/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
+ * modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
- *
+ *
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
import org.exolab.castor.xml.*;
-import uk.ac.vamsas.objects.utils.MapList;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
import jalview.schemes.*;
-import jalview.structure.StructureSelectionManager;
import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
+import jalview.ws.jws2.AAConsClient;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.dm.AAConsSettings;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.AutoCalcSetting;
+import jalview.ws.params.WsParamSetI;
/**
* Write out the current jalview desktop state as a Jalview XML stream.
- *
+ *
* Note: the vamsas objects referred to here are primitive versions of the
* VAMSAS project schema elements - they are not the same and most likely never
* will be :)
- *
+ *
* @author $author$
* @version $Revision: 1.134 $
*/
{
/**
* create/return unique hash string for sq
- *
+ *
* @param sq
* @return new or existing unique string for sq
*/
/**
* Writes a jalview project archive to the given Jar output stream.
- *
+ *
* @param jout
*/
public void SaveState(JarOutputStream jout)
/**
* create a JalviewModel from an algnment view and marshall it to a
* JarOutputStream
- *
+ *
* @param ap
* panel to create jalview model for
* @param fileName
}
JSeq jseq;
+ Set<String> calcIdSet=new HashSet<String>();
// SAVE SEQUENCES
String id = "";
if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
{
- jalview.datamodel.SequenceI[] reps = av.getRepresentedSequences(jal.getSequenceAt(i)).getSequencesInOrder(jal);
+ jalview.datamodel.SequenceI[] reps = av.getRepresentedSequences(
+ jal.getSequenceAt(i)).getSequencesInOrder(jal);
for (int h = 0; h < reps.length; h++)
{
for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++)
{
-// if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
- if (jds==jmol.jmb.sequence[peid][smap])
+ // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+ if (jds == jmol.jmb.sequence[peid][smap])
{
StructureState state = new StructureState();
state.setVisible(true);
}
}
}
-
// SAVE ANNOTATIONS
/**
* store forward refs from an annotationRow to any groups
{
annotationIds.put(aa[i].annotationId, aa[i]);
}
-
+
an.setId(aa[i].annotationId);
an.setVisible(aa[i].visible);
an.setDescription(aa[i].description);
-
+
if (aa[i].sequenceRef != null)
{
// TODO later annotation sequenceRef should be the XML ID of the
an.setLabel(aa[i].label);
- if (aa[i] == av.getAlignmentQualityAnnot() || aa[i] == av.getAlignmentConservationAnnotation()
- || aa[i] == av.getAlignmentConsensusAnnotation() || aa[i].autoCalculated)
+ if (aa[i] == av.getAlignmentQualityAnnot()
+ || aa[i] == av.getAlignmentConservationAnnotation()
+ || aa[i] == av.getAlignmentConsensusAnnotation()
+ || aa[i].autoCalculated)
{
// new way of indicating autocalculated annotation -
an.setAutoCalculated(aa[i].autoCalculated);
an.setScore(aa[i].getScore());
}
- if (aa[i].getCalcId()!=null)
+ if (aa[i].getCalcId() != null)
{
+ calcIdSet.add(aa[i].getCalcId());
an.setCalcId(aa[i].getCalcId());
}
{
JGroup[] groups = new JGroup[jal.getGroups().size()];
int i = -1;
- for (jalview.datamodel.SequenceGroup sg:jal.getGroups())
+ for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
{
groups[++i] = new JGroup();
}
// Make sure we save none displayed feature settings
- Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
- .keys();
- while (en.hasMoreElements())
+ Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
+ .keySet().iterator();
+ while (en.hasNext())
{
- String key = en.nextElement().toString();
+ String key = en.next().toString();
if (settingsAdded.contains(key))
{
continue;
fs.addSetting(setting);
settingsAdded.addElement(key);
}
- en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
+ en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+ .keySet().iterator();
Vector groupsAdded = new Vector();
- while (en.hasMoreElements())
+ while (en.hasNext())
{
- String grp = en.nextElement().toString();
+ String grp = en.next().toString();
if (groupsAdded.contains(grp))
{
continue;
}
}
}
+ if (calcIdSet.size() > 0)
+ {
+ for (String calcId : calcIdSet)
+ {
+ if (calcId.trim().length() > 0)
+ {
+ CalcIdParam cidp = createCalcIdParam(calcId, av);
+ // Some calcIds have no parameters.
