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Merge branch 'JAL-1164_disorderforselection' into Release_2_8_1_Branch
[jalview.git]
/
src
/
jalview
/
ws
/
jws2
/
JabawsCalcWorker.java
diff --git
a/src/jalview/ws/jws2/JabawsCalcWorker.java
b/src/jalview/ws/jws2/JabawsCalcWorker.java
index
4a78209
..
8515dbc
100644
(file)
--- a/
src/jalview/ws/jws2/JabawsCalcWorker.java
+++ b/
src/jalview/ws/jws2/JabawsCalcWorker.java
@@
-23,6
+23,7
@@
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
@@
-126,7
+127,7
@@
public abstract class JabawsCalcWorker extends AlignCalcWorker
return;
}
List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(alignViewport
return;
}
List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(alignViewport
- .getAlignment());
+ .getAlignment(), bySequence ? alignViewport.getSelectionGroup() : null);
if (seqs == null)
{
if (seqs == null)
{
@@
-349,19
+350,24
@@
public abstract class JabawsCalcWorker extends AlignCalcWorker
protected Map<String, SequenceI> seqNames;
protected boolean[] gapMap;
int realw;
protected Map<String, SequenceI> seqNames;
protected boolean[] gapMap;
int realw;
+ int start,end;
- public List<FastaSequence> getInputSequences(AlignmentI alignment)
+ public List<FastaSequence> getInputSequences(AlignmentI alignment, AnnotatedCollectionI inputSeqs)
{
if (alignment == null || alignment.getWidth() <= 0
|| alignment.getSequences() == null
{
if (alignment == null || alignment.getWidth() <= 0
|| alignment.getSequences() == null
- // || (alignedSeqs && !alignment.isAligned() && !submitGaps)
|| alignment.isNucleotide() ? !nucleotidesAllowed
: !proteinAllowed)
{
return null;
}
|| alignment.isNucleotide() ? !nucleotidesAllowed
: !proteinAllowed)
{
return null;
}
+ if (inputSeqs==null || inputSeqs.getWidth()<=0 || inputSeqs.getSequences()==null || inputSeqs.getSequences().size()<1)
+ {
+ inputSeqs = alignment;
+ }
+
List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
List<compbio.data.sequence.FastaSequence> seqs = new ArrayList<compbio.data.sequence.FastaSequence>();
-
+
int minlen = 10;
int ln = -1;
if (bySequence)
int minlen = 10;
int ln = -1;
if (bySequence)
@@
-369,9
+375,13
@@
public abstract class JabawsCalcWorker 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>) alignment.getSequences()))
{
for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
{
- if (sq.getEnd() - sq.getStart() > minlen - 1)
+ if (bySequence ? sq.findPosition(end+1) -sq.findPosition(start+1) > minlen - 1 : sq.getEnd() - sq.getStart() > 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
@@
-403,7
+413,7
@@
public abstract class JabawsCalcWorker 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)
{