/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import uk.ac.vamsas.objects.utils.MapList;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
* will be :)
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.134 $
*/
public class Jalview2XML
{
{
if (frames[f] instanceof AppJmol)
{
- // TODO: revise schema to allow many:one PDB id binding to viewer
jmol = (AppJmol) frames[f];
for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++)
{
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);
state.setWidth(jmol.getWidth());
state.setHeight(jmol.getHeight());
state.setViewId(jmol.getViewId());
+ state.setAlignwithAlignPanel(jmol.isUsedforaligment(ap));
+ state.setColourwithAlignPanel(jmol
+ .isUsedforcolourby(ap));
+ state.setColourByJmol(jmol.isColouredByJmol());
if (!jmolViewIds.contains(state.getViewId()))
{
// Make sure we only store a Jmol state once in each XML
}
an.setGroupRef(groupIdr.toString());
}
- if (aa[i] == av.quality || aa[i] == av.conservation
- || aa[i] == av.consensus || aa[i].autoCalculated)
- {
- // new way of indicating autocalculated annotation -
- an.setAutoCalculated(aa[i].autoCalculated);
- // write a stub for this annotation - indicate presence of autocalc
- // rows
- an.setLabel(aa[i].label);
- an.setGraph(true);
- vamsasSet.addAnnotation(an);
- continue;
- }
+
+ // store all visualization attributes for annotation
+ an.setGraphHeight(aa[i].graphHeight);
+ an.setCentreColLabels(aa[i].centreColLabels);
+ an.setScaleColLabels(aa[i].scaleColLabel);
+ an.setShowAllColLabels(aa[i].showAllColLabels);
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)
+ {
+ // new way of indicating autocalculated annotation -
+ an.setAutoCalculated(aa[i].autoCalculated);
+ }
if (aa[i].hasScore())
{
an.setScore(aa[i].getScore());
}
an.addAnnotationElement(ae);
+ if (aa[i].autoCalculated)
+ {
+ // only write one non-null entry into the annotation row -
+ // sufficient to get the visualization attributes necessary to
+ // display data
+ continue;
+ }
}
}
else
Vector settingsAdded = new Vector();
Object gstyle = null;
GraduatedColor gcol = null;
- for (int ro = 0; ro < renderOrder.length; ro++)
+ if (renderOrder != null)
{
- gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getFeatureStyle(renderOrder[ro]);
- Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
- if (gstyle instanceof GraduatedColor)
- {
- gcol = (GraduatedColor) gstyle;
- setting.setColour(gcol.getMaxColor().getRGB());
- setting.setMincolour(gcol.getMinColor().getRGB());
- setting.setMin(gcol.getMin());
- setting.setMax(gcol.getMax());
- setting.setColourByLabel(gcol.isColourByLabel());
- setting.setAutoScale(gcol.isAutoScale());
- setting.setThreshold(gcol.getThresh());
- setting.setThreshstate(gcol.getThreshType());
- }
- else
+ for (int ro = 0; ro < renderOrder.length; ro++)
{
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getColour(renderOrder[ro]).getRGB());
- }
+ gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getFeatureStyle(renderOrder[ro]);
+ Setting setting = new Setting();
+ setting.setType(renderOrder[ro]);
+ if (gstyle instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) gstyle;
+ setting.setColour(gcol.getMaxColor().getRGB());
+ setting.setMincolour(gcol.getMinColor().getRGB());
+ setting.setMin(gcol.getMin());
+ setting.setMax(gcol.getMax());
+ setting.setColourByLabel(gcol.isColourByLabel());
+ setting.setAutoScale(gcol.isAutoScale());
+ setting.setThreshold(gcol.getThresh());
+ setting.setThreshstate(gcol.getThreshType());
+ }
+ else
+ {
+ setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(renderOrder[ro]).getRGB());
+ }
- setting.setDisplay(av.featuresDisplayed
- .containsKey(renderOrder[ro]));
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
- renderOrder[ro]);
- if (rorder > -1)
- {
- setting.setOrder(rorder);
+ setting.setDisplay(av.featuresDisplayed
+ .containsKey(renderOrder[ro]));
