viewer.getHeight(), viewer.getDividerLocation()); + safeInt(viewer.getXpos()), safeInt(viewer.getYpos()), + safeInt(viewer.getWidth()), safeInt(viewer.getHeight()), + safeInt(viewer.getDividerLocation())); AppVarna varna = new AppVarna(model, ap); return varna; @@ -3898,10 +4329,10 @@ public class Jalview2XML 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()); + tp = af.showNewickTree(new NewickFile(tree.getNewick()), + tree.getTitle(), safeInt(tree.getWidth()), + safeInt(tree.getHeight()), safeInt(tree.getXpos()), + safeInt(tree.getYpos())); if (tree.getId() != null) { // perhaps bind the tree id to something ? @@ -3913,15 +4344,15 @@ public class Jalview2XML // 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.setViewport(av); // af.viewport; // TODO: verify 'associate with all - // views' - // works still + tp.setBounds(new Rectangle(safeInt(tree.getXpos()), + safeInt(tree.getYpos()), safeInt(tree.getWidth()), + safeInt(tree.getHeight()))); + tp.setViewport(av); // af.viewport; + // 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" @@ -3929,27 +4360,29 @@ public class Jalview2XML continue; } - tp.fitToWindow.setState(tree.isFitToWindow()); + tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow())); tp.fitToWindow_actionPerformed(null); if (tree.getFontName() != null) { - tp.setTreeFont(new java.awt.Font(tree.getFontName(), - tree.getFontStyle(), tree.getFontSize())); + tp.setTreeFont( + new Font(tree.getFontName(), safeInt(tree.getFontStyle()), + safeInt(tree.getFontSize()))); } else { - tp.setTreeFont(new java.awt.Font(view.getFontName(), - view.getFontStyle(), tree.getFontSize())); + tp.setTreeFont( + new Font(view.getFontName(), safeInt(view.getFontStyle()), + safeInt(view.getFontSize()))); } - tp.showPlaceholders(tree.isMarkUnlinked()); - tp.showBootstrap(tree.isShowBootstrap()); - tp.showDistances(tree.isShowDistances()); + tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked())); + tp.showBootstrap(safeBoolean(tree.isShowBootstrap())); + tp.showDistances(safeBoolean(tree.isShowDistances())); - tp.getTreeCanvas().setThreshold(tree.getThreshold()); + tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold())); - if (tree.isCurrentTree()) + if (safeBoolean(tree.isCurrentTree())) { af.getViewport().setCurrentTree(tp.getTree()); } @@ -4003,13 +4436,13 @@ public class Jalview2XML loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile())); jpdb.setId(pdbid.getId()); - int x = structureState.getXpos(); - int y = structureState.getYpos(); - int width = structureState.getWidth(); - int height = structureState.getHeight(); + int x = safeInt(structureState.getXpos()); + int y = safeInt(structureState.getYpos()); + int width = safeInt(structureState.getWidth()); + int height = safeInt(structureState.getHeight()); // Probably don't need to do this anymore... - // Desktop.desktop.getComponentAt(x, y); + // Desktop.getDesktop().getComponentAt(x, y); // TODO: NOW: check that this recovers the PDB file correctly. String pdbFile = loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()); @@ -4328,9 +4761,9 @@ public class Jalview2XML final AlignFrame alf = af; final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(), svattrib.getWidth(), svattrib.getHeight()); - try - { - javax.swing.SwingUtilities.invokeAndWait(new Runnable() + // try + // { + javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() @@ -4357,14 +4790,14 @@ public class Jalview2XML } } }); - } catch (InvocationTargetException ex) - { - warn("Unexpected error when opening Jmol view.", ex); - - } catch (InterruptedException e) - { - // e.printStackTrace(); - } + // } catch (InvocationTargetException ex) + // { + // warn("Unexpected error when opening Jmol view.", ex); + // + // } catch (InterruptedException e) + // { + // // e.printStackTrace(); + // } } @@ -4493,7 +4926,7 @@ public class