X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=913dffe52030868a1beb41543024d8df3072d1fe;hb=fdde9a078d7bdb46ed9fb7fe115ea83c84a19c81;hp=351fc041bc1ba1af534dd2e123243f1b9b0cb467;hpb=5afdbcf85bf0a52dbb3124f47d05be659284c93c;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 351fc04..913dffe 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -26,6 +26,7 @@ import static jalview.math.RotatableMatrix.Axis.Z; import java.awt.Color; import java.awt.Font; +import java.awt.FontMetrics; import java.awt.Rectangle; import java.io.BufferedReader; import java.io.ByteArrayInputStream; @@ -44,6 +45,7 @@ import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; +import java.util.BitSet; import java.util.Collections; import java.util.Enumeration; import java.util.GregorianCalendar; @@ -89,6 +91,8 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ContactMatrix; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLocus; import jalview.datamodel.GraphLine; @@ -112,6 +116,7 @@ import jalview.gui.AppVarna; import jalview.gui.Desktop; import jalview.gui.JvOptionPane; import jalview.gui.OOMWarning; +import jalview.gui.OverviewPanel; import jalview.gui.PCAPanel; import jalview.gui.PaintRefresher; import jalview.gui.SplitFrame; @@ -147,6 +152,7 @@ import jalview.viewmodel.ViewportRanges; import jalview.viewmodel.seqfeatures.FeatureRendererModel; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.dm.AAConSettings; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -185,11 +191,13 @@ import jalview.xml.binding.jalview.JalviewModel.UserColours; import jalview.xml.binding.jalview.JalviewModel.Viewport; import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam; import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns; +import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview; import jalview.xml.binding.jalview.JalviewUserColours; import jalview.xml.binding.jalview.JalviewUserColours.Colour; import jalview.xml.binding.jalview.MapListType.MapListFrom; import jalview.xml.binding.jalview.MapListType.MapListTo; import jalview.xml.binding.jalview.Mapping; +import jalview.xml.binding.jalview.MatrixType; import jalview.xml.binding.jalview.NoValueColour; import jalview.xml.binding.jalview.ObjectFactory; import jalview.xml.binding.jalview.PcaDataType; @@ -625,7 +633,7 @@ public class Jalview2XML if (Cache.getDefault("DEBUG_DELAY_SAVE", false)) { - int n = 20; + int n = debugDelaySave; int i = 0; while (i < n) { @@ -791,7 +799,7 @@ public class Jalview2XML if (Cache.getDefault("DEBUG_DELAY_SAVE", false)) { - int n = 20; + int n = debugDelaySave; int i = 0; while (i < n) { @@ -1317,6 +1325,13 @@ public class Jalview2XML tree.setLinkToAllViews( tp.getTreeCanvas().isApplyToAllViews()); + // columnWiseTree + if (tp.isColumnWise()) + { + tree.setColumnWise(true); + String annId = tp.getAssocAnnotation().annotationId; + tree.setColumnReference(annId); + } // jms.addTree(tree); object.getTree().add(tree); } @@ -1492,6 +1507,23 @@ public class Jalview2XML view.setStartRes(vpRanges.getStartRes()); view.setStartSeq(vpRanges.getStartSeq()); + OverviewPanel ov = ap.getOverviewPanel(); + if (ov != null) + { + Overview overview = new Overview(); + overview.setTitle(ov.getTitle()); + Rectangle bounds = ov.getFrameBounds(); + overview.setXpos(bounds.x); + overview.setYpos(bounds.y); + overview.setWidth(bounds.width); + overview.setHeight(bounds.height); + overview.setShowHidden(ov.isShowHiddenRegions()); + overview.setGapColour(ov.getCanvas().getGapColour().getRGB()); + overview.setResidueColour( + ov.getCanvas().getResidueColour().getRGB()); + overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB()); + view.setOverview(overview); + } if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) { view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(), @@ -1532,6 +1564,8 @@ public class Jalview2XML view.setConservationSelected(av.getConservationSelected()); view.setPidSelected(av.getAbovePIDThreshold()); + view.setCharHeight(av.getCharHeight()); + view.setCharWidth(av.getCharWidth()); final Font font = av.getFont(); view.setFontName(font.getName()); view.setFontSize(font.getSize()); @@ -2270,6 +2304,45 @@ public class Jalview2XML line.setColour(annotation.getThreshold().colour.getRGB()); an.setThresholdLine(line); } + if (annotation.graph == AlignmentAnnotation.CONTACT_MAP) + { + if (annotation.sequenceRef.getContactMaps() != null) + { + ContactMatrixI cm = annotation.sequenceRef + .getContactMatrixFor(annotation); + if (cm != null) + { + MatrixType xmlmat = new MatrixType(); + xmlmat.setType(cm.getType()); + xmlmat.setRows(BigInteger.valueOf(cm.getWidth())); + xmlmat.setCols(BigInteger.valueOf(cm.getHeight())); + // consider using an opaque to/from -> allow instance to control + // its representation ? + xmlmat.setElements(ContactMatrix.contactToFloatString(cm)); + if (cm.hasGroups()) + { + for (BitSet gp : cm.getGroups()) + { + BigInteger val = new BigInteger(gp.toByteArray()); + xmlmat.getGroups().add(val.toString()); + } + } + if (cm.hasTree()) + { + // provenance object for tree ? + xmlmat.getNewick().add(cm.getNewick()); + xmlmat.setTreeMethod(cm.getTreeMethod()); + } + if (cm.hasCutHeight()) + { + xmlmat.setCutHeight(cm.getCutHeight()); + } + + // set/get properties + an.getContactmatrix().add(xmlmat); + } + } + } } else { @@ -2300,10 +2373,9 @@ public class Jalview2XML { for (String pr : annotation.getProperties()) { - jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property(); + jalview.xml.binding.jalview.Property prop = new jalview.xml.binding.jalview.Property(); prop.setName(pr); prop.setValue(annotation.getProperty(pr)); - // an.addProperty(prop); an.getProperty().add(prop); } } @@ -3878,11 +3950,78 @@ public class Jalview2XML jaa.setCalcId(annotation.getCalcId()); if (annotation.getProperty().size() > 0) { - for (Annotation.Property prop : annotation.getProperty()) + for (jalview.xml.binding.jalview.Property prop : annotation + .getProperty()) { jaa.setProperty(prop.getName(), prop.getValue()); } } + if (jaa.graph == AlignmentAnnotation.CONTACT_MAP) + { + if (annotation.getContactmatrix() != null + && annotation.getContactmatrix().size() > 0) + { + for (MatrixType xmlmat : annotation.getContactmatrix()) + { + if (PAEContactMatrix.PAEMATRIX.equals(xmlmat.getType())) + { + if (!xmlmat.getRows().equals(xmlmat.getCols())) + { + Console.error("Can't handle non square PAE Matrices"); + } + else + { + float[][] elements = ContactMatrix + .fromFloatStringToContacts(xmlmat.getElements(), + xmlmat.getCols().intValue(), + xmlmat.getRows().intValue()); + + PAEContactMatrix newpae = new PAEContactMatrix( + jaa.sequenceRef, elements); + List newgroups = new ArrayList(); + if (xmlmat.getGroups().size() > 0) + { + for (String sgroup : xmlmat.getGroups()) + { + try + { + BigInteger group = new BigInteger(sgroup); + newgroups.add(BitSet.valueOf(group.toByteArray())); + } catch (NumberFormatException nfe) + { + Console.error( + "Problem parsing groups for a contact matrix (\"" + + sgroup + "\"", + nfe); + } + } + } + String nwk = xmlmat.getNewick().size() > 0 + ? xmlmat.getNewick().get(0) + : null; + if (xmlmat.getNewick().size() > 1) + { + Console.log.info( + "Ignoring additional clusterings for contact matrix"); + } + + String treeMethod = xmlmat.getTreeMethod(); + double thresh = xmlmat.getCutHeight() != null + ? xmlmat.getCutHeight() + : 0; + newpae.restoreGroups(newgroups, treeMethod, nwk, thresh); + jaa.sequenceRef.addContactListFor(jaa, newpae); + } + } + else + { + Console.error("Ignoring CONTACT_MAP annotation with type " + + xmlmat.getType()); + } + } + } + } + if (jaa.autoCalculated) { autoAlan.add(new JvAnnotRow(i, jaa)); @@ -4093,7 +4232,7 @@ public class Jalview2XML } /* - * Load any trees, PDB structures and viewers + * Load any trees, PDB structures and viewers, Overview * * Not done if flag is false (when this method is used for New View) */ @@ -4103,12 +4242,49 @@ public class Jalview2XML loadPCAViewers(jalviewModel, ap); loadPDBStructures(jprovider, jseqs, af, ap); loadRnaViewers(jprovider, jseqs, ap); + loadOverview(view, jalviewModel.getVersion(), af); } // and finally return. return af; } /** + * Load Overview window, restoring colours, 'show hidden regions' flag, title + * and geometry as saved + * + * @param view + * @param af + */ + protected void loadOverview(Viewport view, String version, AlignFrame af) + { + if (!isVersionStringLaterThan("2.11.3", version) + && view.getOverview() == null) + { + return; + } + /* + * first close any Overview that was opened automatically + * (if so configured in Preferences) so that the view is + * restored in the same state as saved + */ + af.alignPanel.closeOverviewPanel(); + + Overview overview = view.getOverview(); + if (overview != null) + { + OverviewPanel overviewPanel = af + .openOverviewPanel(overview.isShowHidden()); + overviewPanel.setTitle(overview.getTitle()); + overviewPanel.setFrameBounds(overview.getXpos(), overview.getYpos(), + overview.getWidth(), overview.getHeight()); + Color gap = new Color(overview.getGapColour()); + Color residue = new Color(overview.getResidueColour()); + Color hidden = new Color(overview.getHiddenColour()); + overviewPanel.getCanvas().setColours(gap, residue, hidden); + } + } + + /** * Instantiate and link any saved RNA (Varna) viewers. The state of the Varna * panel is restored from separate jar entries, two (gapped and trimmed) per * sequence and secondary structure. @@ -4227,10 +4403,28 @@ public class Jalview2XML TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId()); if (tp == null) { - tp = af.showNewickTree(new NewickFile(tree.getNewick()), - tree.getTitle(), safeInt(tree.getWidth()), - safeInt(tree.getHeight()), safeInt(tree.getXpos()), - safeInt(tree.getYpos())); + if (tree.isColumnWise()) + { + AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds + .get(tree.getColumnReference()); + if (aa == null) + { + Console.warn( + "Null alignment annotation when restoring columnwise tree"); + } + tp = af.showColumnWiseTree(new NewickFile(tree.getNewick()), aa, + tree.getTitle(), safeInt(tree.getWidth()), + safeInt(tree.getHeight()), safeInt(tree.getXpos()), + safeInt(tree.getYpos())); + + } + else + { + 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 ? @@ -4625,7 +4819,7 @@ public class Jalview2XML * - minimum version we are comparing against * @param version * - version of data being processsed - * @return + * @return true if version is equal to or later than supported */ public static boolean isVersionStringLaterThan(String supported, String version) @@ -4770,9 +4964,15 @@ public class Jalview2XML 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); + viewport.setFont( + new Font(view.getFontName(), safeInt(view.getFontStyle()), + safeInt(view.getFontSize())), + (view.getCharWidth() != null) ? false : true); + if (view.getCharWidth() != null) + { + viewport.setCharWidth(view.getCharWidth()); + viewport.setCharHeight(view.getCharHeight()); + } ViewStyleI vs = viewport.getViewStyle(); vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna()); viewport.setViewStyle(vs); @@ -5031,6 +5231,7 @@ public class Jalview2XML { splitFrameCandidates.put(view, af); } + return af; } @@ -5094,7 +5295,10 @@ public class Jalview2XML + annotationId); return null; } - if (matchedAnnotation.getThreshold() == null) + // belt-and-braces create a threshold line if the + // colourscheme needs one but the matchedAnnotation doesn't have one + if (safeInt(viewAnnColour.getAboveThreshold()) != 0 + && matchedAnnotation.getThreshold() == null) { matchedAnnotation.setThreshold( new GraphLine(safeFloat(viewAnnColour.getThreshold()), @@ -6602,13 +6806,24 @@ public class Jalview2XML return true; AlignFrame[] frames = Desktop.getAlignFrames(); - for (int i = 0; i < frames.length; i++) + if (frames != null) { - if (frames[i] == null) - continue; - if (!frames[i].getViewport().savedUpToDate()) - return false; // at least one alignment is not individually saved + for (int i = 0; i < frames.length; i++) + { + if (frames[i] == null) + continue; + if (!frames[i].getViewport().savedUpToDate()) + return false; // at least one alignment is not individually saved + } } return true; } + + // used for debugging and tests + private static int debugDelaySave = 20; + + public static void setDebugDelaySave(int n) + { + debugDelaySave = n; + } }