*/
package jalview.viewmodel;
-import jalview.analysis.AAFrequency;
import jalview.analysis.Conservation;
import jalview.api.AlignCalcManagerI;
import jalview.api.AlignViewportI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.ClustalxColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.PIDColourScheme;
import jalview.schemes.ResidueProperties;
+import jalview.util.MappingUtils;
import jalview.workers.AlignCalcManager;
import jalview.workers.ConsensusThread;
import jalview.workers.StrucConsensusThread;
import java.awt.Color;
import java.util.ArrayList;
import java.util.BitSet;
+import java.util.HashMap;
import java.util.Hashtable;
import java.util.List;
import java.util.Map;
*/
public abstract class AlignmentViewport implements AlignViewportI
{
+ /*
+ * A viewport that hosts the cDna view of this (protein), or vice versa (if
+ * set).
+ */
+ AlignViewportI codingComplement = null;
+
/**
* alignment displayed in the viewport. Please use get/setter
*/
AlignmentAnnotation alignmentAnnotation)
{
if (!alignmentAnnotation.autoCalculated)
+ {
return false;
+ }
if (calculator.workingInvolvedWith(alignmentAnnotation))
{
// System.err.println("grey out ("+alignmentAnnotation.label+")");
protected boolean showConsensus = true;
- Hashtable sequenceColours;
+ private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
/**
* Property change listener for changes in alignment
selectionGroup = new SequenceGroup();
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- Vector tmp = alignment.getHiddenSequences().showAll(
+ List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
hiddenRepSequences);
- for (int t = 0; t < tmp.size(); t++)
+ for (SequenceI seq : tmp)
{
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ selectionGroup.addSequence(seq, false);
+ setSequenceAnnotationsVisible(seq, true);
}
hasHiddenRows = false;
public void showSequence(int index)
{
- Vector tmp = alignment.getHiddenSequences().showSequence(index,
+ List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
+ index,
hiddenRepSequences);
if (tmp.size() > 0)
{
selectionGroup.setEndRes(alignment.getWidth() - 1);
}
- for (int t = 0; t < tmp.size(); t++)
+ for (SequenceI seq : tmp)
{
- selectionGroup.addSequence((SequenceI) tmp.elementAt(t), false);
+ selectionGroup.addSequence(seq, false);
+ setSequenceAnnotationsVisible(seq, true);
}
// JBPNote: refactor: only update flag if we modified visiblity (used to
// do this regardless)
hideSequence(seqs);
+ AlignViewportI peer = getCodingComplement();
+ if (peer != null)
+ {
+ SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(
+ selectionGroup, this, peer);
+ ((AlignmentViewport) peer).hideSequence(mappedGroup
+ .getSequencesInOrder(peer.getAlignment()));
+ peer.setSelectionGroup(null);
+
+ }
+
setSelectionGroup(null);
}
for (int i = 0; i < seq.length; i++)
{
alignment.getHiddenSequences().hideSequence(seq[i]);
+ setSequenceAnnotationsVisible(seq[i], false);
}
hasHiddenRows = true;
firePropertyChange("alignment", null, alignment.getSequences());
}
}
+ /**
+ * Set visibility for any annotations for the given sequence.
+ *
+ * @param sequenceI
+ */
+ protected void setSequenceAnnotationsVisible(SequenceI sequenceI,
+ boolean visible)
+ {
+ for (AlignmentAnnotation ann : alignment.getAlignmentAnnotation())
+ {
+ if (ann.sequenceRef == sequenceI)
+ {
+ ann.visible = visible;
+ }
+ }
+ }
+
public void hideRepSequences(SequenceI repSequence, SequenceGroup sg)
{
int sSize = sg.getSize();
}
+ @Override
+ public List<AlignmentAnnotation> getVisibleAlignmentAnnotation(boolean selectedOnly)
+ {
+ ArrayList<AlignmentAnnotation> ala = new ArrayList<AlignmentAnnotation>();
+ AlignmentAnnotation[] aa;
+ if ((aa=alignment.getAlignmentAnnotation())!=null)
+ {
+ for (AlignmentAnnotation annot:aa)
+ {
+ AlignmentAnnotation clone = new AlignmentAnnotation(annot);
+ if (selectedOnly && selectionGroup!=null)
+ {
+ colSel.makeVisibleAnnotation(selectionGroup.getStartRes(), selectionGroup.getEndRes(),clone);
+ } else {
+ colSel.makeVisibleAnnotation(clone);
+ }
+ ala.add(clone);
+ }
+ }
+ return ala;
+ }
+
/**
* @return the padGaps
*/
@Override
public Color getSequenceColour(SequenceI seq)
{
- Color sqc = Color.white;
- if (sequenceColours != null)
- {
- sqc = (Color) sequenceColours.get(seq);
- if (sqc == null)
- {
- sqc = Color.white;
- }
- }
- return sqc;
+ Color sqc = sequenceColours.get(seq);
+ return (sqc == null ? Color.white : sqc);
}
@Override
public void setSequenceColour(SequenceI seq, Color col)
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
-
if (col == null)
{
sequenceColours.remove(seq);
@Override
public void updateSequenceIdColours()
{
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
for (SequenceGroup sg : alignment.getGroups())
{
if (sg.idColour != null)
@Override
public void clearSequenceColours()
{
- sequenceColours = null;
+ sequenceColours.clear();
};
+
+ @Override
+ public AlignViewportI getCodingComplement()
+ {
+ return this.codingComplement;
+ }
+
+ /**
+ * Set this as the (cDna/protein) complement of the given viewport. Also
+ * ensures the reverse relationship is set on the given viewport.
+ */
+ @Override
+ public void setCodingComplement(AlignViewportI av)
+ {
+ if (this == av)
+ {
+ System.err.println("Ignoring recursive setCodingComplement request");
+ }
+ else
+ {
+ this.codingComplement = av;
+ // avoid infinite recursion!
+ if (av.getCodingComplement() != this)
+ {
+ av.setCodingComplement(this);
+ }
+ }
+ }
+
+ @Override
+ public boolean isNucleotide()
+ {
+ return getAlignment() == null ? false : getAlignment().isNucleotide();
+ }
}