Alogirthm working, but still giving slightly off results

diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index 81d44f5..de89953 100755 (executable)
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -35,6 +35,7 @@ import jalview.viewmodel.AlignmentViewport;
 
 
 import java.io.PrintStream;
+import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -216,8 +217,8 @@ System.out.println(see.getName());
       float[][] scores = new float[nSeqs][nSeqs];      // rows, cols
 
       int nSplits = 1;
-      //while ((nSeqs / nSplits) > 300)                // heap full at 341
-      while (((float) nSeqs / nSplits) > 5f)           // heap full at 341
+      while (((float) nSeqs / nSplits) > 300f)         // heap full at 341
+      //while (((float) nSeqs / nSplits) > 5f)         // heap full at 341
        nSplits++;
       int splitSeqs = (int) Math.ceil((float) nSeqs / nSplits);
 System.out.println(String.format("%d -> %d splits into %d seqs", nSeqs, nSplits, splitSeqs));
@@ -245,14 +246,13 @@ pairwiseScores.print(System.out, "%1.4f ");
 
       pairwiseScores = new Matrix(scores);
 pairwiseScores.print(System.out, "%1.4f ");
-/*
+*/
       pairwiseScores.fillDiagonal();
 
       eigenMatrix = pairwiseScores.copy();
 
       ccAnalysis cc = new ccAnalysis(pairwiseScores, dim);
       eigenMatrix = cc.run();
-*/
 
     } catch (Exception q)
     {
@@ -288,7 +288,7 @@ pairwiseScores.print(System.out, "%1.4f ");
     int g = 0; // group count
     for (int[] group : allGroups)
     {
-      HashSet<SequenceI> sg = new HashSet<SequenceI>();
+      ArrayList<SequenceI> sg = new ArrayList<SequenceI>();
       //SequenceGroup sg = new SequenceGroup();
       for (int index : group)
       {
@@ -312,6 +312,7 @@ pairwiseScores.print(System.out, "%1.4f ");
        result.put(new int[]{s1 + g * s, s1 + g * s}, Float.NaN);       // self score = Float.NaN
        for (int s2 = 0; s2 < s1; s2++)                 // col
        {
+System.out.println(String.format("%s x %s -> [%d][%d] (%f)", sgArray[s1].getName(), sgArray[s2].getName(), s1+g*s, s2+g*s, scores[s1][s2]));
          result.put(new int[]{s1 + g * s, s2 + g * s}, scores[s1][s2]);
        }
       }   
@@ -340,16 +341,17 @@ pairwiseScores.print(System.out, "%1.4f ");
     // align each subsplit with subsplits from other split groups
     for (int subsplitN = 0; subsplitN < newGroups.length; subsplitN++)
     {
-      int c = 1;               // current split block
+      int c = 1;               // current subsplit block
       while (newGroups[subsplitN][0] > smallS * c)
       {
        c++;
       }
       for (int nextSplit = subsplitN + 1; nextSplit < newGroups.length; nextSplit++)
       {
-       if (newGroups[nextSplit][0] >= s * c)   // if next subsplit of next split group -> align seqs
+System.out.println(String.format("subsplitN %d, nextSplit %d, %d > %d * %d", subsplitN, nextSplit, allGroups[(int) Math.floor((float) nextSplit / 2)][0], smallS, c));
+       if (allGroups[(int) Math.floor((float) nextSplit / 2)][0] > smallS * c)
        {
-          HashSet<SequenceI> sg = new HashSet<SequenceI>();
+          ArrayList<SequenceI> sg = new ArrayList<SequenceI>();
           //SequenceGroup sg = new SequenceGroup();
           for (int index : newGroups[subsplitN])
           {
@@ -380,6 +382,7 @@ pairwiseScores.print(System.out, "%1.4f ");
            for (int s2 = 0; s2 < s1; s2++)                     // col
            {
              if (s1 >= smallS && s2 < smallS)
+System.out.println(String.format("%s x %s -> [%d][%d] (%f)", sgArray[s1].getName(), sgArray[s2].getName(), s1+(nextSplit-1)*smallS, s2+subsplitN*smallS, scores[s1][s2]));
                result.put(new int[]{s1 + (nextSplit-1) * smallS, s2 + subsplitN * smallS}, scores[s1][s2]);
            }
           }   

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index fc862fe..2379e27 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -139,6 +139,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
         first = false;
         as.printAlignment(System.out);
         scores[i][j] = as.getMaxScore() / as.getASeq1().length;
+System.out.println(String.format("%s x %s -> [%d][%d] (%f)", seqs[i].getName(), seqs[j].getName(), i, j, as.getAlignmentScore()));
         alignmentScores[i][j] = as.getAlignmentScore();
         totscore = totscore + scores[i][j];