inlcude progress

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 1b5dab4..bcb7bd5 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -145,6 +145,11 @@ public class AlignSeq
    * @param type
    *          molecule type, either AlignSeq.PEP or AlignSeq.DNA
    */
+  public AlignSeq(int opencost, int extcost)
+  {
+    GAP_OPEN_COST = opencost;
+    GAP_EXTEND_COST = extcost;
+  }
   public AlignSeq(SequenceI s1, SequenceI s2, String type)
   {
     seqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(),
@@ -1459,4 +1464,38 @@ public class AlignSeq
     float minScore = 0f;
     this.alignmentScore = (score <= minScore) ? Float.NaN : score;
   }
+
+  public void clear()
+  {
+    score = null;
+    alignmentScore = 0f;
+    E = null;
+    F = null;
+    traceback = null; // todo is this actually used?
+    seq1 = null;
+    seq2 = null;
+    s1 = null;
+    s2 = null;
+    s1str = null;
+    s2str = null;
+    maxi = 0;
+    maxj = 0;
+    aseq1 = null;
+    aseq2 = null;
+    astr1 = "";
+    astr2 = "";
+    indelfreeAstr1 = "";
+    indelfreeAstr2 = "";
+    seq1start = 0;
+    seq1end = 0;
+    seq2start = 0;
+    seq2end = 0;
+    count = 0;
+    maxscore = 0f;
+    meanScore = 0f;    //needed for PaSiMap
+    hypotheticMaxScore = 0;    // needed for PaSiMap
+    prev = 0;
+    StringBuffer output = new StringBuffer();
+    String type = null; // AlignSeq.PEP or AlignSeq.DNA
+  }
 }

diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java
index de89953..8e8d423 100755 (executable)
--- a/src/jalview/analysis/PaSiMap.java
+++ b/src/jalview/analysis/PaSiMap.java
@@ -31,9 +31,9 @@ import jalview.gui.PairwiseAlignPanel;
 import jalview.gui.PaSiMapPanel;
 import jalview.math.Matrix;
 import jalview.math.MatrixI;
+import jalview.math.MiscMath;
 import jalview.viewmodel.AlignmentViewport;
 
-
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.Hashtable;
@@ -58,6 +58,17 @@ public class PaSiMap implements Runnable
 
   final private byte dim = 3;
 
+  final private int openCost = 100;
+
+  final private int extendCost = 5;
+
+  /*
+  * other
+  */
+  private long total;  // total number of combinations
+
+  private long count;  // current iteration number
+
   /*
    * outputs
    */
@@ -81,6 +92,9 @@ public class PaSiMap implements Runnable
     this.seqs = sequences;
     this.scoreModel = sm;
     this.similarityParams = options;
+    int nseqs = seqs.getAlignment().getHeight();
+    this.total = (long) MiscMath.permutations(nseqs, 2) / 2;   // n!/(n-r)!
+    this.count = 0l;
   }
 
   /**
@@ -213,11 +227,12 @@ for (SequenceI see : seqs.getAlignment().getSequencesArray())
 System.out.println(see.getName());
 }
 
+/*
       int nSeqs = seqs.getAlignment().getHeight();
       float[][] scores = new float[nSeqs][nSeqs];      // rows, cols
 
       int nSplits = 1;
-      while (((float) nSeqs / nSplits) > 300f)         // heap full at 341
+      while (((float) nSeqs / nSplits) > 20f)          // heap full at 341
       //while (((float) nSeqs / nSplits) > 5f)         // heap full at 341
        nSplits++;
       int splitSeqs = (int) Math.ceil((float) nSeqs / nSplits);
@@ -237,8 +252,8 @@ System.out.println(String.format("%d -> %d splits into %d seqs", nSeqs, nSplits,
       }
 pairwiseScores = new Matrix(scores);
 pairwiseScores.print(System.out, "%1.4f ");
+*/
 
-/*
       alignment = new PairwiseAlignPanel(seqs, true, 100, 5);
       float[][] scores = alignment.getAlignmentScores();       //bigger index first -- eg scores[14][13]
 
