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.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;
}
} 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.");
}
}
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)
{
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(),
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());
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);
});
} 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));
}
{
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;
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()));
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);
}
}
// 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.");
}
*/
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 = annotationIds
+ .get(tree.getColumnReference());
if (aa == null)
{
Console.warn(
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);
//
// }
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());
}
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
+ // 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)
}
// 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");
}
}
}
git://source.jalview.org / jalview.git / blobdiff