+ float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getOrder(renderOrder[ro]);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(renderOrder[ro]);
}
- fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
}
// Make sure we save none displayed feature settings
}
;
out.close();
-
- alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
- return outFile.getAbsolutePath();
+ String t=outFile.toURI().getPath().substring(1);
+ alreadyLoadedPDB.put(pdbId, t);
+ return t;
}
else
{
return null;
}
+ private class JvAnnotRow
+ {
+ public JvAnnotRow(int i, AlignmentAnnotation jaa)
+ {
+ order = i;
+ template = jaa;
+ }
+
+ /**
+ * persisted version of annotation row from which to take vis properties
+ */
+ public jalview.datamodel.AlignmentAnnotation template;
+
+ /**
+ * original position of the annotation row in the alignment
+ */
+ public int order;
+ }
+
/**
* Load alignment frame from jalview XML DOM object
*
// ////////////////////////////////
// LOAD ANNOTATIONS
- boolean hideQuality = true, hideConservation = true, hideConsensus = true;
+ ArrayList<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
/**
* store any annotations which forward reference a group's ID
*/
- Hashtable groupAnnotRefs = new Hashtable();
+ Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>>();
if (vamsasSet.getAnnotationCount() > 0)
{
for (int i = 0; i < an.length; i++)
{
- // set visibility for automatic annotation for this view
- if (an[i].getLabel().equals("Quality"))
- {
- hideQuality = false;
- continue;
- }
- else if (an[i].getLabel().equals("Conservation"))
- {
- hideConservation = false;
- continue;
+ /**
+ * test if annotation is automatically calculated for this view only
+ */
+ boolean autoForView = false;
+ if (an[i].getLabel().equals("Quality")
+ || an[i].getLabel().equals("Conservation")
+ || an[i].getLabel().equals("Consensus"))
+ {
+ // Kludge for pre 2.5 projects which lacked the autocalculated flag
+ autoForView = true;
+ if (!an[i].hasAutoCalculated())
+ {
+ an[i].setAutoCalculated(true);
+ }
}
- else if (an[i].getLabel().equals("Consensus"))
+ if (autoForView
+ || (an[i].hasAutoCalculated() && an[i].isAutoCalculated()))
{
- hideConsensus = false;
- continue;
+ // remove ID - we don't recover annotation from other views for
+ // view-specific annotation
+ an[i].setId(null);
}
+
// set visiblity for other annotation in this view
if (an[i].getId() != null
&& annotationIds.containsKey(an[i].getId()))
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)
if (an[i].getGraph())
{
+ float llim = 0, hlim = 0;
+ // if (autoForView || an[i].isAutoCalculated()) {
+ // hlim=11f;
+ // }
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
+ an[i].getDescription(), anot, llim, hlim,
+ an[i].getGraphType());
jaa.graphGroup = an[i].getGraphGroup();
an[i].getThresholdLine().getColour())));
}
-
+ if (autoForView || an[i].isAutoCalculated())
+ {
+ // Hardwire the symbol display line to ensure that labels for
+ // histograms are displayed
+ jaa.hasText = true;
+ }
}
else
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot);
}
- // register new annotation
- if (an[i].getId() != null)
+ if (autoForView)
{
- 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)
+ // 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)
{
- jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
- 1, true);
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ if (al.findName(an[i].getSequenceRef()) != null)
+ {
+ 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].getGroupRef() != null && an[i].getGroupRef().length() > 0)
{
- groupAnnotRefs.put(an[i].getGroupRef(), jaa);
+ ArrayList<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
+ .get(an[i].getGroupRef());
+ if (aal == null)
+ {
+ aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
+ groupAnnotRefs.put(an[i].getGroupRef(), aal);
+ }
+ aal.add(jaa);
}
if (an[i].hasScore())
jaa.autoCalculated = true; // means annotation will be marked for
// update at end of load.
