From 26816cdcb7617e74fad006d2c675efb298e0d9b1 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 22 Sep 2020 15:09:51 +0100
Subject: [PATCH] =?utf8?q?JAL-3748=20don=E2=80=99t=20trash=20start/end=20on=20?=
 =?utf8?q?SequenceI=20reconstructed=20from=20a=20SeqCigar=20via=20SeqsetUtil?=
 =?utf8?q?s.SeqCharacterUnhash?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 src/jalview/analysis/SeqsetUtils.java |   20 +++++++++++++++++---
 src/jalview/datamodel/SeqCigar.java   |    2 +-
 2 files changed, 18 insertions(+), 4 deletions(-)

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index fdca89d..891e295 100755
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -84,6 +84,20 @@ public class SeqsetUtils
    */
   public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo)
   {
+    return SeqCharacterUnhash(sq, sqinfo, false, false);
+  }
+
+  /**
+   * restore some characteristics for a sequence from its hash
+   * @param sq
+   * @param sqinfo
+   * @param excludeLimits - when true, start/end is left unmodified
+   * @param excludeFeatures - when true, features are not restored from stashed vector
+   * @return true if sequence's name was modified
+   */
+          
+  public static boolean SeqCharacterUnhash(SequenceI sq, Hashtable sqinfo, boolean excludeLimits,boolean excludeFeatures)
+  {
     boolean namePresent = true;
     if (sqinfo == null)
     {
@@ -110,13 +124,13 @@ public class SeqsetUtils
       sq.setPDBId(pdbid);
     }
 
-    if ((start != null) && (end != null))
+    if (!excludeLimits && (start != null) && (end != null))
     {
       sq.setStart(start.intValue());
       sq.setEnd(end.intValue());
     }
-
-    if (sfeatures != null && !sfeatures.isEmpty())
+    // TODO: drop this completely since we should not manipulate sequenceFeatures as a vector any more
+    if (!excludeFeatures && sfeatures != null && !sfeatures.isEmpty())
     {
       sq.setSequenceFeatures(sfeatures);
     }
diff --git a/src/jalview/datamodel/SeqCigar.java b/src/jalview/datamodel/SeqCigar.java
index c282d6e..34697b3 100644
--- a/src/jalview/datamodel/SeqCigar.java
+++ b/src/jalview/datamodel/SeqCigar.java
@@ -587,7 +587,7 @@ public class SeqCigar extends CigarSimple
                       + (bounds[2] == 0 ? -1 : bounds[2]));
       seqs[i].setDatasetSequence(ref);
       seqs[i].setDescription(ref.getDescription());
-      SeqsetUtils.SeqCharacterUnhash(seqs[i],alseqs[i].seqProps);
+      SeqsetUtils.SeqCharacterUnhash(seqs[i],alseqs[i].seqProps,true,true);
     }
     if (segments != null)
     {
-- 
1.7.10.2