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Implemented least-squares optimisation in ccAnalysis
[jalview.git]
/
src
/
jalview
/
viewmodel
/
PaSiMapModel.java
diff --git
a/src/jalview/viewmodel/PaSiMapModel.java
b/src/jalview/viewmodel/PaSiMapModel.java
index
c9545a8
..
1f5e2dc
100644
(file)
--- a/
src/jalview/viewmodel/PaSiMapModel.java
+++ b/
src/jalview/viewmodel/PaSiMapModel.java
@@
-101,14
+101,19
@@
public class PaSiMapModel
ii++;
}
ii++;
}
+ int width = pasimap.getWidth();
int height = pasimap.getHeight();
// top = pasimap.getM().height() - 1;
int height = pasimap.getHeight();
// top = pasimap.getM().height() - 1;
- top = height - 1;
+ //&!
+ //top = height - 1;
+ top = height;
points = new Vector<>();
points = new Vector<>();
- Point[] scores = pasimap.getComponents(top - 1, top - 2, top - 3, 100);
+ //&!
+ //Point[] scores = pasimap.getComponents(top - 1, top - 2, top - 3, 100);
+ Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3, 1);
- for (int i = 0; i < height; i++)
+ for (int i = 0; i < top; i++)
{
SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
points.add(sp);
{
SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
points.add(sp);
@@
-158,9
+163,11
@@
public class PaSiMapModel
public void updateRcView(int dim1, int dim2, int dim3)
{
// note: actual indices for components are dim1-1, etc (patch for JAL-1123)
public void updateRcView(int dim1, int dim2, int dim3)
{
// note: actual indices for components are dim1-1, etc (patch for JAL-1123)
- Point[] scores = pasimap.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
+ //&!
+ //Point[] scores = pasimap.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
+ Point[] scores = pasimap.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 1);
- for (int i = 0; i < pasimap.getHeight(); i++)
+ for (int i = 0; i < pasimap.getWidth(); i++)
{
points.get(i).coord = scores[i];
}
{
points.get(i).coord = scores[i];
}