X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=af3b2c8e4ba5df144d5452c4c53bc17092895ec1;hb=e75315ad5faf541f6943e9395c81a078369f2f63;hp=913dffe52030868a1beb41543024d8df3072d1fe;hpb=fdde9a078d7bdb46ed9fb7fe115ea83c84a19c81;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 913dffe..af3b2c8 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -26,7 +26,6 @@ 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; @@ -87,6 +86,7 @@ import jalview.api.analysis.SimilarityParamsI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; import jalview.bin.Console; +import jalview.bin.Jalview; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@ -96,6 +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; @@ -152,6 +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; @@ -194,6 +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; @@ -517,7 +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(); @@ -531,29 +534,30 @@ 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."); } } @@ -933,7 +937,7 @@ 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")); @@ -1000,14 +1004,14 @@ 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 { @@ -1136,38 +1140,55 @@ public class Jalview2XML * only view *should* be coped with sensibly. */ // This must have been loaded, is it still visible? - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - String matchedFile = null; - for (int f = frames.length - 1; f > -1; f--) + List viewFrames = new ArrayList<>(); + if (Desktop.desktop != null) { - if (frames[f] instanceof StructureViewerBase) + JInternalFrame[] jifs = Desktop.desktop.getAllFrames(); + if (jifs != null) { - StructureViewerBase viewFrame = (StructureViewerBase) frames[f]; - matchedFile = saveStructureViewer(ap, jds, pdb, entry, - viewIds, matchedFile, viewFrame); - /* - * Only store each structure viewer's state once in the project - * jar. First time through only (storeDS==false) - */ - String viewId = viewFrame.getViewId(); - String viewerType = viewFrame.getViewerType().toString(); - if (!storeDS && !viewIds.contains(viewId)) + for (JInternalFrame jif : jifs) { - viewIds.add(viewId); - File viewerState = viewFrame.saveSession(); - if (viewerState != null) - { - copyFileToJar(jout, viewerState.getPath(), - getViewerJarEntryName(viewId), viewerType); - } - else + if (jif instanceof JalviewStructureDisplayI) { - Console.error( - "Failed to save viewer state for " + viewerType); + viewFrames.add((JalviewStructureDisplayI) jif); } } } } + else if (Jalview.isHeadlessMode() + && Jalview.getInstance().getCommands() != null) + { + viewFrames.addAll( + StructureViewerBase.getAllStructureViewerBases()); + } + + String matchedFile = null; + for (JalviewStructureDisplayI viewFrame : viewFrames) + { + matchedFile = saveStructureViewer(ap, jds, pdb, entry, viewIds, + matchedFile, viewFrame); + /* + * Only store each structure viewer's state once in the project + * jar. First time through only (storeDS==false) + */ + String viewId = viewFrame.getViewId(); + String viewerType = viewFrame.getViewerType().toString(); + if (!storeDS && !viewIds.contains(viewId)) + { + viewIds.add(viewId); + File viewerState = viewFrame.saveSession(); + if (viewerState != null) + { + copyFileToJar(jout, viewerState.getPath(), + getViewerJarEntryName(viewId), viewerType); + } + else + { + Console.error( + "Failed to save viewer state for " + viewerType); + } + } + } if (matchedFile != null || entry.getFile() != null) { @@ -1760,7 +1781,7 @@ 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( @@ -1781,7 +1802,7 @@ 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(); } } @@ -2095,7 +2116,7 @@ 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); @@ -2144,7 +2165,7 @@ public class Jalview2XML */ protected String saveStructureViewer(AlignmentPanel ap, SequenceI jds, Pdbids pdb, PDBEntry entry, List viewIds, - String matchedFile, StructureViewerBase viewFrame) + String matchedFile, JalviewStructureDisplayI viewFrame) { final AAStructureBindingModel bindingModel = viewFrame.getBinding(); @@ -2189,7 +2210,7 @@ public class Jalview2XML { StructureState state = new StructureState(); state.setVisible(true); - state.setXpos(viewFrame.getX()); + state.setXpos(viewFrame.getY()); state.setYpos(viewFrame.getY()); state.setWidth(viewFrame.getWidth()); state.setHeight(viewFrame.getHeight()); @@ -2323,8 +2344,7 @@ public class Jalview2XML { for (BitSet gp : cm.getGroups()) { - BigInteger val = new BigInteger(gp.toByteArray()); - xmlmat.getGroups().add(val.toString()); + xmlmat.getGroups().add(stringifyBitset(gp)); } } if (cm.hasTree()) @@ -2337,8 +2357,39 @@ public class Jalview2XML { 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); } } @@ -2446,6 +2497,44 @@ 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); @@ -2889,7 +2978,8 @@ 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; @@ -2928,19 +3018,22 @@ 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)); } @@ -3047,11 +3140,12 @@ 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) { @@ -3063,18 +3157,19 @@ 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(); } @@ -3178,8 +3273,8 @@ 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() - + " to split frame"); + jalview.bin.Console.errPrintln("Failed to restore view " + + view.getTitle() + " to split frame"); } } @@ -3257,7 +3352,8 @@ public class Jalview2XML } else { - System.err.println("Problem loading Jalview file: " + errorMessage); + jalview.bin.Console.errPrintln( + "Problem loading Jalview file: " + errorMessage); } } errorMessage = null; @@ -3455,7 +3551,7 @@ 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())); @@ -3975,25 +4071,39 @@ public class Jalview2XML .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(); + } - PAEContactMatrix newpae = new PAEContactMatrix( - jaa.sequenceRef, elements); + 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()) { - 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); - } + newgroups.add(deStringifyBitset(sgroup)); } } String nwk = xmlmat.getNewick().size() > 0 @@ -4004,12 +4114,14 @@ public class Jalview2XML 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); + GroupSet grpset = new GroupSet(); + grpset.restoreGroups(newgroups, treeMethod, nwk, thresh); + PAEContactMatrix newpae = new PAEContactMatrix( + jaa.sequenceRef, mapping, elements, grpset); jaa.sequenceRef.addContactListFor(jaa, newpae); } } @@ -4170,7 +4282,7 @@ 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); @@ -4179,13 +4291,13 @@ 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."); } @@ -4405,7 +4517,7 @@ public class Jalview2XML { if (tree.isColumnWise()) { - AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds + AlignmentAnnotation aa = annotationIds .get(tree.getColumnReference()); if (aa == null) { @@ -4625,7 +4737,7 @@ 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 } @@ -4829,7 +4941,7 @@ 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; @@ -4876,7 +4988,7 @@ 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); // // } @@ -5291,8 +5403,9 @@ public class Jalview2XML } if (matchedAnnotation == null) { - System.err.println("Failed to match annotation colour scheme for " - + annotationId); + jalview.bin.Console + .errPrintln("Failed to match annotation colour scheme for " + + annotationId); return null; } // belt-and-braces create a threshold line if the @@ -5750,7 +5863,7 @@ 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" : "")); @@ -5943,7 +6056,7 @@ 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 @@ -6624,7 +6737,7 @@ 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 @@ -6705,7 +6818,8 @@ public class Jalview2XML } else { - System.err.println("Malformed compound filter condition"); + jalview.bin.Console + .errPrintln("Malformed compound filter condition"); } } }