X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=928d35e46ccc5199bf76dfa03a5506c2f9d48d62;hb=c1f777a6a4a74ee1573e5f3f883e0de902818ae7;hp=a9c87872d4962c6e5a16f6656d17a4de318fd0d4;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index a9c8787..928d35e 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,43 +1,37 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.viewmodel;
-import java.util.Vector;
-
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;
-import jalview.api.RotatableCanvasI;
+
+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;
@@ -45,31 +39,42 @@ public class PCAModel
AlignmentView seqstrings;
SequenceI[] seqs;
-
- /**
- * Score matrix used to calculate PC
- */
- String score_matrix;
- /**
- * use the identity matrix for calculating similarity between sequences.
+ /*
+ * Name of score model used to calculate PCA
*/
+ ScoreModelI scoreModel;
+
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
@@ -80,32 +85,23 @@ 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()
@@ -143,9 +139,9 @@ 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];
}
}
@@ -225,19 +221,14 @@ public class PCAModel
return pts;
}
- public void setJvCalcMode(boolean state)
+ public String getScoreModelName()
{
- jvCalcMode = state;
+ return scoreModel == null ? "" : scoreModel.getName();
}
- public String getScore_matrix()
+ public void setScoreModel(ScoreModelI sm)
{
- return score_matrix;
+ this.scoreModel = sm;
}
- public void setScore_matrix(String score_matrix)
- {
- this.score_matrix = score_matrix;
- }
-
}