/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* 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
* 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
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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.Jws2Discoverer;
+import jalview.ws.jws2.dm.AAConSettings;
+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.
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
- jalview.datamodel.AlignmentI jal = av.alignment;
+ jalview.datamodel.AlignmentI jal = av.getAlignment();
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
jal = jal.getHiddenSequences().getFullAlignment();
}
}
JSeq jseq;
+ Set<String> calcIdSet = new HashSet<String>();
// SAVE SEQUENCES
String id = "";
jseq.setId(id); // jseq id should be a string not a number
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
+ jseq.setHidden(av.getAlignment().getHiddenSequences().isHidden(jds));
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
+ if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
{
- jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
- .get(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 (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+ if (jds == jmol.jmb.sequence[peid][smap])
{
StructureState state = new StructureState();
state.setVisible(true);
jms.addJSeq(jseq);
}
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- jal = av.alignment;
+ jal = av.getAlignment();
}
// SAVE MAPPINGS
if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.treeCanvas.av.alignment == jal)
+ if (tp.treeCanvas.av.getAlignment() == jal)
{
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
}
}
}
-
// SAVE ANNOTATIONS
/**
* store forward refs from an annotationRow to any groups
an.setCentreColLabels(aa[i].centreColLabels);
an.setScaleColLabels(aa[i].scaleColLabel);
an.setShowAllColLabels(aa[i].showAllColLabels);
+ an.setBelowAlignment(aa[i].belowAlignment);
if (aa[i].graph > 0)
{
an.setLabel(aa[i].label);
- if (aa[i] == av.quality || aa[i] == av.conservation
- || aa[i] == av.consensus || 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)
+ {
+ calcIdSet.add(aa[i].getCalcId());
+ an.setCalcId(aa[i].getCalcId());
+ }
+
AnnotationElement ae;
if (aa[i].annotations != null)
{
if (jal.getGroups() != null)
{
JGroup[] groups = new JGroup[jal.getGroups().size()];
-
- for (int i = 0; i < groups.length; i++)
+ int i = -1;
+ for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
{
- groups[i] = new JGroup();
+ groups[++i] = new JGroup();
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
- .getGroups().elementAt(i);
groups[i].setStart(sg.getStartRes());
groups[i].setEnd(sg.getEndRes());
groups[i].setName(sg.getName());
groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
+ groups[i].setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
for (int s = 0; s < sg.getSize(); s++)
{
jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
view.setTextColThreshold(av.thresholdTextColour);
view.setShowConsensusHistogram(av.isShowConsensusHistogram());
view.setShowSequenceLogo(av.isShowSequenceLogo());
+ view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
view.setShowGroupConsensus(av.isShowGroupConsensus());
view.setShowGroupConservation(av.isShowGroupConservation());
view.setShowNPfeatureTooltip(av.isShowNpFeats());
}
// 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 (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
if (av.getColumnSelection() == null
|| av.getColumnSelection().getHiddenColumns() == null)
}
}
}
+ 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 AACon -
+ // otherwise we'll need to create a new preset
+ }
+ }
+ else
+ {
+ argList = parmSet.getArguments();
+ parmSet = null;
+ }
+ AAConSettings settings = new AAConSettings(
+ 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
try
{
+ // create list to store references for any new Jmol viewers created
+ newStructureViewers=new Vector<AppJmol>();
// UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
// Workaround is to make sure caller implements the JarInputStreamProvider
// interface
jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
af = LoadJalviewAlign(jprovider);
+
} catch (MalformedURLException e)
{
errorMessage = "Invalid URL format for '" + file + "'";
reportErrors();
}
+ finally {
+ try
+ {
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+ public void run()
+ {
+ setLoadingFinishedForNewStructureViewers();
+ };
+ });
+ } catch (Exception x)
+ {
+
+ }
+ }
return af;
}
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();
-
- alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
- return outFile.getAbsolutePath();
+ String t = outFile.getAbsolutePath();
+ alreadyLoadedPDB.put(pdbId, t);
+ return t;
}
else
{
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(
- ae[aa].getColour());
+ 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;
+ }
+ // register new annotation
+ if (an[i].getId() != null)
+ {
+ annotationIds.put(an[i].getId(), jaa);
+ jaa.annotationId = an[i].getId();
}
- if (autoForView)
+ // recover sequence association
+ if (an[i].getSequenceRef() != null)
{
- // register new annotation
- if (an[i].getId() != null)
+ if (al.findName(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)
- {
- 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
{
jaa.graphHeight = an[i].getGraphHeight();
}
+ if (an[i].hasBelowAlignment())
+ {
+ jaa.belowAlignment = an[i].isBelowAlignment();
+ }
+ jaa.setCalcId(an[i].getCalcId());
+
if (jaa.autoCalculated)
{
autoAlan.add(new JvAnnotRow(i, jaa));
{
sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
}
+ if (groups[i].hasNormaliseSequenceLogo())
+ {
+ sg.setNormaliseSequenceLogo(groups[i].isNormaliseSequenceLogo());
+ }
if (groups[i].hasIgnoreGapsinConsensus())
{
sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
// 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());
Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
- .get(ids[p].getFile());
+ .get(mapkey);
if (seqstrmaps == null)
{
- ((Hashtable) jmoldat[2]).put(
- new File(ids[p].getFile()).toString(),
+ ((Hashtable) jmoldat[2]).put(mapkey,
seqstrmaps = new Object[]
{ pdbFile, ids[p].getId(), new Vector(),
new Vector() });
}
else
{
- errorMessage = ("The Jmol views in the Jalview 2 project may\nnot be correctly bound to sequences in the alignment.\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
+ errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
warn(errorMessage);
}
}
Object[] svattrib = entry.getValue();
int[] geom = (int[]) svattrib[0];
String state = (String) svattrib[1];
- Hashtable<String, Object[]> oldFiles = (Hashtable<String, Object[]>) svattrib[2];
+ Hashtable<File, Object[]> oldFiles = (Hashtable<File, Object[]>) svattrib[2];
final boolean useinJmolsuperpos = ((boolean[]) svattrib[3])[0], usetoColourbyseq = ((boolean[]) svattrib[3])[1], jmolColouring = ((boolean[]) svattrib[3])[2];
int x = geom[0], y = geom[1], width = geom[2], height = geom[3];
// collate the pdbfile -> sequence mappings from this view
{
newFileLoc = new StringBuffer();
}
- 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)
- .toString());
- newFileLoc.append(((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.
+ 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(((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)
{
.print("Ignoring incomplete Jmol state for PDB ids: ");
newFileLoc = new StringBuffer(state);
newFileLoc.append("; load append ");
- for (String id : oldFiles.keySet())
+ for (File id : oldFiles.keySet())
{
// add this and any other pdb files that should be present in
// the viewer
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;
sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
useinJmolsuperpos, usetoColourbyseq,
jmolColouring, fileloc, rect, vid);
+ addNewStructureViewer(sview);
} catch (OutOfMemoryError ex)
{
new OOMWarning("restoring structure view for PDB id "
// add mapping for sequences in this view to an already open Jmol
// instance
- for (String id : oldFiles.keySet())
+ for (File id : oldFiles.keySet())
{
// add this and any other pdb files that should be present in the
// 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);
}
}
}
// and finally return.
