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
{
- /*
- * Jalview 2.10.1 treated gaps as X (peptide) or N (nucleotide)
- * for pairwise scoring; 2.10.2 uses gap score (last column) in
- * score matrix (JAL-2397)
- * Set this flag to true (via Groovy) for 2.10.1 behaviour
- */
- private static boolean scoreGapAsAny = false;
-
- public PCAModel(AlignmentView seqstrings2, SequenceI[] seqs2,
- boolean nucleotide2)
- {
- seqstrings = seqstrings2;
- seqs = seqs2;
- nucleotide = nucleotide2;
- score_matrix = nucleotide2 ? "DNA" : "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()
{
- char gapChar = scoreGapAsAny ? (nucleotide ? 'N' : 'X') : ' ';
- String[] sequenceStrings = seqstrings.getSequenceStrings(gapChar);
- pca = new PCA(sequenceStrings, nucleotide,
- score_matrix);
- pca.setJvCalcMode(jvCalcMode);
+ pca = new PCA(seqstrings, scoreModel, similarityParams);
pca.run();
// Now find the component coordinates
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;
}
}