import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactMatrix;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.FloatContactMatrix;
import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
import jalview.datamodel.GroupSet;
+import jalview.datamodel.GroupSetI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import jalview.datamodel.RnaViewerModel;
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.MapOnAMatrixType;
import jalview.xml.binding.jalview.Mapping;
import jalview.xml.binding.jalview.MatrixType;
import jalview.xml.binding.jalview.NoValueColour;
{
String cmId = contactMatrices.get(cm);
MatrixType xmlmat=null;
- if (cmId==null)
+
+ // first create an xml ref for the matrix data, if none exist
+ 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 = 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())
{
- xmlmat.getGroups().add(stringifyBitset(gp));
+ 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));
+ 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(cmId = makeHashCode(cm, null));
+ contactMatrices.put(cm, cmId);
+ contactMatrixRefs.put(cmId, cm);
root.getMatrices().add(xmlmat);
}
- else {
-
- }
- // set/get properties
+
+ // now store mapping
+
+ MapOnAMatrixType xmlmatmapping = new MapOnAMatrixType();
+ xmlmatmapping.setMatrix(cmId);
+
+ // Pretty much all matrices currently managed in this way are
+ // mappableContactMatrixI implementations - but check anyway
if (cm instanceof MappableContactMatrixI)
{
jalview.util.MapList mlst = ((MappableContactMatrixI) cm)
// mp.addMapListTo(mto);
mp.getMapListTo().add(mto);
}
- mp.setMapFromUnit(
- BigInteger.valueOf(mlst.getFromRatio()));
+ mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
- xmlmat.setMapping(mp);
+ xmlmatmapping.setMapping(mp);
}
}
// and add to model
- an.getContactmatrix().add(xmlmat);
+ an.getContactmatrix().add(xmlmatmapping);
}
private String stringifyBitset(BitSet gp)
}
// ////////////////////////////////
+ // LOAD MATRICES (IF ANY)
+
+ if (vamsasSet.getMatrices()!=null && vamsasSet.getMatrices().size()>0)
+ {
+ importMatrixData(vamsasSet.getMatrices());
+ }
+
+ // ////////////////////////////////
// LOAD SEQUENCES
List<SequenceI> hiddenSeqs = null;
if (annotation.getContactmatrix() != null
&& annotation.getContactmatrix().size() > 0)
{
- for (MatrixType xmlmat : annotation.getContactmatrix())
+ for (MapOnAMatrixType 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());
- 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<MapListFrom> 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<MapListTo> 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<BitSet> newgroups = new ArrayList<BitSet>();
- 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, mapping, elements, grpset);
- jaa.sequenceRef.addContactListFor(jaa, newpae);
- }
- }
- else
- {
- Console.error("Ignoring CONTACT_MAP annotation with type "
- + xmlmat.getType());
- }
- }
+ restoreMatrixFor(jaa.sequenceRef, jaa, xmlmat);
+ }
}
}
return af;
}
+ private void importMatrixData(List<MatrixType> xmlmatrices)
+ {
+ for (MatrixType xmlmat:xmlmatrices)
+ {
+ if (!PAEContactMatrix.PAEMATRIX.equals(xmlmat.getType()))
+ {
+ Console.error("Ignoring matrix '"+xmlmat.getId()+"' of type '"+xmlmat.getType());
+ continue;
+ }
+
+ if (!xmlmat.getRows().equals(xmlmat.getCols()))
+ {
+ Console.error("Can't handle non square matrices");
+ continue;
+ }
+
+ float[][] elements = ContactMatrix
+ .fromFloatStringToContacts(xmlmat.getElements(),
+ xmlmat.getCols().intValue(),
+ xmlmat.getRows().intValue());
+
+ List<BitSet> newgroups = new ArrayList<BitSet>();
+ 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);
+
+ FloatContactMatrix newcm = new FloatContactMatrix(elements, grpset);
+ contactMatrixRefs.put(xmlmat.getId(), newcm);
+ Console.trace("Restored base contact matrix "+xmlmat.getId());
+ }
+ }
+
+ private void restoreMatrixFor(SequenceI sequenceRef,
+ AlignmentAnnotation jaa, MapOnAMatrixType xmlmatmapping)
+ {
+ MatrixType xmlmat;
+
+ // locate matrix data in project XML and import
+ ContactMatrixI cm = contactMatrixRefs.get(xmlmatmapping.getMatrix());
+ if (cm == null)
+ {
+ Console.error("Cannot restore mapping to matrix "
+ + xmlmatmapping.getMatrix() + " - not found in project.");
+ }
+
+ // restore mapping data to matrix data
+ jalview.util.MapList mapping = null;
+ if (xmlmatmapping.getMapping() != null)
+ {
+ MapListType m = xmlmatmapping.getMapping();
+ // Mapping m = dr.getMapping();
+ int fr[] = new int[m.getMapListFrom().size() * 2];
+ Iterator<MapListFrom> 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<MapListTo> 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());
+ }
+ PAEContactMatrix newpae = new PAEContactMatrix(jaa.sequenceRef, mapping,
+ cm);
+
+ jaa.sequenceRef.addContactListFor(jaa, newpae);
+
+ return;
+ }
+
/**
* Load Overview window, restoring colours, 'show hidden regions' flag, title
* and geometry as saved
git://source.jalview.org / jalview.git / blobdiff