{
public static final String PROPERTY_ALIGNMENT = "alignment";
public static final String PROPERTY_SEQUENCE = "sequence";
-
protected ViewportRanges ranges;
protected ViewStyleI viewStyle = new ViewStyle();
* alignment
*/
protected boolean isDataset = false;
+
public void setDataset(boolean b)
{
{
autoCalculateStrucConsensus = b;
}
-
-
protected boolean ignoreGapsInConsensusCalculation = false;
protected ResidueShaderI residueShading = new ResidueShader();
+
@Override
public void setGlobalColourScheme(ColourSchemeI cs)
{
return residueShading;
}
+
protected AlignmentAnnotation consensus;
protected Hashtable<String, Object>[] hStrucConsensus = null;
protected Conservation hconservation = null;
+
@Override
public void setConservation(Conservation cons)
calculator.registerWorker(new InformationThread(this, ap));
}
}
-
// --------START Structure Conservation
public void updateStrucConsensus(final AlignmentViewPanel ap)
{
}
this.hmmShowSequenceLogo = showHMMSequenceLogo;
}
-
/**
* @param showConsensusHistogram
* the showConsensusHistogram to set
{
return infoLetterHeight;
}
-
// property change stuff
// JBPNote Prolly only need this in the applet version.
private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
}
}
+
// common hide/show column stuff
public void hideSelectedColumns()
}
}
-
public void showSequence(int index)
{
int startSeq = ranges.getStartSeq();
}
ranges.setStartEndSeq(startSeq, endSeq + tmp.size());
+
notifyAlignment();
sendSelection();
}
MessageManager.getString("label.consensus_descr"),
new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
initConsensus(consensus);
-
initGapCounts();
initComplementConsensus();
}
return false;
}
-
@Override
public void setCurrentTree(TreeModel tree)
{
codingComplement.setUpdateStructures(needToUpdateStructureViews);
}
}
+
+ @Override
+ public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
+ {
+ int start = 0;
+ int end = 0;
+ if (selectedRegionOnly && selectionGroup != null)
+ {
+ start = selectionGroup.getStartRes();
+ end = selectionGroup.getEndRes() + 1;
+ }
+ else
+ {
+ end = alignment.getWidth();
+ }
+ return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+ false));
+ }
/**
* Filters out sequences with an eValue higher than the specified value. The
* filtered sequences are hidden or deleted. Sequences with no eValues are also