{
BinaryNode lf = leaves.elementAt(i);
- if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder())
+ if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder())
{
has_placeholders = true;
}
g.drawString(nodeLabel, xstart + 2, ypos - 2);
}
- String name = (markPlaceholders && ((node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder())))
- ? (PLACEHOLDER + node.getName())
- : node.getName();
+ String name = (markPlaceholders && ((node instanceof SequenceNode
+ && ((SequenceNode) node).isPlaceholder())))
+ ? (PLACEHOLDER + node.getName())
+ : node.getName();
int charWidth = fm.stringWidth(name) + 3;
int charHeight = font.getSize();
int ystart = (node.left() == null ? 0
: (int) (((BinaryNode) node.left()).ycount * chunk)) + offy;
int yend = (node.right() == null ? 0
- : (int) (((BinaryNode) node.right()).ycount * chunk))
- + offy;
+ : (int) (((BinaryNode) node.right()).ycount * chunk)) + offy;
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
nodeHash.put(node, pos);
else
{
Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
- if (tp.isColumnWise()) {
- markColumnsFor(getAssociatedPanels(), leaves, Color.red);
- } else {
- for (int i = 0; i < leaves.size(); i++)
+ if (tp.isColumnWise())
{
- SequenceI seq = (SequenceI) leaves.elementAt(i).element();
- treeSelectionChanged(seq);
+ markColumnsFor(getAssociatedPanels(), leaves, Color.red);
}
+ else
+ {
+ for (int i = 0; i < leaves.size(); i++)
+ {
+ SequenceI seq = (SequenceI) leaves.elementAt(i).element();
+ treeSelectionChanged(seq);
+ }
}
av.sendSelection();
}
{
AlignmentPanel[] aps = getAssociatedPanels();
List<BitSet> colGroups = new ArrayList<>();
- Map<BitSet,Color> colors=new HashMap();
+ Map<BitSet, Color> colors = new HashMap();
for (int i = 0; i < groups.size(); i++)
{
Color col = new Color((int) (Math.random() * 255),
setColor(groups.get(i), col.brighter());
Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
- if (!tp.isColumnWise()) {
+ if (!tp.isColumnWise())
+ {
createSeqGroupFor(aps, l, col);
- } else {
- BitSet gp=createColumnGroupFor(l,col);
+ }
+ else
+ {
+ BitSet gp = createColumnGroupFor(l, col);
colGroups.add(gp);
colors.put(gp, col);
if (tp.isColumnWise())
{
AlignmentAnnotation aa = tp.getAssocAnnotation();
- if (aa!=null) {
+ if (aa != null)
+ {
ContactMatrixI cm = av.getContactMatrix(aa);
- if (cm!=null)
+ if (cm != null)
{
cm.updateGroups(colGroups);
- for (BitSet gp:colors.keySet())
+ for (BitSet gp : colors.keySet())
{
cm.setColorForGroup(gp, colors.get(gp));
}
}
// stash colors in linked annotation row.
// doesn't work yet. TESTS!
- int sstart=aa.sequenceRef!=null ? aa.sequenceRef.getStart()-1 : 0;
+ int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1
+ : 0;
Annotation ae;
Color gpcol = null;
- int[] seqpos=null;
+ int[] seqpos = null;
for (BitSet gp : colors.keySet())
{
gpcol = colors.get(gp);
- for (int p = gp.nextSetBit(0); p >= 0 && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
+ for (int p = gp.nextSetBit(0); p >= 0
+ && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1))
{
if (cm instanceof MappableContactMatrixI)
{
MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
- seqpos = mcm.getMappedPositionsFor(aa.sequenceRef,p);
- if (seqpos==null)
+ seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p);
+ if (seqpos == null)
{
// no mapping for this column.
continue;
}
// TODO: handle ranges...
ae = aa.getAnnotationForPosition(seqpos[0]);
- } else {
- ae = aa.getAnnotationForPosition(p+sstart);
+ }
+ else
+ {
+ ae = aa.getAnnotationForPosition(p + sstart);
}
if (ae != null)
{
{
return false;
}
- if (av==null||av.getAlignment()==null)
+ if (av == null || av.getAlignment() == null)
{
// alignment is closed
return false;
}
ColumnSelection cs = av.getColumnSelection();
-
+
HiddenColumns hc = av.getAlignment().getHiddenColumns();
int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
: colm;
if (!av.hasHiddenColumns())
{
- return cs.contains(offp-1);
+ return cs.contains(offp - 1);
}
- if (hc.isVisible(offp-1))
+ if (hc.isVisible(offp - 1))
{
- return cs.contains(offp-1);
-// return cs.contains(hc.absoluteToVisibleColumn(offp));
+ return cs.contains(offp - 1);
+ // return cs.contains(hc.absoluteToVisibleColumn(offp));
}
return false;
}
-
- private BitSet createColumnGroupFor(Vector<BinaryNode> l,
- Color col)
+
+ private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col)
{
- BitSet gp=new BitSet();
- for (BinaryNode bn:l)
+ BitSet gp = new BitSet();
+ for (BinaryNode bn : l)
{
- int colm=-1;
- if (bn.element()!=null && bn.element()instanceof Integer)
- { colm = (Integer)bn.element();
- } else {
- // parse out from nodename
- try {
- colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1));
- } catch (Exception e)
+ int colm = -1;
+ if (bn.element() != null && bn.element() instanceof Integer)
{
- continue;
+ colm = (Integer) bn.element();
}
+ else
+ {
+ // parse out from nodename
+ try
+ {
+ colm = Integer.parseInt(
+ bn.getName().substring(bn.getName().indexOf("c") + 1));
+ } catch (Exception e)
+ {
+ continue;
+ }
}
gp.set(colm);
}
Color col)
{
SequenceI rseq = tp.assocAnnotation.sequenceRef;
-
+
if (av == null || av.getAlignment() == null)
{
// alignment is closed
continue;
}
// TODO - sort indices for faster lookup
-
+
ColumnSelection cs = av.getColumnSelection();
HiddenColumns hc = av.getAlignment().getHiddenColumns();
ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation);
if (cm instanceof MappableContactMatrixI)
{
mcm = (MappableContactMatrixI) cm;
- int[] seqpos = mcm.getMappedPositionsFor(tp.assocAnnotation.sequenceRef,colm);
- if (seqpos==null)
+ int[] seqpos = mcm.getMappedPositionsFor(
+ tp.assocAnnotation.sequenceRef, colm);
+ if (seqpos == null)
{
// no mapping for this column.
continue;
}
// TODO: handle ranges...
- offp=seqpos[0];
+ offp = seqpos[0];
}
else
{
git://source.jalview.org / jalview.git / blobdiff