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JAL-1517 update copyright to version 2.8.2
[jalview.git]
/
src
/
jalview
/
ws
/
DBRefFetcher.java
diff --git
a/src/jalview/ws/DBRefFetcher.java
b/src/jalview/ws/DBRefFetcher.java
index
d742eaa
..
f46779b
100644
(file)
--- a/
src/jalview/ws/DBRefFetcher.java
+++ b/
src/jalview/ws/DBRefFetcher.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
@@
-658,6
+658,11
@@
public class DBRefFetcher implements Runnable
// unknownSequences.remove(sequence);
int absEnd = absStart + nonGapped.length();
absStart += 1;
// unknownSequences.remove(sequence);
int absEnd = absStart + nonGapped.length();
absStart += 1;
+ if (!trimDatasetSeqs) {
+ // insert full length sequence from record
+ sequence.setSequence(entry.getSequenceAsString());
+ sequence.setStart(entry.getStart());
+ }
if (updateRefFrame)
{
// finally, update local sequence reference frame if we're allowed
if (updateRefFrame)
{
// finally, update local sequence reference frame if we're allowed
@@
-665,9
+670,6
@@
public class DBRefFetcher implements Runnable
// just fix start/end
sequence.setStart(absStart);
sequence.setEnd(absEnd);
// just fix start/end
sequence.setStart(absStart);
sequence.setEnd(absEnd);
- } else {
- // insert full length sequence from record
- sequence.setSequence(entry.getSequenceAsString());
}
// search for alignment sequences to update coordinate frame for
for (int alsq = 0; alsq < alseqs.length; alsq++)
}
// search for alignment sequences to update coordinate frame for
for (int alsq = 0; alsq < alseqs.length; alsq++)