X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=b0af302d84617ea3dbcefd76267a54e57e39b69f;hb=ecdc8f7020e2fe1b510e03635801528a08480ec8;hp=31fce1581c7b491787b381c1f18b9b1d59798d54;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index 31fce15..b0af302 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,29 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
-import jalview.api.RotatableCanvasI;
+
+import java.util.Vector;
public class PCAModel
{
@@ -34,6 +37,7 @@ public class PCAModel
seqstrings = seqstrings2;
seqs = seqs2;
nucleotide = nucleotide2;
+ score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
}
private volatile PCA pca;
@@ -45,6 +49,11 @@ public class PCAModel
SequenceI[] seqs;
/**
+ * Score matrix used to calculate PC
+ */
+ String score_matrix;
+
+ /**
* use the identity matrix for calculating similarity between sequences.
*/
private boolean nucleotide = false;
@@ -61,7 +70,8 @@ public class PCAModel
public void run()
{
- pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide);
+ pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide,
+ score_matrix);
pca.setJvCalcMode(jvCalcMode);
pca.run();
@@ -223,4 +233,14 @@ public class PCAModel
jvCalcMode = state;
}
+ public String getScore_matrix()
+ {
+ return score_matrix;
+ }
+
+ public void setScore_matrix(String score_matrix)
+ {
+ this.score_matrix = score_matrix;
+ }
+
}