Inlcude 8 dimensions

diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index 89bfff0..07256a3 100755 (executable)
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -52,7 +52,7 @@ public class PaSiMap implements Runnable
 
   final private SimilarityParamsI similarityParams;
 
-  final private byte dim = 3;
+  final private byte dim = 8;
 
   /*
    * outputs
@@ -215,7 +215,7 @@ public class PaSiMap implements Runnable
       eigenMatrix = pairwiseScores.copy();
 
       ccAnalysis cc = new ccAnalysis(pairwiseScores, dim);
-      eigenMatrix = cc.run();
+      eigenMatrix = cc.run().mirrorCol();
 
     } catch (Exception q)
     {

diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java
index 832bbad..b3b5750 100644 (file)
--- a/src/jalview/gui/PaSiMapPanel.java
+++ b/src/jalview/gui/PaSiMapPanel.java
@@ -91,7 +91,7 @@ public class PaSiMapPanel extends GPaSiMapPanel
   public PaSiMapPanel(AlignmentPanel alignPanel, String modelName,
           SimilarityParamsI params)
   {
-    super(3);  // dim = 3
+    super(8);  // dim = 8
     this.av = alignPanel.av;
     this.ap = alignPanel;
     boolean nucleotide = av.getAlignment().isNucleotide();

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 7870c14..b7d225a 100755 (executable)
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -1415,4 +1415,23 @@ public class Matrix implements MatrixI
     return result;
   }
 
+  /**
+  * mirrors columns of the matrix
+  *
+  * @return
+  */
+  @Override
+  public MatrixI mirrorCol()
+  {
+    double[][] result = new double[rows][cols];
+    for (int i = 0; i < rows; i++)
+    {
+      int k = cols - 1;        // reverse col
+      for (int j = 0; j < cols; j++)
+      {
+       result[i][k--] = this.getValue(i,j);
+      }
+    }
+    return new Matrix(result);
+  }
 }

diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index a42c75c..7faac73 100644 (file)
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.java
@@ -307,4 +307,11 @@ public interface MatrixI
   *    if this.cols and v do not have the same length
   */
   double[] sumProduct(double[] v);
+
+  /**
+  * mirrors the columns of this matrix
+  *
+  * @return
+  */
+  MatrixI mirrorCol();
 }