From a1f00ef5e877d63fe0463710baecfc458dc0907c Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Fri, 15 Dec 2023 13:56:07 +0000
Subject: [PATCH] JAL-4366 compute coverage on each side of the pairwise
 alignment

---
 src/jalview/analysis/AlignSeq.java |   37 +++++++++++++++++++++++++++++++++---
 1 file changed, 34 insertions(+), 3 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 36d2482..75ccdfc 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -93,6 +93,11 @@ public class AlignSeq
   int[] aseq1;
 
   int[] aseq2;
+  
+  /*
+   * matches in alignment
+   */
+  int match=-1;
 
   public String astr1 = "";
 
@@ -281,6 +286,30 @@ public class AlignSeq
             s2.getDatasetSequence() == null ? s2 : s2.getDatasetSequence());
     return alSeq2;
   }
+  /**
+   * fraction of seq2 matched in the alignment
+   * @return NaN or [0..1]
+   */
+  public double getS2Coverage()
+  {
+    if (match>=0)
+    {
+      return ((double)match)/((double)s2.getEnd()-s2.getStart()+1);
+    }
+    return Double.NaN;
+  }
+  /**
+   * fraction of seq1 matched in the alignment
+   * @return NaN or [0..1]
+   */
+  public double getS1Coverage()
+  {
+    if (match>=0)
+    {
+      return ((double)match)/((double)s1.getEnd()-s1.getStart()+1);
+    }
+    return Double.NaN;
+  }
 
   /**
    * Construct score matrix for sequences with standard DNA or PEPTIDE matrix
@@ -390,7 +419,7 @@ public class AlignSeq
 
     aseq1 = new int[seq1.length + seq2.length];
     aseq2 = new int[seq1.length + seq2.length];
-
+    match=0;
     StringBuilder sb1 = new StringBuilder(aseq1.length);
     StringBuilder sb2 = new StringBuilder(aseq2.length);
 
@@ -402,11 +431,11 @@ public class AlignSeq
       sb1.append(s1str.charAt(i));
       aseq2[count] = seq2[j];
       sb2.append(s2str.charAt(j));
-
       trace = findTrace(i, j);
 
       if (trace == 0)
       {
+        match++;
         i--;
         j--;
       }
@@ -439,8 +468,10 @@ public class AlignSeq
     {
       aseq2[count] = seq2[j];
       sb2.append(s2str.charAt(j));
+      if (aseq1[count]!=GAP_INDEX) {
+        match++;
+      }
     }
-
     /*
      * we built the character strings backwards, so now
      * reverse them to convert to sequence strings
-- 
1.7.10.2