import java.awt.Color;
import java.awt.Font;
-import java.awt.FontMetrics;
import java.awt.Rectangle;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
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;
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;
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;
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(),
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()));
- // consider using an opaque to/from -> allow instance to control its representation ?
+ // 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())
+ for (BitSet gp : cm.getGroups())
{
- BigInteger val = new BigInteger(gp.toByteArray());
- xmlmat.getGroups().add(val.toString());
+ xmlmat.getGroups().add(stringifyBitset(gp));
}
}
if (cm.hasTree())
{
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<int[]> 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);
jaa.setCalcId(annotation.getCalcId());
if (annotation.getProperty().size() > 0)
{
- for (jalview.xml.binding.jalview.Property prop : annotation.getProperty())
+ for (jalview.xml.binding.jalview.Property prop : annotation
+ .getProperty())
{
jaa.setProperty(prop.getName(), prop.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<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();
+ }
- PAEContactMatrix newpae = new PAEContactMatrix(
- jaa.sequenceRef, elements);
- List<BitSet> newgroups=new ArrayList<BitSet>();
- if (xmlmat.getGroups().size()>0)
+ 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())
+ 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 ? xmlmat.getNewick().get(0):null;
- if (xmlmat.getNewick().size()>1)
+ 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);
+ 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);
}
}
*/
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;
}
{
if (tree.isColumnWise())
{
- AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds.get(tree
- .getColumnReference());
+ AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds
+ .get(tree.getColumnReference());
if (aa == null)
{
Console.warn(
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())),
- (view.getCharWidth()!=null) ? false : true);
- 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());
+ 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)
git://source.jalview.org / jalview.git / blobdiff