scrollPane = scroller;
addMouseListener(this);
addMouseMotionListener(this);
-
+
ToolTipManager.sharedInstance().registerComponent(this);
}
PaintRefresher.Refresh(tp, av.getSequenceSetId());
repaint();
}
+
/**
* DOCUMENT ME!
*
longestName = "";
AlignmentAnnotation aa = tp.getAssocAnnotation();
- ContactMatrixI cm = (aa!=null) ? av.getContactMatrix(aa) : null;
- if (cm!=null && cm.hasCutHeight())
+ ContactMatrixI cm = (aa != null) ? av.getContactMatrix(aa) : null;
+ if (cm != null && cm.hasCutHeight())
{
- threshold=(float) cm.getCutHeight();
+ threshold = (float) cm.getCutHeight();
}
-
+
for (int i = 0; i < leaves.size(); i++)
{
BinaryNode lf = leaves.elementAt(i);
longestName = TreeCanvas.PLACEHOLDER
+ ((Sequence) lf.element()).getName();
}
- if (tp.isColumnWise() && cm!=null)
+ if (tp.isColumnWise() && cm != null)
{
// get color from group colours, if they are set for the matrix
- try {
+ try
+ {
Color col = cm.getGroupColorForPosition(parseColumnNode(lf));
- setColor(lf,col.brighter());
- } catch (NumberFormatException ex) {};
+ setColor(lf, col.brighter());
+ } catch (NumberFormatException ex)
+ {
+ }
+ ;
}
}
if (top.count == 0)
{
- top.count = top.left().count
- + top.right().count;
+ top.count = top.left().count + top.right().count;
}
float chunk = (float) (height - (offy)) / top.count;
Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
if (tp.isColumnWise())
{
- markColumnsFor(getAssociatedPanels(), leaves, Color.red,false);
+ markColumnsFor(getAssociatedPanels(), leaves, Color.red, false);
}
else
{
for (int i = 0; i < groups.size(); i++)
{
Color col = ColorUtils.getARandomColor();
-
+
setColor(groups.get(i), col.brighter());
Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
}
}
}
+
private int parseColumnNode(BinaryNode bn) throws NumberFormatException
{
return Integer.parseInt(
bn.getName().substring(bn.getName().indexOf("c") + 1));
}
+
private boolean isColumnForNodeSelected(BinaryNode bn)
{
SequenceI rseq = tp.assocAnnotation.sequenceRef;
ColumnSelection cs = av.getColumnSelection();
HiddenColumns hc = av.getAlignment().getHiddenColumns();
AlignmentAnnotation aa = tp.getAssocAnnotation();
- int offp=-1;
+ int offp = -1;
if (aa != null)
{
ContactMatrixI cm = av.getContactMatrix(aa);
- // generally, we assume cm has 1:1 mapping to annotation row - probably wrong
+ // generally, we assume cm has 1:1 mapping to annotation row - probably
+ // wrong
// but.. if
if (cm instanceof MappableContactMatrixI)
{
int[] pos;
- // use the mappable's mapping - always the case for PAE Matrices so good
+ // use the mappable's mapping - always the case for PAE Matrices so good
// for 2.11.3
MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
pos = mcm.getMappedPositionsFor(rseq, colm + 1);
{
offp = rseq.findIndex(pos[0]);
}
- } else {
+ }
+ else
+ {
offp = colm;
}
}
- if (offp<=0)
+ if (offp <= 0)
{
return false;
}
- offp-=2;
+ offp -= 2;
if (!av.hasHiddenColumns())
{
return cs.contains(offp);
}
return false;
}
+
private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col)
{
BitSet gp = new BitSet();
{
continue;
}
- if (mcm!=null)
+ if (mcm != null)
{
- int[] seqpos = mcm.getMappedPositionsFor(
- rseq, colm);
+ int[] seqpos = mcm.getMappedPositionsFor(rseq, colm);
if (seqpos == null)
{
// no mapping for this column.
continue;
}
// TODO: handle ranges...
- offp = rseq.findIndex(seqpos[0])-1;
+ offp = rseq.findIndex(seqpos[0]) - 1;
}
else
{