+ if (cidp != null)
+ {
+ view.addCalcIdParam(cidp);
+ }
+ }
+ }
+ }
jms.addViewport(view);
return object;
}
+ private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
+ {
+ AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
+ if (settings != null)
+ {
+ CalcIdParam vCalcIdParam = new CalcIdParam();
+ vCalcIdParam.setCalcId(calcId);
+ vCalcIdParam.addServiceURL(settings.getServiceURI());
+ // generic URI allowing a third party to resolve another instance of the
+ // service used for this calculation
+ for (String urls : settings.getServiceURLs())
+ {
+ vCalcIdParam.addServiceURL(urls);
+ }
+ vCalcIdParam.setVersion("1.0");
+ if (settings.getPreset() != null)
+ {
+ WsParamSetI setting = settings.getPreset();
+ vCalcIdParam.setName(setting.getName());
+ vCalcIdParam.setDescription(setting.getDescription());
+ }
+ else
+ {
+ vCalcIdParam.setName("");
+ vCalcIdParam.setDescription("Last used parameters");
+ }
+ // need to be able to recover 1) settings 2) user-defined presets or
+ // recreate settings from preset 3) predefined settings provided by
+ // service - or settings that can be transferred (or discarded)
+ vCalcIdParam.setParameters(settings.getWsParamFile().replace("\n",
+ "|\\n|"));
+ vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
+ // todo - decide if updateImmediately is needed for any projects.
+
+ return vCalcIdParam;
+ }
+ return null;
+ }
+
+ private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
+ AlignViewport av)
+ {
+ if (calcIdParam.getVersion().equals("1.0"))
+ {
+ Jws2Instance service = Jws2Discoverer.getDiscoverer()
+ .getPreferredServiceFor(calcIdParam.getServiceURL());
+ if (service != null)
+ {
+ WsParamSetI parmSet = null;
+ try
+ {
+ parmSet = service.getParamStore().parseServiceParameterFile(
+ calcIdParam.getName(), calcIdParam.getDescription(),
+ calcIdParam.getServiceURL(),
+ calcIdParam.getParameters().replace("|\\n|", "\n"));
+ } catch (IOException x)
+ {
+ warn("Couldn't parse parameter data for "
+ + calcIdParam.getCalcId(), x);
+ return false;
+ }
+ List<ArgumentI> argList = null;
+ if (calcIdParam.getName().length() > 0)
+ {
+ parmSet = service.getParamStore()
+ .getPreset(calcIdParam.getName());
+ if (parmSet != null)
+ {
+ // TODO : check we have a good match with settings in AACons -
+ // otherwise we'll need to create a new preset
+ }
+ }
+ else
+ {
+ argList = parmSet.getArguments();
+ parmSet = null;
+ }
+ AAConsSettings settings = new AAConsSettings(
+ calcIdParam.isAutoUpdate(), service, parmSet, argList);
+ av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
+ calcIdParam.isNeedsUpdate());
+ return true;
+ }
+ else
+ {
+ warn("Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ return false;
+ }
+ }
+ throw new Error("Unsupported Version for calcIdparam "
+ + calcIdParam.toString());
+ }
+
/**
* External mapping between jalview objects and objects yielding a valid and
* unique object ID string. This is null for normal Jalview project IO, but
return new jarInputStreamProvider()
{
+ @Override
public JarInputStream getJarInputStream() throws IOException
{
if (_url != null)
}
}
+ @Override
public String getFilename()
{
return file;
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
* Currently (28th Sep 2008) things will go horribly wrong in vamsas document
* sync if this is set to true.
*/
- private boolean updateLocalViews = false;
+ private final boolean updateLocalViews = false;
String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
{
}
;
out.close();
- String t=outFile.getAbsolutePath();
+ String t = outFile.getAbsolutePath();
alreadyLoadedPDB.put(pdbId, t);
return t;
}
if (seqRefIds.get(seqId) != null)
{
- tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ tmpseqs.add(seqRefIds.get(seqId));
multipleView = true;
}
else
hiddenSeqs = new Vector();
}
- hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
- .get(seqId));
+ hiddenSeqs.addElement(seqRefIds.get(seqId));
}
}
// Construct new annotation from model.