Jalview2XML { try { - frames = Desktop.desktop.getAllFrames(); + frames = Desktop.getDesktopPane().getAllFrames(); } catch (ArrayIndexOutOfBoundsException e) { // occasional No such child exceptions are thrown here... @@ -4569,17 +5002,28 @@ public class Jalview2XML String viewId, List autoAlan) { AlignFrame af = null; - af = new AlignFrame(al, view.getWidth(), view.getHeight(), - uniqueSeqSetId, viewId); - + af = new AlignFrame(al, safeInt(view.getWidth()), + safeInt(view.getHeight()), uniqueSeqSetId, viewId) +// { +// +// @Override +// protected void processKeyEvent(java.awt.event.KeyEvent e) { +// System.out.println("Jalview2XML AF " + e); +// super.processKeyEvent(e); +// +// } +// +// } + ; + af.alignPanel.setHoldRepaint(true); af.setFileName(file, FileFormat.Jalview); final AlignViewport viewport = af.getViewport(); for (int i = 0; i < JSEQ.size(); i++) { - viewport.setSequenceColour( - viewport.getAlignment().getSequenceAt(i), - new java.awt.Color(JSEQ.get(i).getColour())); + int colour = safeInt(JSEQ.get(i).getColour()); + viewport.setSequenceColour(viewport.getAlignment().getSequenceAt(i), + new Color(colour)); } if (al.hasSeqrep()) @@ -4588,7 +5032,7 @@ public class Jalview2XML viewport.setDisplayReferenceSeq(true); } - viewport.setGatherViewsHere(view.isGatheredViews()); + viewport.setGatherViewsHere(safeBoolean(view.isGatheredViews())); if (view.getSequenceSetId() != null) { @@ -4640,49 +5084,58 @@ public class Jalview2XML } // recover view properties and display parameters - viewport.setShowAnnotation(view.isShowAnnotation()); - viewport.setAbovePIDThreshold(view.isPidSelected()); - final int pidThreshold = view.getPidThreshold() == null ? 0 - : view.getPidThreshold().intValue(); + viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation())); + viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected())); + final int pidThreshold = safeInt(view.getPidThreshold()); viewport.setThreshold(pidThreshold); - viewport.setColourText(view.isShowColourText()); + viewport.setColourText(safeBoolean(view.isShowColourText())); viewport - .setConservationSelected(view.isConservationSelected()); - viewport.setIncrement(view.getConsThreshold() == null ? 0 - : view.getConsThreshold().intValue()); - viewport.setShowJVSuffix(view.isShowFullId()); - viewport.setRightAlignIds(view.isRightAlignIds()); - viewport.setFont(new java.awt.Font(view.getFontName(), - view.getFontStyle(), view.getFontSize()), true); + .setConservationSelected( + safeBoolean(view.isConservationSelected())); + viewport.setIncrement(safeInt(view.getConsThreshold())); + viewport.setShowJVSuffix(safeBoolean(view.isShowFullId())); + viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds())); + viewport.setFont(new Font(view.getFontName(), + safeInt(view.getFontStyle()), safeInt(view.getFontSize())), + true); ViewStyleI vs = viewport.getViewStyle(); vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna()); viewport.setViewStyle(vs); // TODO: allow custom charWidth/Heights to be restored by updating them // after setting font - which means set above to false - viewport.setRenderGaps(view.isRenderGaps()); - viewport.setWrapAlignment(view.isWrapAlignment()); - viewport.setShowAnnotation(view.isShowAnnotation()); + viewport.setRenderGaps(safeBoolean(view.isRenderGaps())); + viewport.setWrapAlignment(safeBoolean(view.isWrapAlignment())); + viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation())); - viewport.setShowBoxes(view.isShowBoxes()); + viewport.setShowBoxes(safeBoolean(view.isShowBoxes())); - viewport.setShowText(view.isShowText()); + viewport.setShowText(safeBoolean(view.isShowText())); - viewport.setTextColour(new java.awt.Color(view.getTextCol1())); - viewport.setTextColour2(new