import jalview.analysis.PCA;
import jalview.api.RotatableCanvasI;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
public class PCAModel
{
-
- public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
- boolean nucleotide2)
- {
- seqstrings = seqstrings2;
- seqs = seqs2;
- nucleotide = nucleotide2;
- score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
- }
-
private volatile PCA pca;
int top;
SequenceI[] seqs;
- /**
- * Score matrix used to calculate PC
+ /*
+ * Name of score model used to calculate PCA
*/
- String score_matrix;
+ ScoreModelI scoreModel;
- /**
- * use the identity matrix for calculating similarity between sequences.
- */
private boolean nucleotide = false;
private Vector<SequencePoint> points;
- private boolean jvCalcMode = true;
+ private SimilarityParamsI similarityParams;
- public boolean isJvCalcMode()
+ /**
+ * Constructor given sequence data, score model and score calculation
+ * parameter options.
+ *
+ * @param seqData
+ * @param sqs
+ * @param nuc
+ * @param modelName
+ * @param params
+ */
+ public PCAModel(AlignmentView seqData, SequenceI[] sqs, boolean nuc,
+ ScoreModelI modelName, SimilarityParamsI params)
{
- return jvCalcMode;
+ seqstrings = seqData;
+ seqs = sqs;
+ nucleotide = nuc;
+ scoreModel = modelName;
+ similarityParams = params;
}
public void run()
{
- pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide,
- score_matrix);
- pca.setJvCalcMode(jvCalcMode);
+ pca = new PCA(seqstrings, scoreModel, similarityParams);
pca.run();
// Now find the component coordinates
ii++;
}
- top = pca.getM().height() - 1;
+ int height = pca.getHeight();
+ // top = pca.getM().height() - 1;
+ top = height - 1;
points = new Vector<SequencePoint>();
float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100);
- for (int i = 0; i < pca.getM().height(); i++)
+ for (int i = 0; i < height; i++)
{
SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
points.addElement(sp);
public void updateRc(RotatableCanvasI rc)
{
- rc.setPoints(points, pca.getM().height());
+ rc.setPoints(points, pca.getHeight());
}
public boolean isNucleotide()
// note: actual indices for components are dim1-1, etc (patch for JAL-1123)
float[][] scores = pca.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 100);
- for (int i = 0; i < pca.getM().height(); i++)
+ for (int i = 0; i < pca.getHeight(); i++)
{
points.elementAt(i).coord = scores[i];
}
return pts;
}
- public void setJvCalcMode(boolean state)
- {
- jvCalcMode = state;
- }
-
- public String getScore_matrix()
+ public String getScoreModelName()
{
- return score_matrix;
+ return scoreModel == null ? "" : scoreModel.getName();
}
- public void setScore_matrix(String score_matrix)
+ public void setScoreModel(ScoreModelI sm)
{
- this.score_matrix = score_matrix;
+ this.scoreModel = sm;
}
}