From 3a8bdc94ec8366d687d7693a7e71948878c05fa5 Mon Sep 17 00:00:00 2001
From: MorellThomas <morellth@yahoo.co.jp>
Date: Sun, 1 Oct 2023 17:29:13 +0200
Subject: [PATCH] Fix Reset Button for PaSiMap and issue with indelfreeAstr in
 AlignSeq

---
 src/jalview/analysis/AlignSeq.java      |   26 ++++++++------------------
 src/jalview/viewmodel/PaSiMapModel.java |    6 +++---
 2 files changed, 11 insertions(+), 21 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 7165096..fa90f74 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -517,7 +517,6 @@ public class AlignSeq
     seq1end = i + 1;
     seq2end = j + 1;
 
-
     aseq1 = new int[seq1.length + seq2.length];
     aseq2 = new int[seq1.length + seq2.length];
 
@@ -545,7 +544,6 @@ public class AlignSeq
       j--;
     }
 
-
     while (i > 0 && j > 0)
     {
       aseq1[count] = seq1[i];
@@ -579,17 +577,10 @@ public class AlignSeq
     seq1start = i + 1;
     seq2start = j + 1;
 
-    if (aseq1[count] != GAP_INDEX)
-    {
-      aseq1[count] = seq1[i];
-      sb1.append(s1str.charAt(i));
-    }
-
-    if (aseq2[count] != GAP_INDEX)
-    {
-      aseq2[count] = seq2[j];
-      sb2.append(s2str.charAt(j));
-    }
+    aseq1[count] = seq1[i];
+    sb1.append(s1str.charAt(i));
+    aseq2[count] = seq2[j];
+    sb2.append(s2str.charAt(j));
 
     //get initial gaps
     while (j > 0 || i > 0)
@@ -1304,7 +1295,6 @@ public class AlignSeq
   */
   public void meanScore()
   {
-    //int length = (indelfreeAstr1.length() > indelfreeAstr2.length()) ? indelfreeAstr1.length() : indelfreeAstr2.length();
     int length = indelfreeAstr1.length();	//both have the same length
     //create HashMap for counting residues in each sequence
     HashMap<Character, Integer> seq1ResCount = new HashMap<Character, Integer>();
@@ -1392,7 +1382,7 @@ public class AlignSeq
   * if preprescore < 1 ~ alignmentScore = Float.NaN 	>
   * alignmentScore = ((preprescore - meanScore) / (hypotheticMaxScore - meanScore)) * coverage
   */
-  public void scoreAlignment() throws RuntimeException
+  public void scoreAlignment()
   {
 
     getIndelfreeAstr();
@@ -1401,9 +1391,9 @@ public class AlignSeq
     // cannot calculate score because denominator would be zero
     if (this.hypotheticMaxScore == this.meanScore)
     {
-      throw new IllegalArgumentException(String.format("hypotheticMaxScore (%8.2f) == meanScore (%8.2f) - division by 0", hypotheticMaxScore, meanScore));
+      this.alignmentScore = Float.NaN;
+      return;
     }
-    //int n = (astr1.length() > astr2.length()) ? astr1.length() : astr2.length();
     int n = indelfreeAstr1.length();
 
     float score = 0;
@@ -1436,7 +1426,7 @@ public class AlignSeq
     float prescore = score;	// only debug
     score *= coverage;
 
-    System.out.println(String.format("prepre-score: %f, pre-score: %f, longlength: %d\nscore: %1.16f, mean: %f, max: %d", preprescore, prescore, _max[1], score, this.meanScore, this.hypotheticMaxScore));
+    //System.out.println(String.format("prepre-score: %f, pre-score: %f, longlength: %d\nscore: %1.16f, mean: %f, max: %d", preprescore, prescore, _max[1], score, this.meanScore, this.hypotheticMaxScore));
     float minScore = 1f;
     this.alignmentScore = (preprescore < minScore) ? Float.NaN : score;
   }
diff --git a/src/jalview/viewmodel/PaSiMapModel.java b/src/jalview/viewmodel/PaSiMapModel.java
index 4bb6d8a..4cc831a 100644
--- a/src/jalview/viewmodel/PaSiMapModel.java
+++ b/src/jalview/viewmodel/PaSiMapModel.java
@@ -99,12 +99,12 @@ public class PaSiMapModel
 
     int width = pasimap.getWidth();
     int height = pasimap.getHeight();
-    top = height;
+    top = width;
 
     points = new Vector<>();
     Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3, 1);
 
-    for (int i = 0; i < top; i++)
+    for (int i = 0; i < height; i++)
     {
       SequencePoint sp = new SequencePoint(seqs[i], scores[i]);
       points.add(sp);
@@ -156,7 +156,7 @@ public class PaSiMapModel
     // note: actual indices for components are dim1-1, etc (patch for JAL-1123)
     Point[] scores = pasimap.getComponents(dim1 - 1, dim2 - 1, dim3 - 1, 1);
 
-    for (int i = 0; i < pasimap.getWidth(); i++)
+    for (int i = 0; i < pasimap.getHeight(); i++)
     {
       points.get(i).coord = scores[i];
     }
-- 
1.7.10.2