java.awt.Color(view.getTextCol2())); - viewport.setThresholdTextColour(view.getTextColThreshold()); - viewport.setShowUnconserved( - view.isShowUnconserved() ? view.isShowUnconserved() : false); - viewport.getRanges().setStartRes(view.getStartRes()); + viewport.setTextColour(new Color(safeInt(view.getTextCol1()))); + viewport.setTextColour2(new Color(safeInt(view.getTextCol2()))); + viewport.setThresholdTextColour(safeInt(view.getTextColThreshold())); + viewport.setShowUnconserved(view.isShowUnconserved()); + viewport.getRanges().setStartRes(safeInt(view.getStartRes())); if (view.getViewName() != null) { viewport.setViewName(view.getViewName()); af.setInitialTabVisible(); } - af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), - view.getHeight()); + int x = safeInt(view.getXpos()); + int y = safeInt(view.getYpos()); + int w = safeInt(view.getWidth()); + int h = safeInt(view.getHeight()); + // // BH we cannot let the title bar go off the top + // if (Platform.isJS()) + // { + // x = Math.max(50 - w, x); + // y = Math.max(0, y); + // } + + af.setBounds(x, y, w, h); // startSeq set in af.alignPanel.updateLayout below af.alignPanel.updateLayout(); ColourSchemeI cs = null; @@ -4703,91 +5156,44 @@ 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 (view.isConservationSelected() && cs != null) + if (safeBoolean(view.isConservationSelected()) && cs != null) { viewport.getResidueShading() - .setConservationInc(view.getConsThreshold()); + .setConservationInc(safeInt(view.getConsThreshold())); } - af.changeColour(cs); - viewport.setColourAppliesToAllGroups(true); viewport - .setShowSequenceFeatures(view.isShowSequenceFeatures()); + .setShowSequenceFeatures( + safeBoolean(view.isShowSequenceFeatures())); - // if (view.hasCentreColumnLabels()) - // { viewport.setCentreColumnLabels(view.isCentreColumnLabels()); - // } - // if (view.hasIgnoreGapsinConsensus()) - // { viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null); - // } - // if (view.hasFollowHighlight()) - // { - viewport.setFollowHighlight(view.isFollowHighlight()); - // } - // if (view.hasFollowSelection()) - // { viewport.followSelection = view.isFollowSelection(); - // } - // if (view.hasShowConsensusHistogram()) - // { viewport.setShowConsensusHistogram(view.isShowConsensusHistogram()); - // } - // else - // { - // viewport.setShowConsensusHistogram(true); - // } - // if (view.hasShowSequenceLogo()) - // { viewport.setShowSequenceLogo(view.isShowSequenceLogo()); - // } - // else - // { - // viewport.setShowSequenceLogo(false); - // } - // if (view.hasNormaliseSequenceLogo()) - // { viewport.setNormaliseSequenceLogo(view.isNormaliseSequenceLogo()); - // } - if (view.isShowDbRefTooltip() != null) - { - viewport.setShowDBRefs(view.isShowDbRefTooltip()); - } - if (view.isShowNPfeatureTooltip() != null) - { - viewport.setShowNPFeats(view.isShowNPfeatureTooltip()); - } - // if (view.hasShowGroupConsensus()) - // { + viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip())); + viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip())); viewport.setShowGroupConsensus(view.isShowGroupConsensus()); - // } - // else - // { - // viewport.setShowGroupConsensus(false); - // } - // if (view.hasShowGroupConservation()) - // { viewport.setShowGroupConservation(view.isShowGroupConservation()); - // } - // else - // { - // viewport.setShowGroupConservation(false); - // } // recover feature settings if (jm.getFeatureSettings() != null) @@ -4815,7 +5221,7 @@ public class Jalview2XML if (filters != null) { FeatureMatcherSetI filter = Jalview2XML - .unmarshalFilter(featureType, filters); + .parseFilter(featureType, filters); if (!filter.isEmpty()) { fr.setFeatureFilter(featureType, filter); @@ -4843,13 +5249,11 @@ public class Jalview2XML { noValueColour = maxColour; } - float min = setting.getMin() != null - ? setting.getMin().floatValue() - : 0f; - float max = setting.getMin() != null - ? setting.getMax().floatValue() - : 1f; - FeatureColourI gc = new FeatureColour(minColour, maxColour, + float min = safeFloat(safeFloat(setting.getMin())); + float max = setting.getMax() == null ? 