From c9296c060f69f3eeab1f6da2a07dbdb87c946e52 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Wed, 16 Sep 2020 17:33:26 +0100
Subject: [PATCH] =?utf8?q?JAL-3700=20JAL-3748=20AlignedCodonFrame.covers(seq?=
 =?utf8?q?,true)=20to=20verify=20mapping=20matches=20seq=E2=80=99s=20dataset?=
 =?utf8?q?=20sequence=20start/end=20rather=20than=20seq?=
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---
 src/jalview/datamodel/AlignedCodonFrame.java |   26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 6103df5..9fa11cc 100644
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -118,14 +118,36 @@ public class AlignedCodonFrame
      */
     public boolean covers(SequenceI seq)
     {
+      return covers(seq,false);
+    }
+    /**
+     * 
+     * @param seq
+     * @param localCover - when true - compare extent of seq's dataset sequence rather than the local extent 
+     * @return true if mapping covers full length of given sequence 
+     */
+    public boolean covers(SequenceI seq, boolean localCover)
+    {
       List<int[]> mappedRanges = null;
       MapList mapList = mapping.getMap();
+      int mstart=seq.getStart(),mend=seq.getEnd()
+              ;
       if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
       {
+        if (localCover && fromSeq !=seq)
+        {
+          mstart=fromSeq.getStart();
+          mend=fromSeq.getEnd();
+        }
         mappedRanges = mapList.getFromRanges();
       }
       else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
       {
+        if (localCover && mapping.to !=seq)
+        {
+          mstart=mapping.to.getStart();
+          mend=mapping.to.getEnd();
+        }
         mappedRanges = mapList.getToRanges();
       }
       else
@@ -143,14 +165,14 @@ public class AlignedCodonFrame
       {
         int from = Math.min(range[0], range[1]);
         int to = Math.max(range[0], range[1]);
-        if (from < seq.getStart() || to > seq.getEnd())
+        if (from < mstart || to > mend)
         {
           return false;
         }
         length += (to - from + 1);
       }
       // add 1 to mapped length to allow for a mapped stop codon
-      if (length + 1 < (seq.getEnd() - seq.getStart() + 1))
+      if (length + 1 < (mend - mstart + 1))
       {
         return false;
       }
-- 
1.7.10.2