import jalview.analysis.Conservation;
import jalview.analysis.TreeModel;
import jalview.api.AlignViewportI;
+import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.BinaryNode;
import jalview.gui.JalviewColourChooser.ColourChooserListener;
import jalview.schemes.ColourSchemeI;
import jalview.structure.SelectionSource;
+import jalview.util.ColorUtils;
import jalview.util.Format;
import jalview.util.MessageManager;
import jalview.ws.datamodel.MappableContactMatrixI;
scrollPane = scroller;
addMouseListener(this);
addMouseMotionListener(this);
-
+
ToolTipManager.sharedInstance().registerComponent(this);
}
PaintRefresher.Refresh(tp, av.getSequenceSetId());
repaint();
}
+
/**
* DOCUMENT ME!
*
boolean has_placeholders = false;
longestName = "";
+ AlignmentAnnotation aa = tp.getAssocAnnotation();
+ ContactMatrixI cm = (aa != null) ? av.getContactMatrix(aa) : null;
+ if (cm != null && cm.hasCutHeight())
+ {
+ 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)
+ {
+ // get color from group colours, if they are set for the matrix
+ try
+ {
+ Color col = cm.getGroupColorForPosition(parseColumnNode(lf));
+ setColor(lf, col.brighter());
+ } catch (NumberFormatException ex)
+ {
+ }
+ ;
+ }
}
setMarkPlaceholders(has_placeholders);
* @param offy
* DOCUMENT ME!
*/
- public void drawNode(Graphics g, BinaryNode node, float chunk,
+ public void drawNode(Graphics g, BinaryNode node, double chunk,
double wscale, int width, int offx, int offy)
{
if (node == null)
}
int ystart = (node.left() == null ? 0
- : (int) (((BinaryNode) node.left()).ycount * chunk)) + offy;
+ : (int) (node.left().ycount * chunk)) + offy;
int yend = (node.right() == null ? 0
- : (int) (((BinaryNode) node.right()).ycount * chunk)) + offy;
+ : (int) (node.right().ycount * chunk)) + offy;
Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
nodeHash.put(node, pos);
if (top.count == 0)
{
- top.count = ((BinaryNode) top.left()).count
- + ((BinaryNode) 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
{
threshold = 0f;
}
}
-
+ Console.log.debug("Tree cut threshold set at:" + threshold);
PaintRefresher.Refresh(tp,
getAssociatedPanel().av.getSequenceSetId());
repaint();
Map<BitSet, Color> colors = new HashMap();
for (int i = 0; i < groups.size(); i++)
{
- Color col = new Color((int) (Math.random() * 255),
- (int) (Math.random() * 255), (int) (Math.random() * 255));
+ Color col = ColorUtils.getARandomColor();
+
setColor(groups.get(i), col.brighter());
Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
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;
- Annotation ae;
- Color gpcol = 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))
- {
- if (cm instanceof MappableContactMatrixI)
- {
- MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
- 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);
- }
- if (ae != null)
- {
- ae.colour = gpcol.brighter().darker();
- }
- }
- }
+ cm.transferGroupColorsTo(aa);
}
}
}
}
+ 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;
int colm = -1;
try
{
- colm = Integer.parseInt(
- bn.getName().substring(bn.getName().indexOf("c") + 1));
+ colm = parseColumnNode(bn);
} catch (Exception e)
{
return false;
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();
// parse out from nodename
try
{
- colm = Integer.parseInt(
- bn.getName().substring(bn.getName().indexOf("c") + 1));
+ colm = parseColumnNode(bn);
} catch (Exception e)
{
continue;
{
continue;
}
- if (mcm!=null)
+ if (mcm != null)
{
- int[] seqpos = mcm.getMappedPositionsFor(
- tp.assocAnnotation.sequenceRef, colm);
+ int[] seqpos = mcm.getMappedPositionsFor(rseq, colm);
if (seqpos == null)
{
// no mapping for this column.
continue;
}
// TODO: handle ranges...
- offp = seqpos[0]-1;
+ offp = rseq.findIndex(seqpos[0]) - 1;
}
else
{
git://source.jalview.org / jalview.git / blobdiff