Correctly working implementation of the PaSiMap pipeline

[jalview.git] / src / jalview / analysis / PaSiMap.java

diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index 4235779..13bc3d2 100755 (executable)
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -114,12 +114,6 @@ public class PaSiMap implements Runnable
       float z = (float) component(i, mm) * factor;
       out[i] = new Point(x, y, z);
     }
-    //&!
-    System.out.println("Points:");
-    for (Point point : out)
-    {
-      System.out.println(point.toString());
-    }
 
     return out;
   }
@@ -174,16 +168,10 @@ public class PaSiMap implements Runnable
     PrintStream ps = wrapOutputBuffer(sb);
 
     /*
-     * pairwise similarity scores
-     */
-    sb.append(" --- OrigT * Orig ---- \n");
-    pairwiseScores.print(ps, "%8.2f");
-
-    /*
-     * eigenvalues matrix, with D vector
+     * coordinates matrix, with D vector
      */
-    sb.append(" --- New diagonalization matrix ---\n");
-    eigenMatrix.print(ps, "%8.2f");
+    sb.append(" --- Coordinates ---\n");
+    eigenMatrix.print(ps, "%8.6f ");
     sb.append(" --- Eigenvalues ---\n");
     eigenMatrix.printD(ps, "%15.4e");
     ps.println();
@@ -219,10 +207,8 @@ public class PaSiMap implements Runnable
       ccAnalysis cc = new ccAnalysis(pairwiseScores, dim);
       pairwiseScores = cc.run();
 
-      /** perform the eigendecomposition for the plot */
       eigenMatrix = pairwiseScores.copy();
       eigenMatrix.setD(pairwiseScores.getD());
-      System.out.println(getDetails());
       
 
     } catch (Exception q)