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 55d32f5..926256d 100644 (file)
--- a/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsAlignCalcWorker.java
@@ -23,6 +23,7 @@ import jalview.api.AlignViewportI;
 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;
@@ -149,7 +150,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         return;
       }
       List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(alignViewport
-              .getAlignment());
+              .getAlignment(), bySequence ? alignViewport.getSelectionGroup() : null);
 
       if (seqs == null)
       {
@@ -176,7 +177,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         } catch (WrongParameterException x)
         {
           throw new JobSubmissionException(
-                  "Invalid paremeter set. Check Jalview implementation.", x);
+                  "Invalid parameter set. Check Jalview implementation.", x);
 
         }
       }
@@ -201,7 +202,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
             }
             else
             {
-              System.err.println("FAILED TO CANCELL AACon job: " + rslt);
+              System.err.println("FAILED TO CANCEL AACon job: " + rslt);
             }
 
           } catch (Exception x)
@@ -379,8 +380,10 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
   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
@@ -390,6 +393,11 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
     {
       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>();
 
     int minlen = 10;
@@ -399,9 +407,12 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
       seqNames = new HashMap<String, SequenceI>();
     }
     gapMap = new boolean[0];
-    for (SequenceI sq : ((List<SequenceI>) alignment.getSequences()))
+    start=inputSeqs.getStartRes();
+    end=inputSeqs.getEndRes();
+    
+    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
@@ -433,7 +444,7 @@ public abstract class JabawsAlignCalcWorker extends AlignCalcWorker
         {
           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)
         {