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.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;
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;
Map<String, SequenceI> incompleteSeqs = null;
- List<SeqFref> frefedSequence = null;
+ List<forwardRef> frefedSequence = null;
boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
* entry names
*/
private Map<RnaModel, String> rnaSessions = new HashMap<>();
+
+ /**
+ * map from contact matrices to their XML ids
+ */
+ private Map<ContactMatrixI,String> contactMatrices = new HashMap<>();
+ private Map<String, ContactMatrixI> contactMatrixRefs = new HashMap<>();
+ private List<jalview.xml.binding.jalview.MatrixType> xmlMatrices= new ArrayList<>();
/**
* A helper method for safely using the value of an optional attribute that
}
/**
- * base class for resolving forward references to sequences by their ID
+ * base class for resolving forward references to an as-yet unmarshalled object referenced by already unmarshalled objects
*
* @author jprocter
*
*/
- abstract class SeqFref
- {
+ abstract class forwardRef {
String sref;
String type;
- public SeqFref(String _sref, String type)
+ public forwardRef(String _sref, String type)
{
sref = _sref;
this.type = type;
return sref;
}
+ public abstract boolean isResolvable();
+ /**
+ * @return true if the forward reference was fully resolved
+ */
+ abstract boolean resolve();
+
+ @Override
+ public String toString()
+ {
+ return type + " reference to " + sref;
+ }
+ }
+ /**
+ * resolve forward references to sequences by their ID
+ * @author jprocter
+ */
+ abstract class SeqFref extends forwardRef
+ {
+ public SeqFref(String _sref, String type)
+ {
+ super(_sref, type);
+ }
public SequenceI getSrefSeq()
{
return seqRefIds.get(sref);
}
return sq;
}
-
- /**
- * @return true if the forward reference was fully resolved
- */
- abstract boolean resolve();
-
- @Override
- public String toString()
- {
- return type + " reference to " + sref;
- }
}
/**
};
return fref;
}
+
+ public forwardRef newMatrixFref(final String matRef,
+ final jalview.util.MapList mapping, final AlignmentAnnotation jaa)
+ {
+ forwardRef fref = new forwardRef(matRef,
+ "Matrix Reference for sequence and annotation")
+ {
+
+ @Override
+ boolean resolve()
+ {
+ ContactMatrixI cm = contactMatrixRefs.get(matRef);
+ PAEContactMatrix newpae = new PAEContactMatrix(jaa.sequenceRef,
+ mapping, cm);
+
+ jaa.sequenceRef.addContactListFor(jaa, newpae);
+ return true;
+ }
+
+ @Override
+ public boolean isResolvable()
+ {
+ return (contactMatrixRefs.get(matRef) != null);
+ }
+ };
+ return fref;
+ }
public void resolveFrefedSequences()
{
- Iterator<SeqFref> nextFref = frefedSequence.iterator();
+ Iterator<forwardRef> nextFref = frefedSequence.iterator();
int toresolve = frefedSequence.size();
int unresolved = 0, failedtoresolve = 0;
while (nextFref.hasNext())
{
- SeqFref ref = nextFref.next();
+ forwardRef ref = nextFref.next();
if (ref.isResolvable())
{
try
}
} catch (Exception x)
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+ ref.getSref());
x.printStackTrace();
}
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.");
}
}
*/
public void saveState(JarOutputStream jout)
{
- AlignFrame[] frames = Desktop.getAlignFrames();
+ AlignFrame[] frames = Desktop.getDesktopAlignFrames();
setStateSavedUpToDate(true);
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"));
// 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
{
* 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<JalviewStructureDisplayI> 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)
{
// jms.addViewport(view);
object.getViewport().add(view);
}
+
+
+ if (storeDS)
+ {
+ // store matrices referenced by any views or annotation in this dataset
+ if (xmlMatrices!=null && xmlMatrices.size()>0)
+ {
+ Console.debug("Adding "+xmlMatrices.size()+" matrices to dataset.");
+ vamsasSet.getMatrix().addAll(xmlMatrices);
+ xmlMatrices.clear();
+ }
+ }
+
+
// object.setJalviewModelSequence(jms);
// object.getVamsasModel().addSequenceSet(vamsasSet);
object.getVamsasModel().getSequenceSet().add(vamsasSet);
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(
} 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();
}
}
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);
*/
protected String saveStructureViewer(AlignmentPanel ap, SequenceI jds,
Pdbids pdb, PDBEntry entry, List<String> viewIds,
- String matchedFile, StructureViewerBase viewFrame)
+ String matchedFile, JalviewStructureDisplayI viewFrame)
{
final AAStructureBindingModel bindingModel = viewFrame.getBinding();
{
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());
.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 ?
