X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=bc2046e8835684a2663d68492df0bfd75091ea0b;hb=c24ec44edbedba55005373c43bf712c047b56faa;hp=2b1b68725bad745622df6dd1794fe1edaa27c09b;hpb=335e6b12c126bcb6825cd3f66422677db7cd91c7;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 2b1b687..bc2046e 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; @@ -94,6 +96,7 @@ import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; import jalview.datamodel.GeneLocus; import jalview.datamodel.GraphLine; +import jalview.datamodel.GroupSet; import jalview.datamodel.PDBEntry; import jalview.datamodel.Point; import jalview.datamodel.RnaViewerModel; @@ -150,6 +153,7 @@ import jalview.viewmodel.ViewportRanges; import jalview.viewmodel.seqfeatures.FeatureRendererModel; import jalview.viewmodel.seqfeatures.FeatureRendererSettings; import jalview.viewmodel.seqfeatures.FeaturesDisplayed; +import jalview.ws.datamodel.MappableContactMatrixI; import jalview.ws.datamodel.alphafold.PAEContactMatrix; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.dm.AAConSettings; @@ -192,6 +196,7 @@ 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; import jalview.xml.binding.jalview.MapListType.MapListFrom; import jalview.xml.binding.jalview.MapListType.MapListTo; import jalview.xml.binding.jalview.Mapping; @@ -515,7 +520,7 @@ public class Jalview2XML } } catch (Exception x) { - System.err.println( + jalview.bin.Console.errPrintln( "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence " + ref.getSref()); x.printStackTrace(); @@ -529,29 +534,29 @@ public class Jalview2XML } if (unresolved > 0) { - System.err.println("Jalview Project Import: There were " + unresolved + jalview.bin.Console.errPrintln("Jalview Project Import: There were " + unresolved + " forward references left unresolved on the stack."); } if (failedtoresolve > 0) { - System.err.println("SERIOUS! " + failedtoresolve + jalview.bin.Console.errPrintln("SERIOUS! " + failedtoresolve + " resolvable forward references failed to resolve."); } if (incompleteSeqs != null && incompleteSeqs.size() > 0) { - System.err.println( + jalview.bin.Console.errPrintln( "Jalview Project Import: There are " + incompleteSeqs.size() + " sequences which may have incomplete metadata."); if (incompleteSeqs.size() < 10) { for (SequenceI s : incompleteSeqs.values()) { - System.err.println(s.toString()); + jalview.bin.Console.errPrintln(s.toString()); } } else { - System.err.println( + jalview.bin.Console.errPrintln( "Too many to report. Skipping output of incomplete sequences."); } } @@ -931,7 +936,7 @@ public class Jalview2XML object.setCreationDate(now); } catch (DatatypeConfigurationException e) { - System.err.println("error writing date: " + e.toString()); + jalview.bin.Console.errPrintln("error writing date: " + e.toString()); } object.setVersion(Cache.getDefault("VERSION", "Development Build")); @@ -998,14 +1003,14 @@ public class Jalview2XML // HAPPEN! (PF00072.15.stk does this) // JBPNote: Uncomment to debug writing out of files that do not read // back in due to ArrayOutOfBoundExceptions. - // System.err.println("vamsasSeq backref: "+id+""); - // System.err.println(jds.getName()+" + // jalview.bin.Console.errPrintln("vamsasSeq backref: "+id+""); + // jalview.bin.Console.errPrintln(jds.getName()+" // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString()); - // System.err.println("Hashcode: "+seqHash(jds)); + // jalview.bin.Console.errPrintln("Hashcode: "+seqHash(jds)); // SequenceI rsq = (SequenceI) seqRefIds.get(id + ""); - // System.err.println(rsq.getName()+" + // jalview.bin.Console.errPrintln(rsq.getName()+" // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString()); - // System.err.println("Hashcode: "+seqHash(rsq)); + // jalview.bin.Console.errPrintln("Hashcode: "+seqHash(rsq)); } else { @@ -1323,6 +1328,13 @@ 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); } @@ -1514,7 +1526,7 @@ public class Jalview2XML 