import jalview.datamodel.SequenceNode;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.util.Format;
import jalview.util.MappingUtils;
}
public void drawNode(Graphics g, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ double scale, int width, int offx, int offy)
{
if (node == null)
{
{
// Drawing leaf node
- float height = node.height;
- float dist = node.dist;
+ double height = node.height;
+ double dist = node.dist;
int xstart = (int) ((height - dist) * scale) + offx;
int xend = (int) (height * scale) + offx;
drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
offy);
- float height = node.height;
- float dist = node.dist;
+ double height = node.height;
+ double dist = node.dist;
int xstart = (int) ((height - dist) * scale) + offx;
int xend = (int) (height * scale) + offx;
SequenceNode top = tree.getTopNode();
- float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
+ double wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
if (top.count == 0)
{
top.count = ((SequenceNode) top.left()).count
}
public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
- float scale, int width, int offx, int offy)
+ double scale, int width, int offx, int offy)
{
if (node == null)
{
if (node.left() == null && node.right() == null)
{
- float height = node.height;
+ double height = node.height;
// float dist = node.dist;
// int xstart = (int) ( (height - dist) * scale) + offx;
// for
// scrollbar
- float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
+ double wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
SequenceNode top = tree.getTopNode();
for (int i = 0; i < leaves.size(); i++)
{
- SequenceI seq = (SequenceI) leaves.elementAt(i)
- .element();
+ SequenceI seq = (SequenceI) leaves.elementAt(i).element();
treeSelectionChanged(seq);
}
}
Color col = new Color((int) (Math.random() * 255),
(int) (Math.random() * 255), (int) (Math.random() * 255));
- setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+ setColor(tree.getGroups().elementAt(i), col.brighter());
- Vector<SequenceNode> l = tree.findLeaves((SequenceNode) tree
- .getGroups().elementAt(i));
+ Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
+ .elementAt(i));
Vector<SequenceI> sequences = new Vector<SequenceI>();
for (int j = 0; j < l.size(); j++)
{
- SequenceI s1 = (SequenceI) l.elementAt(j)
- .element();
+ SequenceI s1 = (SequenceI) l.elementAt(j).element();
if (!sequences.contains(s1))
{
sequences.addElement(s1);
}
else
{
- cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
- .getColourName(av.getGlobalColourScheme()));
+ cs = ColourSchemeProperty.getColourScheme(sg,
+ ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
}
// cs is null if shading is an annotationColourGradient
- if (cs != null)
- {
- cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
- av.isIgnoreGapsConsensus());
- }
+ // if (cs != null)
+ // {
+ // cs.setThreshold(av.getViewportColourScheme().getThreshold(),
+ // av.isIgnoreGapsConsensus());
+ // }
}
// TODO: cs used to be initialized with a sequence collection and
// recalcConservation called automatically
// instead we set it manually - recalc called after updateAnnotation
- sg.cs = cs;
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setThreshold(
+ av.getResidueShading().getThreshold(),
+ av.isIgnoreGapsConsensus());
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
if (av.getGlobalColourScheme() != null
- && av.getGlobalColourScheme().conservationApplied())
+ && av.getResidueShading().conservationApplied())
{
- Conservation c = new Conservation("Group",
- ResidueProperties.propHash, 3, sg.getSequences(null),
+ Conservation c = new Conservation("Group", sg.getSequences(null),
sg.getStartRes(), sg.getEndRes());
c.calculate();
c.verdict(false, av.getConsPercGaps());
- cs.setConservation(c);
-
- sg.cs = cs;
+ sg.setColourScheme(cs);
+ sg.getGroupColourScheme().setConservation(c);
}
av.getAlignment().addGroup(sg);