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fix for JAL-1494 tweaked logic to fix NPEs and modify settings for both background...
[jalview.git]
/
src
/
jalview
/
ws
/
DBRefFetcher.java
diff --git
a/src/jalview/ws/DBRefFetcher.java
b/src/jalview/ws/DBRefFetcher.java
index
a156b2c
..
84eba02
100644
(file)
--- a/
src/jalview/ws/DBRefFetcher.java
+++ b/
src/jalview/ws/DBRefFetcher.java
@@
-577,6
+577,7
@@
public class DBRefFetcher implements Runnable
// mappings are made (but content matches retrieved set)
boolean updateRefFrame = sequence.getDBRef() == null
|| sequence.getDBRef().length == 0;
// mappings are made (but content matches retrieved set)
boolean updateRefFrame = sequence.getDBRef() == null
|| sequence.getDBRef().length == 0;
+ // TODO:
// verify sequence against the entry sequence
String nonGapped = AlignSeq.extractGaps("-. ",
// verify sequence against the entry sequence
String nonGapped = AlignSeq.extractGaps("-. ",
@@
-657,11
+658,19
@@
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
- sequence.setStart(absStart);
- sequence.setEnd(absEnd);
+ if (trimDatasetSeqs) {
+ // just fix start/end
+ sequence.setStart(absStart);
+ sequence.setEnd(absEnd);
+ }
// 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++)
{