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(), @@ -1555,6 +1567,8 @@ 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()); @@ -1749,7 +1763,7 @@ public class Jalview2XML try { fileName = fileName.replace('\\', '/'); - System.out.println("Writing jar entry " + fileName); + jalview.bin.Console.outPrintln("Writing jar entry " + fileName); JarEntry entry = new JarEntry(fileName); jout.putNextEntry(entry); PrintWriter pout = new PrintWriter( @@ -1770,7 +1784,7 @@ public class Jalview2XML } catch (Exception ex) { // TODO: raise error in GUI if marshalling failed. - System.err.println("Error writing Jalview project"); + jalview.bin.Console.errPrintln("Error writing Jalview project"); ex.printStackTrace(); } } @@ -2084,7 +2098,7 @@ public class Jalview2XML File file = new File(infilePath); if (file.exists() && jout != null) { - System.out.println( + jalview.bin.Console.outPrintln( "Writing jar entry " + jarEntryName + " (" + msg + ")"); jout.putNextEntry(new JarEntry(jarEntryName)); copyAll(is, jout); @@ -2293,18 +2307,71 @@ public class Jalview2XML line.setColour(annotation.getThreshold().colour.getRGB()); an.setThresholdLine(line); } - if (annotation.graph==AlignmentAnnotation.CONTACT_MAP) + if (annotation.graph == AlignmentAnnotation.CONTACT_MAP) { - if (annotation.sequenceRef.getContactMaps()!=null) + if (annotation.sequenceRef.getContactMaps() != null) { - ContactMatrixI cm = annotation.sequenceRef.getContactMatrixFor(annotation); - if (cm!=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())); - xmlmat.setValue(ContactMatrix.contactToFloatString(cm)); + // 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()) + { + xmlmat.getGroups().add(stringifyBitset(gp)); + } + } + 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 + if (cm instanceof MappableContactMatrixI) + { + jalview.util.MapList mlst = ((MappableContactMatrixI) cm) + .getMapFor(annotation.sequenceRef); + if (mlst != null) + { + MapListType mp = new MapListType(); + List r = mlst.getFromRanges(); + for (int[] range : r) + { + MapListFrom mfrom = new MapListFrom(); + mfrom.setStart(range[0]); + mfrom.setEnd(range[1]); + // mp.addMapListFrom(mfrom); + mp.getMapListFrom().add(mfrom); + } + r = mlst.getToRanges(); + for (int[] range : r) + { + MapListTo mto = new MapListTo(); + mto.setStart(range[0]); + mto.setEnd(range[1]); + // mp.addMapListTo(mto); + mp.getMapListTo().add(mto); + } + mp.setMapFromUnit( + BigInteger.valueOf(mlst.getFromRatio())); + mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio())); + xmlmat.setMapping(mp); + } + } + // and add to model an.getContactmatrix().add(xmlmat); } } @@ -2339,10 +2406,9 @@ 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); } } @@ -2413,6 +2479,43 @@ public class Jalview2XML } + private String stringifyBitset(BitSet gp) + { + StringBuilder sb = new StringBuilder(); + for (long val : gp.toLongArray()) + { + if (sb.length() > 0) + { + sb.append(","); + } + sb.append(val); + } + return sb.toString(); + } + + private BitSet deStringifyBitset(String stringified) + { + if ("".equals(stringified) || stringified == null) + { + return new BitSet(); + } + String[] longvals = stringified.split(","); + long[] newlongvals = new long[longvals.length]; + for (int lv = 0; lv < longvals.length; lv++) + { + try + { + newlongvals[lv] = Long.valueOf(longvals[lv]); + } catch (Exception x) + { + errorMessage += "Couldn't destringify bitset from: '" + stringified + + "'"; + newlongvals[lv] = 0; + } + } + return BitSet.valueOf(newlongvals); + + } private CalcIdParam createCalcIdParam(String calcId, AlignViewport av) { AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId); @@ -2856,7 +2959,7 @@ public class Jalview2XML }); } catch (Exception x) { - System.err.println("Error loading alignment: " + x.getMessage()); + jalview.bin.Console.errPrintln("Error loading alignment: " + x.getMessage()); } } return af; @@ -2895,19 +2998,19 @@ public