import jalview.datamodel.Point;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
+import jalview.viewmodel.AlignmentViewport;
import java.util.List;
import java.util.Vector;
/*
* inputs
*/
- private AlignmentView inputData;
+ //private AlignmentView inputData;
+ //&!
+ private AlignmentViewport inputData;
private final SequenceI[] seqs;
* @param modelName
* @param params
*/
- public PaSiMapModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+ //public PaSiMapModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+ //&! viewport or panel?
+ public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, boolean nuc,
ScoreModelI modelName, SimilarityParamsI params)
{
inputData = seqData;
ii++;
}
+ int width = pasimap.getWidth();
int height = pasimap.getHeight();
// top = pasimap.getM().height() - 1;
- top = height - 1;
+ //&!
+ //top = height - 1;
+ top = height;
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);
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];
}
return pasimap.getDetails();
}
- public AlignmentView getInputData()
+ //&!
+ //public AlignmentView getInputData()
+ public AlignmentViewport getInputData()
{
return inputData;
}
- public void setInputData(AlignmentView data)
+ //&!
+ //public void setInputData(AlignmentView data)
+ public void setInputData(AlignmentViewport data)
{
inputData = data;
}