- 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<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);
+ storeMatrixFor(vamsasSet, an,annotation, cm);
}
}
}
}
+ private void storeMatrixFor(SequenceSet root, Annotation an, AlignmentAnnotation annotation, ContactMatrixI cm)
+ {
+ String cmId = contactMatrices.get(cm);
+ MatrixType xmlmat=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.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(cmId = "m"+contactMatrices.size()+System.currentTimeMillis());
+ Console.trace("Matrix data stored :"+cmId);
+ contactMatrices.put(cm, cmId);
+ contactMatrixRefs.put(cmId, cm);
+ xmlMatrices.add(xmlmat);
+ } else {
+ Console.trace("Existing Matrix stored :"+cmId);
+ }
+
+ // 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)
+ .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()));
+ xmlmatmapping.setMapping(mp);
+ }
+ }
+ // and add to model
+ an.getContactmatrix().add(xmlmatmapping);
+ }
+
private String stringifyBitset(BitSet gp)
{
StringBuilder sb = new StringBuilder();
return BitSet.valueOf(newlongvals);
}
+
private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
{
AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
});
} catch (Exception x)
{
- System.err.println("Error loading alignment: " + x.getMessage());
+ jalview.bin.Console
+ .errPrintln("Error loading alignment: " + x.getMessage());
}
}
return af;
{
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));
}
initSeqRefs();
}
AlignFrame af = null, _af = null;
+ List<AlignFrame> toRepaint=new ArrayList<AlignFrame>();
IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
final String file = jprovider.getFilename();
if (_af != null && object.getViewport().size() > 0)
// getJalviewModelSequence().getViewportCount() > 0)
{
+ toRepaint.add(_af);
if (af == null)
{
// store a reference to the first view
} while (jarentry != null);
jin.close();
resolveFrefedSequences();
+ for (AlignFrame alignFrame:toRepaint)
+ {
+ alignFrame.repaint();
+ }
} catch (IOException ex)
{
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)
{
}
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();
}
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");
}
}
}
else
{
- System.err.println("Problem loading Jalview file: " + errorMessage);
+ jalview.bin.Console.errPrintln(
+ "Problem loading Jalview file: " + errorMessage);
}
}
errorMessage = null;
}
// ////////////////////////////////
+ // LOAD MATRICES (IF ANY)
+
+ if (vamsasSet.getMatrix()!=null && vamsasSet.getMatrix().size()>0)
+ {
+ importMatrixData(vamsasSet.getMatrix());
+ }
+
+ // ////////////////////////////////
// LOAD SEQUENCES
List<SequenceI> hiddenSeqs = null;
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()));
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);
+ }
}
}
// 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);
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.");
}
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)
+ {
+ // 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());
+ }
+
+ // locate matrix data in project XML and import
+ ContactMatrixI cm = contactMatrixRefs.get(xmlmatmapping.getMatrix());
+ if (cm == null)
+ {
+ frefedSequence
+ .add(newMatrixFref(xmlmatmapping.getMatrix(), mapping, jaa));
+ }
+ else
+ {
+ // create the PAEMatrix now
+ 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
{
if (tree.isColumnWise())
{
- AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds
+ AlignmentAnnotation aa = annotationIds
.get(tree.getColumnReference());
if (aa == null)
{
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
}
|| 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;
//
// @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);
//
// }
}
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
}
// 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" : ""));
}
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
} 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
}
else
{
- System.err.println("Malformed compound filter condition");
+ jalview.bin.Console
+ .errPrintln("Malformed compound filter condition");
}
}
}
if (stateSavedUpToDate()) // nothing happened since last project save
return true;
- AlignFrame[] frames = Desktop.getAlignFrames();
+ AlignFrame[] frames = Desktop.getDesktopAlignFrames();
if (frames != null)
{
for (int i = 0; i < frames.length; i++)
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import jalview.analysis.AlignmentUtils;
import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Mapping;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence;
import jalview.datamodel.Sequence.DBModList;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceFeature;
@Test(groups = { "Functional" })
public void gatherViewsHere() throws Exception
{
- int origCount = Desktop.getAlignFrames() == null ? 0
- : Desktop.getAlignFrames().length;
+ int origCount = Desktop.getDesktopAlignFrames() == null ? 0
+ : Desktop.getDesktopAlignFrames().length;
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
assertNotNull(af, "Didn't read in the example file correctly.");
- assertTrue(Desktop.getAlignFrames().length == 1 + origCount,
+ assertTrue(Desktop.getDesktopAlignFrames().length == 1 + origCount,
"Didn't gather the views in the example file.");
}
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
"examples/exampleFile_2_7.jar", DataSourceType.FILE);
- Assert.assertEquals(Desktop.getAlignFrames().length, 1);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 1);
String afid = af.getViewport().getSequenceSetId();