1f + : setting.getMax().floatValue(); + FeatureColourI gc = new FeatureColour(maxColour, minColour, + maxColour, noValueColour, min, max); if (setting.getAttributeName().size() > 0) { @@ -4859,7 +5263,7 @@ public class Jalview2XML if (setting.getThreshold() != null) { gc.setThreshold(setting.getThreshold().floatValue()); - int threshstate = setting.getThreshstate().intValue(); + int threshstate = safeInt(setting.getThreshstate()); // -1 = None, 0 = Below, 1 = Above threshold if (threshstate == 0) { @@ -4897,7 +5301,7 @@ public class Jalview2XML featureOrder.put(featureType, new Float( fs / jm.getFeatureSettings().getSetting().size())); } - if (setting.isDisplay()) + if (safeBoolean(setting.isDisplay())) { fdi.setVisible(featureType); } @@ -4920,9 +5324,9 @@ public class Jalview2XML { for (int c = 0; c < view.getHiddenColumns().size(); c++) { - viewport.hideColumns(view.getHiddenColumns().get(c).getStart(), - view.getHiddenColumns().get(c).getEnd() // +1 - ); + final HiddenColumns hc = view.getHiddenColumns().get(c); + viewport.hideColumns(safeInt(hc.getStart()), + safeInt(hc.getEnd()) /* +1 */); } } if (view.getCalcIdParam() != null) @@ -4953,8 +5357,8 @@ public class Jalview2XML String complementaryViewId = view.getComplementId(); if (complementaryViewId == null) { - Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), - view.getHeight()); + Desktop.addInternalFrame(af, view.getTitle(), + safeInt(view.getWidth()), safeInt(view.getHeight())); // recompute any autoannotation af.alignPanel.updateAnnotation(false, true); reorderAutoannotation(af, al, autoAlan); @@ -5029,34 +5433,36 @@ public class Jalview2XML } if (matchedAnnotation.getThreshold() == null) { - matchedAnnotation.setThreshold(new GraphLine( - viewAnnColour.getThreshold(), "Threshold", Color.black)); + matchedAnnotation.setThreshold( + new GraphLine(safeFloat(viewAnnColour.getThreshold()), + "Threshold", Color.black)); } AnnotationColourGradient cs = null; if (viewAnnColour.getColourScheme().equals("None")) { cs = new AnnotationColourGradient(matchedAnnotation, - new Color(viewAnnColour.getMinColour()), - new Color(viewAnnColour.getMaxColour()), - viewAnnColour.getAboveThreshold()); + new Color(safeInt(viewAnnColour.getMinColour())), + new Color(safeInt(viewAnnColour.getMaxColour())), + safeInt(viewAnnColour.getAboveThreshold())); } else if (viewAnnColour.getColourScheme().startsWith("ucs")) { cs = new AnnotationColourGradient(matchedAnnotation, getUserColourScheme(model, viewAnnColour.getColourScheme()), - viewAnnColour.getAboveThreshold()); + safeInt(viewAnnColour.getAboveThreshold())); } else { cs = new AnnotationColourGradient(matchedAnnotation, - ColourSchemeProperty.getColourScheme(al, + ColourSchemeProperty.getColourScheme(af.getViewport(), al, viewAnnColour.getColourScheme()), - viewAnnColour.getAboveThreshold()); + safeInt(viewAnnColour.getAboveThreshold())); } - boolean perSequenceOnly = viewAnnColour.isPerSequence(); - boolean useOriginalColours = viewAnnColour.isPredefinedColours(); + boolean perSequenceOnly = safeBoolean(viewAnnColour.isPerSequence()); + boolean useOriginalColours = safeBoolean( + viewAnnColour.isPredefinedColours()); cs.setSeqAssociated(perSequenceOnly); cs.setPredefinedColours(useOriginalColours); @@ -5073,7 +5479,7 @@ public class Jalview2XML AnnotationColourGradient groupScheme = new AnnotationColourGradient( matchedAnnotation, sg.getColourScheme(), - viewAnnColour.getAboveThreshold()); + safeInt(viewAnnColour.getAboveThreshold())); sg.setColourScheme(groupScheme); groupScheme.setSeqAssociated(perSequenceOnly); groupScheme.setPredefinedColours(useOriginalColours); @@ -5238,13 +5644,51 @@ public class Jalview2XML } 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(); } @@ -5259,18 +5703,66 @@ public class Jalview2XML SequenceI[] dsseqs = new SequenceI[dseqs.size()]; dseqs.copyInto(dsseqs); ds = new jalview.datamodel.Alignment(dsseqs); - debug("Created new dataset " + vamsasSet.getDatasetId() - + " for alignment " + System.identityHashCode(al)); +// debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId() +// + " for alignment " + System.identityHashCode(al)); addDatasetRef(vamsasSet.getDatasetId(), ds); } // set the dataset for the newly imported alignment. 