class Jalview2XML { if (bytes != null) { - // System.out.println("Jalview2XML: opening byte jarInputStream for + // jalview.bin.Console.outPrintln("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 " + // jalview.bin.Console.outPrintln("Jalview2XML: opening url jarInputStream for " // + _url); return new JarInputStream(_url.openStream()); } else { - // System.out.println("Jalview2XML: opening file jarInputStream for + // jalview.bin.Console.outPrintln("Jalview2XML: opening file jarInputStream for // " + file); return new JarInputStream(new FileInputStream(file)); } @@ -3014,11 +3117,11 @@ public class Jalview2XML { ex.printStackTrace(); errorMessage = "Couldn't locate Jalview XML file : " + file; - System.err.println( + jalview.bin.Console.errPrintln( "Exception whilst loading jalview XML file : " + ex + "\n"); } catch (Exception ex) { - System.err.println("Parsing as Jalview Version 2 file failed."); + jalview.bin.Console.errPrintln("Parsing as Jalview Version 2 file failed."); ex.printStackTrace(System.err); if (attemptversion1parse) { @@ -3030,18 +3133,18 @@ public class Jalview2XML } if (af != null) { - System.out.println("Successfully loaded archive file"); + jalview.bin.Console.outPrintln("Successfully loaded archive file"); return af; } ex.printStackTrace(); - System.err.println( + jalview.bin.Console.errPrintln( "Exception whilst loading jalview XML file : " + ex + "\n"); } catch (OutOfMemoryError e) { // Don't use the OOM Window here errorMessage = "Out of memory loading jalview XML file"; - System.err.println("Out of memory whilst loading jalview XML file"); + jalview.bin.Console.errPrintln("Out of memory whilst loading jalview XML file"); e.printStackTrace(); } @@ -3145,7 +3248,7 @@ public class Jalview2XML Desktop.addInternalFrame(af, view.getTitle(), safeInt(view.getWidth()), safeInt(view.getHeight())); af.setMenusForViewport(); - System.err.println("Failed to restore view " + view.getTitle() + jalview.bin.Console.errPrintln("Failed to restore view " + view.getTitle() + " to split frame"); } } @@ -3224,7 +3327,7 @@ public class Jalview2XML } else { - System.err.println("Problem loading Jalview file: " + errorMessage); + jalview.bin.Console.errPrintln("Problem loading Jalview file: " + errorMessage); } } errorMessage = null; @@ -3422,7 +3525,7 @@ public class Jalview2XML if (tmpSeq.getStart() != jseq.getStart() || tmpSeq.getEnd() != jseq.getEnd()) { - System.err.println(String.format( + jalview.bin.Console.errPrintln(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())); @@ -3917,7 +4020,8 @@ 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()); } @@ -3938,12 +4042,60 @@ public class Jalview2XML else { float[][] elements = ContactMatrix - .fromFloatStringToContacts(xmlmat.getValue(), + .fromFloatStringToContacts(xmlmat.getElements(), xmlmat.getCols().intValue(), xmlmat.getRows().intValue()); - + jalview.util.MapList mapping = null; + if (xmlmat.getMapping() != null) + { + MapListType m = xmlmat.getMapping(); + // Mapping m = dr.getMapping(); + int fr[] = new int[m.getMapListFrom().size() * 2]; + Iterator from = m.getMapListFrom() + .iterator();// enumerateMapListFrom(); + for (int _i = 0; from.hasNext(); _i += 2) + { + MapListFrom mf = from.next(); + fr[_i] = mf.getStart(); + fr[_i + 1] = mf.getEnd(); + } + int fto[] = new int[m.getMapListTo().size() * 2]; + Iterator to = m.getMapListTo().iterator();// enumerateMapListTo(); + for (int _i = 0; to.hasNext(); _i += 2) + { + MapListTo mf = to.next(); + fto[_i] = mf.getStart(); + fto[_i + 1] = mf.getEnd(); + } + + mapping = new jalview.util.MapList(fr, fto, + m.getMapFromUnit().intValue(), + m.getMapToUnit().intValue()); + } + List newgroups = new ArrayList(); + if (xmlmat.getGroups().size() > 0) + { + for (String sgroup : xmlmat.getGroups()) + { + newgroups.add(deStringifyBitset(sgroup)); + } + } + 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; + GroupSet grpset = new