// check FileLoader returned a reference to the one alignFrame that is
Desktop.explodeViews(af);
- int oldviews = Desktop.getAlignFrames().length;
- Assert.assertEquals(Desktop.getAlignFrames().length,
+ int oldviews = Desktop.getDesktopAlignFrames().length;
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length,
Desktop.getAlignmentPanels(afid).length);
File tfile = File.createTempFile("testStoreAndRecoverExpanded", ".jvp");
try
Assert.fail("Didn't save the expanded view state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
+ if (Desktop.getDesktopAlignFrames() != null)
{
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
}
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
DataSourceType.FILE);
Assert.assertNotNull(af);
- Assert.assertEquals(Desktop.getAlignFrames().length,
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length,
Desktop.getAlignmentPanels(
af.getViewport().getSequenceSetId()).length);
Assert.assertEquals(Desktop
Assert.fail("Didn't save the expanded view state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
+ if (Desktop.getDesktopAlignFrames() != null)
{
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
}
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
Assert.fail("Didn't save the expanded view state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
+ if (Desktop.getDesktopAlignFrames() != null)
{
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
}
af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
Assert.fail("Didn't save the state", e);
}
Desktop.instance.closeAll_actionPerformed(null);
- if (Desktop.getAlignFrames() != null)
+ if (Desktop.getDesktopAlignFrames() != null)
{
- Assert.assertEquals(Desktop.getAlignFrames().length, 0);
+ Assert.assertEquals(Desktop.getDesktopAlignFrames().length, 0);
}
AlignFrame restoredFrame = new FileLoader().LoadFileWaitTillLoaded(
assertNotNull(af);
AlignmentI ds = null;
- for (AlignFrame alignFrame : Desktop.getAlignFrames())
+ for (AlignFrame alignFrame : Desktop.getDesktopAlignFrames())
{
if (ds == null)
{
}
@Test(groups = { "Functional" })
+ public void testMatrixToFloatsAndBack()
+ {
+ int imax=2000;
+ int i=imax;
+ SequenceI sq = new Sequence("dummy","SEQ");
+ while (sq.getLength()<i)
+ {
+ sq.setSequence(sq.getSequenceAsString()+'Q');
+ }
+ float[][] paevals = new float[i][i];
+ for (i = imax - 1; i >= 0; i--)
+ {
+ for (int j = 0; j <= i; j++)
+ {
+ paevals[i][j] = ((i - j < 2)
+ || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f;
+ paevals[j][i] = -paevals[i][j];
+ }
+ }
+ PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
+ String content = ContactMatrix.contactToFloatString(dummyMat);
+ Assert.assertTrue(content.contains("\t1.")); // at least one element must be
+ // 1
+ float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
+ sq.getLength(), sq.getLength());
+ assertEquals(vals[3][4], paevals[3][4]);
+ assertEquals(vals[4][3], paevals[4][3]);
+
+ // test recovery
+ for (i=0;i<imax;i++)
+ {
+ for (int j=0;j<imax;j++)
+ {
+ assertEquals(vals[i][j],paevals[i][j]);
+ }
+ }
+ }
+ @Test(groups = { "Functional" })
public void testPAEsaveRestore() throws Exception
{
Desktop.instance.closeAll_actionPerformed(null);
Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
+ // verify no duplicate PAE matrix data when new view created and saved
+
+ // add reference annotations to view first, then copy
+ AlignmentUtils.addReferenceAnnotationTo(newAl, newAl.getSequenceAt(0), newSeq.getAnnotation()[0],null);
+
+ AlignmentViewPanel newview = af.newView("copy of PAE", true);
+
+ // redundant asserts here check all is good with the new view firest...
+ AlignmentI newviewAl = newview.getAlignment();
+ SequenceI newviewSeq = newviewAl.getSequenceAt(0);
+ // check annotation of the expected type exists
+ Assert.assertEquals(newviewSeq.getAnnotation().length, 1);
+ Assert.assertEquals(newviewSeq.getAnnotation()[0].graph, paeCm.graph);
+ // check we have just one contact matrix mapping
+ Assert.assertEquals(newviewSeq.getContactMaps().size(), 1);
+
+ // and can be found for the annotation on the sequence
+ ContactMatrixI newviewMat = newviewSeq
+ .getContactMatrixFor(newviewSeq.getAnnotation()[0]);
+ Assert.assertNotNull(newviewMat);
+
+ Assert.assertTrue(newviewMat == restoredMat);
+
+ // save the two views and restore. Now look at visible annotation to check all views have shared refs.
+
+ tfile = File.createTempFile("testStoreAndRecoverPAEmatrixTwoViews",
+ ".jvp");
+ new Jalview2XML(false).saveState(tfile);
+ Desktop.instance.closeAll_actionPerformed(null);
+
+ af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+ DataSourceType.FILE);
+ newAl = af.getAlignPanels().get(0).getAlignment();
+ AlignmentAnnotation view1aa = newAl.getSequenceAt(0).getAnnotation()[0];
+
+ newviewAl = af.getAlignPanels().get(1).getAlignment();
+ AlignmentAnnotation view2aa = newviewAl.getSequenceAt(0).getAnnotation()[0];
+
+ // annotations are shared across alignment views - so should still have an identical pair of annotations.
+ Assert.assertTrue(view1aa==view2aa);
+ // identical annotations means identical contact matrix mappings
+ Assert.assertEquals(newAl.getDataset().getSequenceAt(0).getContactMaps().size(), 1);
+
+ // TODO Verify when distinct mappable PAEs are created, only one PAE dataset is actually held.
+ // Assert.assertTrue(view1aa!=view2aa);
+ // restoredMat = newAl.getContactMatrixFor(view1aa);
+ // newviewMat = newviewAl.getContactMatrixFor(view2aa);
+ // Assert.assertTrue(restoredMat!=newviewMat);
+
}
}
git://source.jalview.org / jalview.git / commitdiff