import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.Annotation;
+import jalview.datamodel.CigarArray;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceCollectionI;
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;
ViewStyleI
{
protected ViewStyleI viewStyle = new ViewStyle();
-
-
+
+ /**
+ * A viewport that hosts the cDna view of this (protein), or vice versa (if
+ * set).
+ */
+ AlignViewportI codingComplement = null;
+
/**
* @param name
* @see jalview.api.ViewStyleI#setFontName(java.lang.String)
protected boolean showConsensus = true;
- Hashtable sequenceColours;
+ private Map<SequenceI, Color> sequenceColours = new HashMap<SequenceI, Color>();
/**
* Property change listener for changes in alignment
}
@Override
- public abstract void sendSelection();
-
- @Override
public void invertColumnSelection()
{
colSel.invertColumnSelection(0, alignment.getWidth());
@Override
- public jalview.datamodel.CigarArray getViewAsCigars(
+ public CigarArray getViewAsCigars(
boolean selectedRegionOnly)
{
- return new jalview.datamodel.CigarArray(alignment, colSel,
+ return new CigarArray(alignment, colSel,
(selectedRegionOnly ? selectionGroup : null));
}
viewStyle.setDisplayReferenceSeq(displayReferenceSeq);
}
+ @Override
public boolean isColourByReferenceSeq()
{
return alignment.hasSeqrep() && viewStyle.isColourByReferenceSeq();
}
-
@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();
+ }
+
FeaturesDisplayedI featuresDisplayed = null;
@Override
{
return viewStyle.isShowColourText();
}
-
/**
* @return
* @see jalview.api.ViewStyleI#isShowSeqFeaturesHeight()