AnnotationElement[] ae = an[i].getAnnotationElement();
jalview.datamodel.Annotation[] anot = null;
-
+ java.awt.Color firstColour=null;
+ int anpos;
if (!an[i].getScoreOnly())
{
anot = new jalview.datamodel.Annotation[al.getWidth()];
for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
{
- if (ae[aa].getPosition() >= anot.length)
+ anpos = ae[aa].getPosition();
+
+ if (anpos >= anot.length)
continue;
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+ anot[anpos] = new jalview.datamodel.Annotation(
ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
(ae[aa].getSecondaryStructure() == null || ae[aa]
// {
// anot[ae[aa].getPosition()].displayCharacter = "";
// }
- anot[ae[aa].getPosition()].colour = new java.awt.Color(
+ anot[anpos].colour = new java.awt.Color(
ae[aa].getColour());
+ if (firstColour==null)
+ {
+ firstColour=anot[anpos].colour;
+ }
}
}
jalview.datamodel.AlignmentAnnotation jaa = null;
an[i].getGraphType());
jaa.graphGroup = an[i].getGraphGroup();
-
+ jaa._linecolour=firstColour;
if (an[i].getThresholdLine() != null)
{
jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot);
+ jaa._linecolour=firstColour;
}
- if (autoForView)
+ // register new annotation
+ if (an[i].getId() != null)
{
- // register new annotation
- if (an[i].getId() != null)
- {
- annotationIds.put(an[i].getId(), jaa);
- jaa.annotationId = an[i].getId();
- }
- // recover sequence association
- if (an[i].getSequenceRef() != null)
+ annotationIds.put(an[i].getId(), jaa);
+ jaa.annotationId = an[i].getId();
+ }
+ // recover sequence association
+ if (an[i].getSequenceRef() != null)
+ {
+ if (al.findName(an[i].getSequenceRef()) != null)
{
- if (al.findName(an[i].getSequenceRef()) != null)
- {
- jaa.createSequenceMapping(
- al.findName(an[i].getSequenceRef()), 1, true);
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(
- jaa);
- }
+ jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
+ 1, true);
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
}
}
// and make a note of any group association
}
if (an[i].hasBelowAlignment())
{
- jaa.belowAlignment=an[i].isBelowAlignment();
+ jaa.belowAlignment = an[i].isBelowAlignment();
}
jaa.setCalcId(an[i].getCalcId());
-
+
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
// file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
// seqs_file 2}, boolean[] {
// linkAlignPanel,superposeWithAlignpanel}} from hash
- Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid);
+ Object[] jmoldat = jmolViewIds.get(sviewid);
((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s)
.hasAlignwithAlignPanel() ? ids[p].getStructureState(
s).getAlignwithAlignPanel() : false;
}
if (ids[p].getFile() != null)
{
- File mapkey=new File(ids[p].getFile());
+ File mapkey = new File(ids[p].getFile());
Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
.get(mapkey);
if (seqstrmaps == null)
{
- ((Hashtable) jmoldat[2]).put(
- mapkey,
+ ((Hashtable) jmoldat[2]).put(mapkey,
seqstrmaps = new Object[]
{ pdbFile, ids[p].getId(), new Vector(),
new Vector() });
{
newFileLoc = new StringBuffer();
}
- do {
+ do
+ {
// look for next filename in load statement
- newFileLoc.append(state.substring(cp,
- ncp = (state.indexOf("\"", ncp + 1) + 1)));
- String oldfilenam = state.substring(ncp,
- ecp = state.indexOf("\"", ncp));
- // recover the new mapping data for this old filename
- // have to normalize filename - since Jmol and jalview do filename
- // translation differently.
- Object[] filedat = oldFiles.get(new File(oldfilenam));
- newFileLoc.append(Platform.escapeString((String) filedat[0]));
- pdbfilenames.addElement((String) filedat[0]);
- pdbids.addElement((String) filedat[1]);
- seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
- .toArray(new SequenceI[0]));
- newFileLoc.append("\"");
- cp = ecp + 1; // advance beyond last \" and set cursor so we can
- // look for next file statement.
- } while ((ncp=state.indexOf("/*file*/",cp))>-1);
+ newFileLoc.append(state.substring(cp,
+ ncp = (state.indexOf("\"", ncp + 1) + 1)));
+ String oldfilenam = state.substring(ncp,
+ ecp = state.indexOf("\"", ncp));
+ // recover the new mapping data for this old filename
+ // have to normalize filename - since Jmol and jalview do
+ // filename
+ // translation differently.
+ Object[] filedat = oldFiles.get(new File(oldfilenam));
+ newFileLoc.append(Platform
+ .escapeString((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement(((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]));
+ newFileLoc.append("\"");
+ cp = ecp + 1; // advance beyond last \" and set cursor so we can
+ // look for next file statement.
+ } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
}
if (cp > 0)
{
newFileLoc.append(((String) filedat[0]));
pdbfilenames.addElement((String) filedat[0]);
pdbids.addElement((String) filedat[1]);
- seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
+ seqmaps.addElement(((Vector<SequenceI>) filedat[2])
.toArray(new SequenceI[0]));
newFileLoc.append(" \"");
newFileLoc.append((String) filedat[0]);
// TODO: assemble String[] { pdb files }, String[] { id for each
// file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
// seqs_file 2}} from hash
- final String[] pdbf = (String[]) pdbfilenames
- .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids
+ final String[] pdbf = pdbfilenames
+ .toArray(new String[pdbfilenames.size()]), id = pdbids
.toArray(new String[pdbids.size()]);
- final SequenceI[][] sq = (SequenceI[][]) seqmaps
+ final SequenceI[][] sq = seqmaps
.toArray(new SequenceI[seqmaps.size()][]);
final String fileloc = newFileLoc.toString(), vid = sviewid;
final AlignFrame alf = af;
{
javax.swing.SwingUtilities.invokeAndWait(new Runnable()
{
+ @Override
public void run()
{
AppJmol sview = null;
// viewer
Object[] filedat = oldFiles.get(id);
String pdbFile = (String) filedat[0];
- SequenceI[] seq = (SequenceI[]) ((Vector<SequenceI>) filedat[2])
+ SequenceI[] seq = ((Vector<SequenceI>) filedat[2])
.toArray(new SequenceI[0]);
- ((AppJmol) comp).jmb.ssm.setMapping(seq, null, pdbFile,
+ comp.jmb.ssm.setMapping(seq, null, pdbFile,
jalview.io.AppletFormatAdapter.FILE);
- ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq);
+ comp.jmb.addSequenceForStructFile(pdbFile, seq);
}
// and add the AlignmentPanel's reference to the Jmol view
- ((AppJmol) comp).addAlignmentPanel(ap);
+ comp.addAlignmentPanel(ap);
if (useinJmolsuperpos)
{
- ((AppJmol) comp).useAlignmentPanelForSuperposition(ap);
+ comp.useAlignmentPanelForSuperposition(ap);
}
else
{
- ((AppJmol) comp).excludeAlignmentPanelForSuperposition(ap);
+ comp.excludeAlignmentPanelForSuperposition(ap);
}
if (usetoColourbyseq)
{
- ((AppJmol) comp).useAlignmentPanelForColourbyseq(ap,
- !jmolColouring);
+ comp.useAlignmentPanelForColourbyseq(ap, !jmolColouring);
}
else
{
- ((AppJmol) comp).excludeAlignmentPanelForColourbyseq(ap);
+ comp.excludeAlignmentPanelForColourbyseq(ap);
}
}
}
for (int i = 0; i < JSEQ.length; i++)
{
- af.viewport.setSequenceColour(af.viewport.getAlignment().getSequenceAt(i),
- new java.awt.Color(JSEQ[i].getColour()));
+ af.viewport.setSequenceColour(af.viewport.getAlignment()
+ .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
}
af.viewport.gatherViewsHere = view.getGatheredViews();
if (view.getAnnotationColours().getColourScheme()
.equals("None"))
{
- cs = new AnnotationColourGradient(
- af.viewport.getAlignment().getAlignmentAnnotation()[i],
+ cs = new AnnotationColourGradient(af.viewport
+ .getAlignment().getAlignmentAnnotation()[i],
new java.awt.Color(view.getAnnotationColours()
.getMinColour()), new java.awt.Color(view
.getAnnotationColours().getMaxColour()),
else if (view.getAnnotationColours().getColourScheme()
.startsWith("ucs"))
{
- cs = new AnnotationColourGradient(
- af.viewport.getAlignment().getAlignmentAnnotation()[i],
+ cs = new AnnotationColourGradient(af.viewport
+ .getAlignment().getAlignmentAnnotation()[i],
GetUserColourScheme(jms, view
.getAnnotationColours().getColourScheme()),
view.getAnnotationColours().getAboveThreshold());
}
else
{
- cs = new AnnotationColourGradient(
- af.viewport.getAlignment().getAlignmentAnnotation()[i],
+ cs = new AnnotationColourGradient(af.viewport
+ .getAlignment().getAlignmentAnnotation()[i],
ColourSchemeProperty.getColour(al, view
.getAnnotationColours().getColourScheme()),
view.getAnnotationColours().getAboveThreshold());
{
for (int g = 0; g < al.getGroups().size(); g++)
{
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
- .getGroups().elementAt(g);
+ jalview.datamodel.SequenceGroup sg = al.getGroups()
+ .get(g);
if (sg.cs == null)
{
* view.getAnnotationColours().getAboveThreshold()); } else
*/
{
- sg.cs = new AnnotationColourGradient(
- af.viewport.getAlignment().getAlignmentAnnotation()[i],
+ sg.cs = new AnnotationColourGradient(af.viewport
+ .getAlignment().getAlignmentAnnotation()[i],
sg.cs, view.getAnnotationColours()
.getAboveThreshold());
}
}
if (view.hasIgnoreGapsinConsensus())
{
- af.viewport.setIgnoreGapsConsensus(view
- .getIgnoreGapsinConsensus(), null);
+ af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
+ null);
}
if (view.hasFollowHighlight())
{
);
}
}
-
+ if (view.getCalcIdParam() != null)
+ {
+ for (CalcIdParam calcIdParam : view.getCalcIdParam())
+ {
+ if (calcIdParam != null)
+ {
+ if (recoverCalcIdParam(calcIdParam, af.viewport))
+ {
+ }
+ else
+ {
+ warn("Couldn't recover parameters for "
+ + calcIdParam.getCalcId());
+ }
+ }
+ }
+ }
af.setMenusFromViewport(af.viewport);
// TODO: we don't need to do this if the viewport is aready visible.