return af;
}
+ Vector<AppJmol> newStructureViewers=null;
+ protected void addNewStructureViewer(AppJmol sview)
+ {
+ if (newStructureViewers!=null)
+ {
+ sview.jmb.setFinishedLoadingFromArchive(false);
+ newStructureViewers.add(sview);
+ }
+ }
+ protected void setLoadingFinishedForNewStructureViewers()
+ {
+ if (newStructureViewers!=null)
+ {
+ for (AppJmol sview:newStructureViewers)
+ {
+ sview.jmb.setFinishedLoadingFromArchive(true);
+ }
+ newStructureViewers.clear();
+ newStructureViewers=null;
+ }
+ }
AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
Alignment al, JalviewModelSequence jms, Viewport view,
for (int i = 0; i < JSEQ.length; i++)
{
- af.viewport.setSequenceColour(af.viewport.alignment.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();
jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
.get(uniqueSeqSetId);
- af.viewport.sequenceSetID = uniqueSeqSetId;
+ af.viewport.setSequenceSetId(uniqueSeqSetId);
if (av != null)
{
// propagate shared settings to this new view
else if (view.getBgColour().startsWith("Annotation"))
{
// int find annotation
- if (af.viewport.alignment.getAlignmentAnnotation() != null)
+ if (af.viewport.getAlignment().getAlignmentAnnotation() != null)
{
- for (int i = 0; i < af.viewport.alignment
+ for (int i = 0; i < af.viewport.getAlignment()
.getAlignmentAnnotation().length; i++)
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i].label
+ if (af.viewport.getAlignment().getAlignmentAnnotation()[i].label
.equals(view.getAnnotationColours().getAnnotation()))
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i]
+ if (af.viewport.getAlignment().getAlignmentAnnotation()[i]
.getThreshold() == null)
{
- af.viewport.alignment.getAlignmentAnnotation()[i]
+ af.viewport.getAlignment().getAlignmentAnnotation()[i]
.setThreshold(new jalview.datamodel.GraphLine(view
.getAnnotationColours().getThreshold(),
"Threshold", java.awt.Color.black)
if (view.getAnnotationColours().getColourScheme()
.equals("None"))
{
- cs = new AnnotationColourGradient(
- af.viewport.alignment.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.alignment.getAlignmentAnnotation()[i],
+ cs = new AnnotationColourGradient(af.viewport
+ .getAlignment().getAlignmentAnnotation()[i],
GetUserColourScheme(jms, view
.getAnnotationColours().getColourScheme()),
view.getAnnotationColours().getAboveThreshold());
}
else
{
- cs = new AnnotationColourGradient(
- af.viewport.alignment.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)
{
* if
* (view.getAnnotationColours().getColourScheme().equals("None"
* )) { sg.cs = new AnnotationColourGradient(
- * af.viewport.alignment.getAlignmentAnnotation()[i], new
+ * af.viewport.getAlignment().getAlignmentAnnotation()[i], new
* java.awt.Color(view.getAnnotationColours().
* getMinColour()), new
* java.awt.Color(view.getAnnotationColours().
* view.getAnnotationColours().getAboveThreshold()); } else
*/
{
- sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
+ sg.cs = new AnnotationColourGradient(af.viewport
+ .getAlignment().getAlignmentAnnotation()[i],
sg.cs, view.getAnnotationColours()
.getAboveThreshold());
}
if (cs != null)
{
cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.hconsensus);
+ cs.setConsensus(af.viewport.getSequenceConsensusHash());
}
}
}
if (view.hasIgnoreGapsinConsensus())
{
- af.viewport.ignoreGapsInConsensusCalculation = view
- .getIgnoreGapsinConsensus();
+ af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
+ null);
}
if (view.hasFollowHighlight())
{
}
if (view.hasShowSequenceLogo())
{
- af.viewport.showSequenceLogo = view.getShowSequenceLogo();
+ af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
}
else
{
- af.viewport.showSequenceLogo = false;
+ af.viewport.setShowSequenceLogo(false);
+ }
+ if (view.hasNormaliseSequenceLogo())
+ {
+ af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
}
if (view.hasShowDbRefTooltip())
{
);
}
}
-
+ 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(),
view.getHeight());
- af.alignPanel.updateAnnotation(false); // recompute any autoannotation
+ af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
reorderAutoannotation(af, al, autoAlan);
return af;
}
}
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)
jalview.datamodel.SequenceI dsq = null;
if (sq != null && sq.getDatasetSequence() != null)
{
- dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
+ dsq = sq.getDatasetSequence();
}
String sqid = vamsasSeq.getDsseqid();
af.closeMenuItem_actionPerformed(true);
/*
- * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
- * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
- * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
- * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
- * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
+ * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
+ * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
+ * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
+ * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
+ * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
*/
return af.alignPanel;
* 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;
*
* @see java.lang.Object#finalize()
*/
+ @Override
protected void finalize() throws Throwable
{
// really make sure we have no buried refs left.
git://source.jalview.org / jalview.git / blobdiff