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.*;
}
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.setGraph(true);
}
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
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"))
- {
- hideConsensus = false;
- continue;
+ if (autoForView || (an[i].hasAutoCalculated() && an[i].isAutoCalculated())) {
+ // 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)
- {
- annotationIds.put(an[i].getId(), jaa);
- jaa.annotationId = an[i].getId();
- }
- // recover sequence association
- if (an[i].getSequenceRef() != null)
+ if (autoForView)
{
- if (al.findName(an[i].getSequenceRef()) != null)
+ // register new annotation
+ if (an[i].getId() != null)
{
- jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
- 1, true);
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ 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);
+ }
}
}
// 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;
}
if (!jmolViewIds.containsKey(sviewid))
{
jmolViewIds.put(sviewid, new Object[]
- {
- new int[]
- { x, y, width, height },
- "",
- new Hashtable<String, Object[]>(),
- new boolean[]
- {
- false,false} });
+ { new int[]
+ { x, y, width, height }, "",
+ new Hashtable<String, Object[]>(), new boolean[]
+ { false, false } });
// Legacy->2.7 conversion: if there is no attribute for
// colouring with the alignPanel then by default we set the
// first encountered view to be the default source of colour
try
{
sview = new AppJmol(pdbf, id, sq, alf.alignPanel,
- useinJmolsuperpos, usetoColourbyseq,
- fileloc,
+ useinJmolsuperpos, usetoColourbyseq, fileloc,
rect, vid);
} catch (OutOfMemoryError ex)
{
}
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 / commitdiff