X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=b9e1f46ccc7e5930db243fafe3b927406c8f20ce;hb=7a48066cfd16ea943eb3dfcc8b2fe353d33ae15a;hp=81424357f88d1fbafb35366d32a425e9de613d0f;hpb=ae447a3691fb85aaf4e27cd6af8a6e0eb3d50530;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 8142435..b9e1f46 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; @@ -278,6 +283,12 @@ public class Jalview2XML * entry names */ private Map rnaSessions = new HashMap<>(); + + /** + * map from contact matrices to their XML ids + */ + private Map contactMatrices = new HashMap<>(); + private Map contactMatrixRefs = new HashMap<>(); /** * A helper method for safely using the value of an optional attribute that @@ -1323,6 +1334,13 @@ 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 +1532,7 @@ 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(), @@ -2295,19 +2313,15 @@ 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)); - an.getContactmatrix().add(xmlmat); + storeMatrixFor(vamsasSet, an,annotation, cm); } } } @@ -2341,10 +2355,9 @@ 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); } } @@ -2415,6 +2428,115 @@ public class Jalview2XML } + private void storeMatrixFor(SequenceSet root, Annotation an, AlignmentAnnotation annotation, ContactMatrixI cm) + { + String cmId = contactMatrices.get(cm); + MatrixType xmlmat=null; + if (cmId==null) + { +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()) + { + 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()); + } + xmlmat.setId(makeHashCode(cm, cm.get)); + root.getMatrices().add(xmlmat); + } + else { + + } + // 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); + } + + 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); @@ -3919,7 +4041,8 @@ 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()); } @@ -3940,12 +4063,60 @@ 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); } } @@ -4193,8 +4364,8 @@ 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; } @@ -4339,10 +4510,28 @@ 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 ? @@ -4882,14 +5071,15 @@ public class Jalview2XML viewport.setIncrement(safeInt(view.getConsThreshold())); viewport.setShowJVSuffix(safeBoolean(view.isShowFullId())); viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds())); - if (view.getCharWidth()!=null) + 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()); } - viewport.setFont(new Font(view.getFontName(), - safeInt(view.getFontStyle()), safeInt(view.getFontSize())), - true); ViewStyleI vs = viewport.getViewStyle(); vs.setScaleProteinAsCdna(view.isScaleProteinAsCdna()); viewport.setViewStyle(vs); @@ -5212,7 +5402,7 @@ public class Jalview2XML + 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)