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
}
for (JvAnnotRow auan : autoAlan)
{
- visan.put(auan.template.label, auan);
+ visan.put(auan.template.label
+ + (auan.template.getCalcId() == null ? "" : "\t"
+ + auan.template.getCalcId()), auan);
}
int hSize = al.getAlignmentAnnotation().length;
ArrayList<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+ // work through any autoCalculated annotation already on the view
+ // removing it if it should be placed in a different location on the
+ // annotation panel.
+ List<String> remains = new ArrayList(visan.keySet());
for (int h = 0; h < hSize; h++)
{
jalview.datamodel.AlignmentAnnotation jalan = al
.getAlignmentAnnotation()[h];
if (jalan.autoCalculated)
{
- JvAnnotRow valan = visan.get(jalan.label);
+ String k;
+ JvAnnotRow valan = visan.get(k = jalan.label);
+ if (jalan.getCalcId() != null)
+ {
+ valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
+ }
+
if (valan != null)
{
// delete the auto calculated row from the alignment
- al.deleteAnnotation(al.getAlignmentAnnotation()[h], false);
+ al.deleteAnnotation(jalan, false);
+ remains.remove(k);
hSize--;
h--;
if (valan != nullAnnot)
}
}
}
+ // Add any (possibly stale) autocalculated rows that were not appended to
+ // the view during construction
+ for (String other : remains)
+ {
+ JvAnnotRow othera = visan.get(other);
+ if (othera != nullAnnot && othera.template.getCalcId() != null
+ && othera.template.getCalcId().length() > 0)
+ {
+ reorder.add(othera);
+ }
+ }
+ // now put the automatic annotation in its correct place
int s = 0, srt[] = new int[reorder.size()];
JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
for (JvAnnotRow jvar : reorder)
/**
* TODO remove this method
- *
+ *
* @param view
* @return AlignFrame bound to sequenceSetId from view, if one exists. private
* AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
/**
* Check if the Jalview view contained in object should be skipped or not.
- *
+ *
* @param object
* @return true if view's sequenceSetId is a key in skipList
*/
}
/**
- *
+ *
* @param vamsasSeq
* sequence definition to create/merge dataset sequence for
* @param ds
jalview.datamodel.SequenceI dsq = null;
if (sq != null && sq.getDatasetSequence() != null)
{
- dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
+ dsq = sq.getDatasetSequence();
}
String sqid = vamsasSeq.getDsseqid();
/**
* make a new dataset ID for this jalview dataset alignment
- *
+ *
* @param dataset
* @return
*/
* flag indicating if hashtables should be cleared on finalization TODO this
* flag may not be necessary
*/
- private boolean _cleartables = true;
+ private final boolean _cleartables = true;
private Hashtable jvids2vobj;
/*
* (non-Javadoc)
- *
+ *
* @see java.lang.Object#finalize()
*/
+ @Override
protected void finalize() throws Throwable
{
// really make sure we have no buried refs left.
* finalize and clearSeqRefs will not clear the tables when the Jalview2XML
* object goes out of scope. - also populates the datasetIds hashtable with
* alignment objects containing dataset sequences
- *
+ *
* @param vobj2jv
* Map from ID strings to jalview datamodel
* @param jv2vobj
* Map from jalview datamodel to ID strings
- *
- *
+ *
+ *
*/
public void setObjectMappingTables(Hashtable vobj2jv,
IdentityHashMap jv2vobj)
* set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
* objects created from the project archive. If string is null (default for
* construction) then suffix will be set automatically.
- *
+ *
* @param string
*/
public void setUniqueSetSuffix(String string)
/**
* uses skipList2 as the skipList for skipping views on sequence sets
* associated with keys in the skipList
- *
+ *
* @param skipList2
*/
public void setSkipList(Hashtable skipList2)