}
- al.addAnnotation(jaa);
+ if (an[i].hasGraphHeight())
+ {
+ jaa.graphHeight = an[i].getGraphHeight();
+ }
+ if (jaa.autoCalculated)
+ {
+ autoAlan.add(new JvAnnotRow(i, jaa));
+ }
+ else
+ // if (!autoForView)
+ {
+ // add autocalculated group annotation and any user created annotation
+ // for the view
+ al.addAnnotation(jaa);
+ }
}
}
if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
{
// re-instate unique group/annotation row reference
- jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs
+ ArrayList<jalview.datamodel.AlignmentAnnotation> jaal = groupAnnotRefs
.get(groups[i].getId());
- if (jaa != null)
+ if (jaal != null)
{
- jaa.groupRef = sg;
+ for (jalview.datamodel.AlignmentAnnotation jaa : jaal)
+ {
+ jaa.groupRef = sg;
+ if (jaa.autoCalculated)
+ {
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Consensus for "))
+ {
+ sg.setConsensus(jaa);
+ }
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Conservation for "))
+ {
+ sg.setConservationRow(jaa);
+ }
+ }
+ }
}
}
al.addGroup(sg);
if (isnewview)
{
- af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
- hideQuality, hideConservation, jms, view, uniqueSeqSetId,
- viewId);
+ af = loadViewport(file, JSEQ, hiddenSeqs, al, jms, view,
+ uniqueSeqSetId, viewId, autoAlan);
av = af.viewport;
ap = af.alignPanel;
}
jmolViewIds.put(sviewid, new Object[]
{ new int[]
{ x, y, width, height }, "",
- new Hashtable<String, Object[]>() });
+ new Hashtable<String, Object[]>(), new boolean[]
+ { false, false, true } });
+ // Legacy pre-2.7 conversion JAL-823 :
+ // do not assume any view has to be linked for colour by
+ // sequence
}
- // TODO: assemble String[] { pdb files }, String[] { id for each
+
+ // assemble String[] { pdb files }, String[] { id for each
// file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
- // seqs_file 2}} from hash
+ // seqs_file 2}, boolean[] {
+ // linkAlignPanel,superposeWithAlignpanel}} from hash
Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid);
+ ((boolean[]) jmoldat[3])[0] |= ids[p].getStructureState(s)
+ .hasAlignwithAlignPanel() ? ids[p].getStructureState(
+ s).getAlignwithAlignPanel() : false;
+ // never colour by linked panel if not specified
+ ((boolean[]) jmoldat[3])[1] |= ids[p].getStructureState(s)
+ .hasColourwithAlignPanel() ? ids[p]
+ .getStructureState(s).getColourwithAlignPanel()
+ : false;
+ // default for pre-2.7 projects is that Jmol colouring is enabled
+ ((boolean[]) jmoldat[3])[2] &= ids[p].getStructureState(s)
+ .hasColourByJmol() ? ids[p].getStructureState(s)
+ .getColourByJmol() : true;
+
if (((String) jmoldat[1]).length() < ids[p]
.getStructureState(s).getContent().length())
{
jmoldat[1] = ids[p].getStructureState(s).getContent();
}
}
- Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
- .get(ids[p].getFile());
- if (seqstrmaps == null)
+ if (ids[p].getFile() != null)
{
- ((Hashtable) jmoldat[2]).put(
- new File(ids[p].getFile()).toString(),
- seqstrmaps = new Object[]
- { pdbFile, ids[p].getId(), new Vector(),
- new Vector() });
+ File mapkey=new File(ids[p].getFile());
+ Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
+ .get(mapkey);
+ if (seqstrmaps == null)
+ {
+ ((Hashtable) jmoldat[2]).put(
+ mapkey,
+ seqstrmaps = new Object[]
+ { pdbFile, ids[p].getId(), new Vector(),
+ new Vector() });
+ }
+ if (!((Vector) seqstrmaps[2]).contains(seq))
+ {
+ ((Vector) seqstrmaps[2]).addElement(seq);
+ // ((Vector)seqstrmaps[3]).addElement(n) :
+ // in principle, chains
+ // should be stored here : do we need to
+ // TODO: store and recover seq/pdb_id :
+ // chain mappings
+ }
}
- if (!((Vector) seqstrmaps[2]).contains(seq))
+ else
{
- ((Vector) seqstrmaps[2]).addElement(seq);
- // ((Vector)seqstrmaps[3]).addElement(n) : in principle, chains
- // should be stored here : do we need to
- // TODO: store and recover seq/pdb_id : chain mappings
+ 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
Vector<String> pdbfilenames = new Vector<String>();
// 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());
+ Object[] filedat = oldFiles.get(new File(oldfilenam));
newFileLoc.append(((String) filedat[0]));
pdbfilenames.addElement((String) filedat[0]);
pdbids.addElement((String) filedat[1]);
.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
{
public void run()
{
- new AppJmol(pdbf, id, sq, alf.alignPanel, fileloc,
- rect, vid);
+ AppJmol sview = null;
+ try
+ {
+ sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
+ useinJmolsuperpos, usetoColourbyseq,
+ jmolColouring, fileloc, rect, vid);
+ } catch (OutOfMemoryError ex)
+ {
+ new OOMWarning("restoring structure view for PDB id "
+ + id, (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
+ {
