X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=5e7fca26507662e2235e774754c6abc8241ff9e9;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=54a492569236b5c1e2e62c5c4b2b8429d033e9ed;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java index 54a4925..5e7fca2 100644 --- a/src/jalview/viewmodel/PCAModel.java +++ b/src/jalview/viewmodel/PCAModel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -22,6 +22,8 @@ package jalview.viewmodel; 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; @@ -30,16 +32,6 @@ import java.util.Vector; 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; @@ -48,31 +40,40 @@ public class PCAModel 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 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 @@ -83,32 +84,23 @@ public class PCAModel ii++; } - double[][] comps = new double[ii][ii]; - - for (int i = 0; i < ii; i++) - { - if (pca.getEigenvalue(i) > 1e-4) - { - comps[i] = pca.component(i); - } - } - - top = pca.getM().rows - 1; + int height = pca.getHeight(); + // top = pca.getM().height() - 1; + top = height - 1; points = new Vector(); float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100); - for (int i = 0; i < pca.getM().rows; 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().rows); + rc.setPoints(points, pca.getHeight()); } public boolean isNucleotide() @@ -146,9 +138,9 @@ public class PCAModel // 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().rows; i++) + for (int i = 0; i < pca.getHeight(); i++) { - ((SequencePoint) points.elementAt(i)).coord = scores[i]; + points.elementAt(i).coord = scores[i]; } } @@ -228,19 +220,14 @@ public class PCAModel 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; } }