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 @@ -5529,15 +6021,16 @@ 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)); @@ -5547,9 +6040,9 @@ public class Jalview2XML frefedSequence.add(newMappingRef(dsfor, jmap)); } } - else + else if (m.getSequence() != null) { - /** + /* * local sequence definition */ Sequence ms = m.getSequence(); @@ -5606,6 +6099,10 @@ public class Jalview2XML 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); @@ -5621,14 +6118,7 @@ public class Jalview2XML AlignFrame af = loadFromObject(jm, null, false, null); af.getAlignPanels().clear(); af.closeMenuItem_actionPerformed(true); - - /* - * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0; - * i 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 * @param fcol * @return */ - protected static Colour marshalColour( + public static Colour marshalColour( String featureType, FeatureColourI fcol) { Colour col = new Colour(); @@ -5930,7 +6542,7 @@ public class Jalview2XML * @param and * if true, conditions are and-ed, else or-ed */ - protected static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter( + public static jalview.xml.binding.jalview.FeatureMatcherSet marshalFilter( FeatureMatcherI firstMatcher, Iterator filters, boolean and) { @@ -5996,14 +6608,14 @@ public class Jalview2XML * @param matcherSetModel * @return */ - protected static FeatureMatcherSetI unmarshalFilter( + public static FeatureMatcherSetI parseFilter( String featureType, jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel) { FeatureMatcherSetI result = new FeatureMatcherSet(); try { - unmarshalFilterConditions(result, matcherSetModel, true); + parseFilterConditions(result, matcherSetModel, true); } catch (IllegalStateException e) { // mixing AND and OR conditions perhaps @@ -6027,7 +6639,7 @@ public class Jalview2XML * @throws IllegalStateException * if AND and OR conditions are mixed */ - protected static void unmarshalFilterConditions( + protected static void parseFilterConditions( FeatureMatcherSetI matcherSet, jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel, boolean and) @@ -6080,13 +6692,12 @@ public class Jalview2XML * compound condition */ List matchers = matcherSetModel - .getCompoundMatcher() - .getMatcherSet(); + .getCompoundMatcher().getMatcherSet(); boolean anded = matcherSetModel.getCompoundMatcher().isAnd(); if (matchers.size() == 2) { - unmarshalFilterConditions(matcherSet, matchers.get(0), anded); - unmarshalFilterConditions(matcherSet, matchers.get(1), anded); + parseFilterConditions(matcherSet, matchers.get(0), anded); + parseFilterConditions(matcherSet, matchers.get(1), anded); } else { @@ -6101,7 +6712,7 @@ public class Jalview2XML * @param colourModel * @return */ - protected static FeatureColourI unmarshalColour(Colour colourModel) + public static FeatureColourI parseColour(Colour colourModel) { FeatureColourI colour = null; @@ -6130,9 +6741,9 @@ public class Jalview2XML noValueColour = maxcol; } - colour = new FeatureColour(mincol, maxcol, noValueColour, - colourModel.getMin(), - colourModel.getMax()); + colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour, + safeFloat(colourModel.getMin()), + safeFloat(colourModel.getMax())); final List attributeName = colourModel.getAttributeName(); String[] attributes = attributeName .toArray(new String[attributeName.size()]);