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JAL-1164 scope bySequence analysis methods to start/end of selected region or alignme...
[jalview.git]
/
src
/
jalview
/
ws
/
jws2
/
JabawsAlignCalcWorker.java
diff --git
a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
index
d6a8d18
..
926256d
100644
(file)
--- a/
src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/
src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@
-380,6
+380,8
@@
public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
boolean[] gapMap;
int realw;
boolean[] gapMap;
int realw;
+
+ int start,end;
public List<FastaSequence> getInputSequences(AlignmentI alignment, AnnotatedCollectionI inputSeqs)
{
public List<FastaSequence> getInputSequences(AlignmentI alignment, AnnotatedCollectionI inputSeqs)
{
@@
-405,9
+407,12
@@
public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
seqNames = new HashMap<String, SequenceI>();
}
gapMap = new boolean[0];
seqNames = new HashMap<String, SequenceI>();
}
gapMap = new boolean[0];
+ start=inputSeqs.getStartRes();
+ end=inputSeqs.getEndRes();
+
for (SequenceI sq : (List<SequenceI>) inputSeqs.getSequences())
{
for (SequenceI sq : (List<SequenceI>) inputSeqs.getSequences())
{
- if (sq.getEnd() - sq.getStart() > minlen - 1)
+ if (sq.findPosition(end+1) -sq.findPosition(start+1) > minlen - 1)
{
String newname = SeqsetUtils.unique_name(seqs.size() + 1);
// make new input sequence with or without gaps
{
String newname = SeqsetUtils.unique_name(seqs.size() + 1);
// make new input sequence with or without gaps
@@
-439,7
+444,7
@@
public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
{
seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
{
seqs.add(seq = new compbio.data.sequence.FastaSequence(newname,
AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
- sq.getSequenceAsString())));
+ sq.getSequenceAsString(start,end+1))));
}
if (seq.getSequence().length() > ln)
{
}
if (seq.getSequence().length() > ln)
{