GroupSet(); + grpset.restoreGroups(newgroups, treeMethod, nwk, thresh); PAEContactMatrix newpae = new PAEContactMatrix( - jaa.sequenceRef, elements); + jaa.sequenceRef, mapping, elements, grpset); jaa.sequenceRef.addContactListFor(jaa, newpae); } } @@ -4104,7 +4256,7 @@ public class Jalview2XML // XML. // and then recover its containing af to allow the settings to be applied. // TODO: fix for vamsas demo - System.err.println( + jalview.bin.Console.errPrintln( "About to recover a viewport for existing alignment: Sequence set ID is " + uniqueSeqSetId); Object seqsetobj = retrieveExistingObj(uniqueSeqSetId); @@ -4113,13 +4265,13 @@ public class Jalview2XML if (seqsetobj instanceof String) { uniqueSeqSetId = (String) seqsetobj; - System.err.println( + jalview.bin.Console.errPrintln( "Recovered extant sequence set ID mapping for ID : New Sequence set ID is " + uniqueSeqSetId); } else { - System.err.println( + jalview.bin.Console.errPrintln( "Warning : Collision between sequence set ID string and existing jalview object mapping."); } @@ -4191,8 +4343,8 @@ public class Jalview2XML */ protected void loadOverview(Viewport view, String version, AlignFrame af) { - if (!isVersionStringLaterThan("2.11.3", - version) && view.getOverview()==null) + if (!isVersionStringLaterThan("2.11.3", version) + && view.getOverview() == null) { return; } @@ -4337,10 +4489,28 @@ 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 ? @@ -4541,7 +4711,7 @@ public class Jalview2XML createOrLinkStructureViewer(entry, af, ap, jprovider); } catch (Exception e) { - System.err.println( + jalview.bin.Console.errPrintln( "Error loading structure viewer: " + e.getMessage()); // failed - try the next one } @@ -4745,7 +4915,7 @@ public class Jalview2XML || version.equalsIgnoreCase("Test") || version.equalsIgnoreCase("AUTOMATED BUILD")) { - System.err.println("Assuming project file with " + jalview.bin.Console.errPrintln("Assuming project file with " + (version == null ? "null" : version) + " is compatible with Jalview version " + supported); return true; @@ -4792,7 +4962,7 @@ public class Jalview2XML // // @Override // protected void processKeyEvent(java.awt.event.KeyEvent e) { - // System.out.println("Jalview2XML AF " + e); + // jalview.bin.Console.outPrintln("Jalview2XML AF " + e); // super.processKeyEvent(e); // // } @@ -4880,9 +5050,15 @@ 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); @@ -5201,11 +5377,11 @@ public class Jalview2XML } if (matchedAnnotation == null) { - System.err.println("Failed to match annotation colour scheme for " + jalview.bin.Console.errPrintln("Failed to match annotation colour scheme for " + annotationId); return null; } - // belt-and-braces create a threshold line if the + // 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) @@ -5660,7 +5836,7 @@ public class Jalview2XML } // TODO: merges will never happen if we 'know' we have the real dataset // sequence - this should be detected when id==dssid - System.err.println( + jalview.bin.Console.errPrintln( "DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // (" // + (pre ? "prepended" : "") + " " // + (post ? "appended" : "")); @@ -5853,7 +6029,7 @@ public class Jalview2XML } else { - System.err.println( + jalview.bin.Console.errPrintln( "Warning - making up dataset sequence id for DbRef sequence map reference"); sqid = ((Object) ms).toString(); // make up a new hascode for // undefined dataset sequence hash @@ -6534,7 +6710,7 @@ public class Jalview2XML } catch (IllegalStateException e) { // mixing AND and OR conditions perhaps - System.err.println( + jalview.bin.Console.errPrintln( String.format("Error reading filter conditions for '%s': %s", featureType, e.getMessage())); // return as much as was parsed up to the error @@ -6615,7 +6791,7 @@ public class Jalview2XML } else { - System.err.println("Malformed compound filter condition"); + jalview.bin.Console.errPrintln("Malformed compound filter condition"); } } }