+ sview.closeViewer();
+ sview.setVisible(false);
+ sview.dispose();
+ }
+ }
}
});
} catch (InvocationTargetException ex)
{
- System.err
- .println("Unexpected error when opening Jmol view.");
- ex.printStackTrace();
+ warn("Unexpected error when opening Jmol view.", ex);
+
} catch (InterruptedException e)
{
// e.printStackTrace();
// 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
String pdbFile = (String) filedat[0];
SequenceI[] seq = (SequenceI[]) ((Vector<SequenceI>) filedat[2])
.toArray(new SequenceI[0]);
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, null, pdbFile,
- jalview.io.AppletFormatAdapter.FILE);
+ ((AppJmol) comp).jmb.ssm.setMapping(seq, null, pdbFile,
+ jalview.io.AppletFormatAdapter.FILE);
((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq);
}
+ // and add the AlignmentPanel's reference to the Jmol view
+ ((AppJmol) comp).addAlignmentPanel(ap);
+ if (useinJmolsuperpos)
+ {
+ ((AppJmol) comp).useAlignmentPanelForSuperposition(ap);
+ }
+ else
+ {
+ ((AppJmol) comp).excludeAlignmentPanelForSuperposition(ap);
+ }
+ if (usetoColourbyseq)
+ {
+ ((AppJmol) comp).useAlignmentPanelForColourbyseq(ap,
+ !jmolColouring);
+ }
+ else
+ {
+ ((AppJmol) comp).excludeAlignmentPanelForColourbyseq(ap);
+ }
}
}
}
}
AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
- Alignment al, boolean hideConsensus, boolean hideQuality,
- boolean hideConservation, JalviewModelSequence jms,
- Viewport view, String uniqueSeqSetId, String viewId)
+ Alignment al, JalviewModelSequence jms, Viewport view,
+ String uniqueSeqSetId, String viewId,
+ ArrayList<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, view.getWidth(), view.getHeight(),
af.viewport.hideSequence(hseqs);
}
- // set visibility of annotation in view
- if ((hideConsensus || hideQuality || hideConservation)
- && al.getAlignmentAnnotation() != null)
- {
- int hSize = al.getAlignmentAnnotation().length;
- for (int h = 0; h < hSize; h++)
- {
- if ((hideConsensus && al.getAlignmentAnnotation()[h].label
- .equals("Consensus"))
- || (hideQuality && al.getAlignmentAnnotation()[h].label
- .equals("Quality"))
- || (hideConservation && al.getAlignmentAnnotation()[h].label
- .equals("Conservation")))
- {
- al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
- hSize--;
- h--;
- }
- }
- af.alignPanel.adjustAnnotationHeight();
- }
// recover view properties and display parameters
if (view.getViewName() != null)
{
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
view.getHeight());
af.alignPanel.updateAnnotation(false); // recompute any autoannotation
+ reorderAutoannotation(af, al, autoAlan);
return af;
}
+ private void reorderAutoannotation(AlignFrame af, Alignment al,
+ ArrayList<JvAnnotRow> autoAlan)
+ {
+ // copy over visualization settings for autocalculated annotation in the
+ // view
+ if (al.getAlignmentAnnotation() != null)
+ {
+ /**
+ * Kludge for magic autoannotation names (see JAL-811)
+ */
+ String[] magicNames = new String[]
+ { "Consensus", "Quality", "Conservation" };
+ JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
+ Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
+ for (String nm : magicNames)
+ {
+ visan.put(nm, nullAnnot);
+ }
+ for (JvAnnotRow auan : autoAlan)
+ {
+ visan.put(auan.template.label, auan);
+ }
+ int hSize = al.getAlignmentAnnotation().length;
+ ArrayList<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+ for (int h = 0; h < hSize; h++)
+ {
+ jalview.datamodel.AlignmentAnnotation jalan = al
+ .getAlignmentAnnotation()[h];
+ if (jalan.autoCalculated)
+ {
+ JvAnnotRow valan = visan.get(jalan.label);
+ if (valan != null)
+ {
+ // delete the auto calculated row from the alignment
+ al.deleteAnnotation(al.getAlignmentAnnotation()[h], false);
+ hSize--;
+ h--;
+ if (valan != nullAnnot)
+ {
+ if (jalan != valan.template)
+ {
+ // newly created autoannotation row instance
+ // so keep a reference to the visible annotation row
+ // and copy over all relevant attributes
+ if (valan.template.graphHeight >= 0)
+
+ {
+ jalan.graphHeight = valan.template.graphHeight;
+ }
+ jalan.visible = valan.template.visible;
+ }
+ reorder.add(new JvAnnotRow(valan.order, jalan));
+ }
+ }
+ }
+ }
+ int s = 0, srt[] = new int[reorder.size()];
+ JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
+ for (JvAnnotRow jvar : reorder)
+ {
+ rws[s] = jvar;
+ srt[s++] = jvar.order;
+ }
+ reorder.clear();
+ jalview.util.QuickSort.sort(srt, rws);
+ // and re-insert the annotation at its correct position
+ for (JvAnnotRow jvar : rws)
+ {
+ al.addAnnotation(jvar.template, jvar.order);
+ }
+ af.alignPanel.adjustAnnotationHeight();
+ }
+ }
+
Hashtable skipList = null;
/**
git://source.jalview.org / jalview.git / blobdiff