From 8afad69b0e7f4b0bb854279fc62b578acbec439e Mon Sep 17 00:00:00 2001
From: MorellThomas <morellth@yahoo.co.jp>
Date: Sat, 16 Sep 2023 13:41:56 +0200
Subject: [PATCH] Correctly working implementation of the PaSiMap pipeline

---
 src/jalview/analysis/PaSiMap.java    |   20 +++-----------------
 src/jalview/analysis/ccAnalysis.java |   13 +++++++------
 2 files changed, 10 insertions(+), 23 deletions(-)

diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index 4235779..13bc3d2 100755
--- 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)
diff --git a/src/jalview/analysis/ccAnalysis.java b/src/jalview/analysis/ccAnalysis.java
index f7d5c58..4922a54 100755
--- a/src/jalview/analysis/ccAnalysis.java
+++ b/src/jalview/analysis/ccAnalysis.java
@@ -337,6 +337,7 @@ public class ccAnalysis
     System.out.println();
     System.out.println("uncorrected eigenvalues");
     eigenMatrix.printD(System.out, "%2.4f ");
+    System.out.println();
 
     double[] eigenVals = eigenMatrix.getD();
 
@@ -445,7 +446,7 @@ public class ccAnalysis
       q.printStackTrace();
     }
     System.out.println("final coordinates:");
-    repMatrix.print(System.out, "%8.2f");
+    repMatrix.print(System.out, "%1.8f ");
     return repMatrix;
   }
 
@@ -744,13 +745,13 @@ public class ccAnalysis
     double alpha = 0.0;		// "Levenberg-Marquardt" parameter
 
     double gNorm = 0;
-    byte terminationStatus = 0;
+    boolean terminationStatus = false;
     int iteration = 0;
 
     while (true)
     {
       gNorm = MiscMath.norm(g);
-      if (terminationStatus != 0 || nfev == maxNfev)
+      if (terminationStatus || nfev == maxNfev)
       {
 	break;
       }
@@ -796,9 +797,9 @@ public class ccAnalysis
 
         // default ftol and xtol = 1e-8
         boolean ftolSatisfied = actualReduction < (1e-8 * cost) && ratio > 0.25;
-        boolean xtolSatisfied = stepHnorm < (1e-8 * (1e-8 + xNorm));
-	terminationStatus = (ftolSatisfied || xtolSatisfied) ? (byte) 1 : (byte) 0;
-	if (terminationStatus != 0)
+        boolean xtolSatisfied = stepHnorm < (1e-8 * (1e-8 + MiscMath.norm(hA)));
+	terminationStatus = ftolSatisfied || xtolSatisfied;
+	if (terminationStatus)
 	{
 	  break;
 	}
-- 
1.7.10.2