X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fviewmodel%2FPCAModel.java;h=93831669a3459a3e1d3ee2e4374502af4bd70b50;hb=c6e8e8ccd10f21698226ae37196cd9680e6804a0;hp=cb6deed5c05aa0b3e2493ccf31b9311a77ee9bc6;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/viewmodel/PCAModel.java b/src/jalview/viewmodel/PCAModel.java
index cb6deed..9383166 100644
--- a/src/jalview/viewmodel/PCAModel.java
+++ b/src/jalview/viewmodel/PCAModel.java
@@ -1,30 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequencePoint;
-import jalview.api.RotatableCanvasI;
+
+import java.util.Vector;
public class PCAModel
{
@@ -35,7 +37,7 @@ public class PCAModel
seqstrings = seqstrings2;
seqs = seqs2;
nucleotide = nucleotide2;
- score_matrix = nucleotide2 ? "PID" : "BLOSUM62";
+ score_matrix = nucleotide2 ? "DNA" : "BLOSUM62";
}
private volatile PCA pca;
@@ -45,7 +47,7 @@ public class PCAModel
AlignmentView seqstrings;
SequenceI[] seqs;
-
+
/**
* Score matrix used to calculate PC
*/
@@ -68,7 +70,8 @@ public class PCAModel
public void run()
{
- pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide, score_matrix);
+ pca = new PCA(seqstrings.getSequenceStrings(' '), nucleotide,
+ score_matrix);
pca.setJvCalcMode(jvCalcMode);
pca.run();
@@ -145,7 +148,7 @@ public class PCAModel
for (int i = 0; i < pca.getM().rows; i++)
{
- ((SequencePoint) points.elementAt(i)).coord = scores[i];
+ points.elementAt(i).coord = scores[i];
}
}
@@ -239,5 +242,5 @@ public class PCAModel
{
this.score_matrix = score_matrix;
}
-
+
}