Correctly working implementation of the PaSiMap pipeline

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

diff --git a/src/jalview/analysis/ccAnalysis.java b/src/jalview/analysis/ccAnalysis.java
index f7d5c58..4922a54 100755 (executable)
--- 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;
        }