From c604058f0c3be7bd38baa8ac01cff87989deecd5 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 8 Oct 2020 15:05:32 +0100
Subject: [PATCH] JAL-3763 always make a new dataset sequence for CDS sequence

---
 src/jalview/analysis/AlignmentUtils.java |   96 +++++++++++++-----------------
 1 file changed, 41 insertions(+), 55 deletions(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 0c40873..9a63eb1 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -20,6 +20,23 @@
  */
 package jalview.analysis;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.NoSuchElementException;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.TreeMap;
+
+import jalview.bin.Cache;
 import jalview.commands.RemoveGapColCommand;
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
@@ -44,22 +61,6 @@ import jalview.util.IntRangeComparator;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.NoSuchElementException;
-import java.util.Set;
-import java.util.SortedMap;
-import java.util.TreeMap;
-
 /**
  * grab bag of useful alignment manipulation operations Expect these to be
  * refactored elsewhere at some point.
@@ -1995,45 +1996,31 @@ public class AlignmentUtils
 
     SequenceI newSeq = null;
 
-    final MapList maplist = mapping.getMap();
-    if (maplist.isContiguous() && maplist.isFromForwardStrand())
-    {
-      /*
-       * just a subsequence, keep same dataset sequence
-       */
-      int start = maplist.getFromLowest();
-      int end = maplist.getFromHighest();
-      newSeq = seq.getSubSequence(start - 1, end);
-      newSeq.setName(seqId);
-    }
-    else
-    {
-      /*
-       * construct by splicing mapped from ranges
-       */
-      char[] seqChars = seq.getSequence();
-      List<int[]> fromRanges = maplist.getFromRanges();
-      int cdsWidth = MappingUtils.getLength(fromRanges);
-      char[] newSeqChars = new char[cdsWidth];
+    /*
+     * construct CDS sequence by splicing mapped from ranges
+     */
+    char[] seqChars = seq.getSequence();
+    List<int[]> fromRanges = mapping.getMap().getFromRanges();
+    int cdsWidth = MappingUtils.getLength(fromRanges);
+    char[] newSeqChars = new char[cdsWidth];
 
-      int newPos = 0;
-      for (int[] range : fromRanges)
+    int newPos = 0;
+    for (int[] range : fromRanges)
+    {
+      if (range[0] <= range[1])
       {
-        if (range[0] <= range[1])
-        {
-          // forward strand mapping - just copy the range
-          int length = range[1] - range[0] + 1;
-          System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
-                  length);
-          newPos += length;
-        }
-        else
+        // forward strand mapping - just copy the range
+        int length = range[1] - range[0] + 1;
+        System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
+                length);
+        newPos += length;
+      }
+      else
+      {
+        // reverse strand mapping - copy and complement one by one
+        for (int i = range[0]; i >= range[1]; i--)
         {
-          // reverse strand mapping - copy and complement one by one
-          for (int i = range[0]; i >= range[1]; i--)
-          {
-            newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
-          }
+          newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
         }
       }
 
@@ -2067,9 +2054,8 @@ public class AlignmentUtils
           }
           else
           {
-            System.err.println(
-                    "JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):"
-                            + mtch.toString());
+            Cache.log.error(
+                    "JAL-2154 regression: warning - found (and ignored) a duplicate CDS sequence:" + mtch.toString());
           }
         }
       }
-- 
1.7.10.2