@@ -246,7 +261,6 @@ pairwiseScores.print(System.out, "%1.4f ");
 
       pairwiseScores = new Matrix(scores);
 pairwiseScores.print(System.out, "%1.4f ");
-*/
       pairwiseScores.fillDiagonal();
 
       eigenMatrix = pairwiseScores.copy();
@@ -341,6 +355,7 @@ System.out.println(String.format("%s x %s -> [%d][%d] (%f)", sgArray[s1].getName
     // align each subsplit with subsplits from other split groups
     for (int subsplitN = 0; subsplitN < newGroups.length; subsplitN++)
     {
+System.gc();
       int c = 1;               // current subsplit block
       while (newGroups[subsplitN][0] > smallS * c)
       {
@@ -377,6 +392,7 @@ System.out.println(String.format("subsplitN %d, nextSplit %d, %d > %d * %d", sub
           //PairwiseAlignPanel pap = new PairwiseAlignPanel(seqs, true, 100, 5);
           //float[][] scores = pap.getAlignmentScores();       //bigger index first -- eg scores[14][13]
           float[][] scores = simulateAlignment(sgArray);
+System.gc();
           for (int s1 = 0; s1 < scores.length; s1++)   // row
           {
            for (int s2 = 0; s2 < s1; s2++)                     // col
@@ -410,12 +426,17 @@ System.out.println(String.format("%s x %s -> [%d][%d] (%f)", sgArray[s1].getName
        seqStrings[0] = seqs[i].getSequenceAsString();
        seqStrings[1] = seqs[j].getSequenceAsString();
 
-       AlignSeq as = new AlignSeq(seqs[i], seqStrings[0], seqs[j], seqStrings[1], AlignSeq.PEP);
+       AlignSeq as = new AlignSeq(seqs[i], seqStrings[0], seqs[j], seqStrings[1], AlignSeq.PEP, openCost, extendCost);
+       as.seqInit(seqs[i], seqStrings[0], seqs[j], seqStrings[1], AlignSeq.PEP);
        as.calcScoreMatrix();
        as.traceAlignmentWithEndGaps();
        as.scoreAlignment();
-       as.printAlignment(System.out);
+       //as.printAlignment(System.out);
        result[i][j] = as.getAlignmentScore();
+       //as.clear();
+
+System.out.println(String.format("%d / %d (%3.2f)", count, total, (float) ((count / total) * 100)));
+       count++;
       }
     }
     return result;

diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java
index 2379e27..ced9cb9 100755 (executable)
--- a/src/jalview/gui/PairwiseAlignPanel.java
+++ b/src/jalview/gui/PairwiseAlignPanel.java
@@ -28,6 +28,7 @@ import jalview.datamodel.SequenceI;
 import jalview.jbgui.GPairwiseAlignPanel;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.math.MiscMath;
 
 import java.awt.event.ActionEvent;
 import java.util.Vector;
@@ -51,6 +52,10 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
   private int GAP_EXTEND_COST;
 
+  //&!
+  private long total = 0l;
+  private long ccount = 0l;
+
   AlignmentViewport av;
 
   Vector<SequenceI> sequences;
@@ -105,6 +110,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
     int count = seqs.length;
     boolean first = true;
     //AlignSeq as = new AlignSeq(seqs[1], seqStrings[1], seqs[0], seqStrings[0], type, gapOpenCost, gapExtendCost);
+//&!
+this.total = (long) MiscMath.permutations(count,2) / 2;
 
     for (int i = 1; i < count; i++)
     {
@@ -116,6 +123,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
                 seqStrings[j], type, gapOpenCost, gapExtendCost);
 //     as.seqInit(seqs[i], seqStrings[i], seqs[j], seqStrings[j], type);
 
+System.out.println(String.format("%d / %d", ccount, total));
+this.ccount++;
         if (as.s1str.length() == 0 || as.s2str.length() == 0)
         {
           continue;
@@ -132,14 +141,14 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel
 
         if (!first)
         {
-          System.out.println(DASHES);
+          //System.out.println(DASHES);
           textarea.append(DASHES);
          sb.append(DASHES);
         }
         first = false;
-        as.printAlignment(System.out);
+        //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()));
+//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];
 

diff --git a/src/jalview/math/MiscMath.java b/src/jalview/math/MiscMath.java
index d3cec30..7593cb0 100755 (executable)
--- a/src/jalview/math/MiscMath.java
+++ b/src/jalview/math/MiscMath.java
@@ -324,4 +324,25 @@ public class MiscMath
     return cnt;
   }
 
+  /**
+  * recursively calculates the permutations of total n items with r items per combination
+  * according to n!/(n-r)! by only multiplying the relevant terms
+  * @param n 
+  * @param r
+  *
+  * @return permutations
+  */
+  public static long permutations(int n, int r)
+  {
+    if (n < r)
+      return permutations(r, n);
+
+    long result = 1l;
+    for (int i = 0; i < r; i++)
+    {
+      result *= (n-i);
+    }
+    return result;
+  }
+
 }