JAL-1517 fix copyright for 2.8.2

[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..add8bd5 100644 (file)
--- a/src/jalview/ws/jws2/JabawsCalcWorker.java
+++ b/src/jalview/ws/jws2/JabawsCalcWorker.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ws.jws2;
 
 import java.util.ArrayList;
@@ -23,6 +43,7 @@ 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;
@@ -126,7 +147,7 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
         return;
       }
       List<compbio.data.sequence.FastaSequence> seqs = getInputSequences(alignViewport
-              .getAlignment());
+              .getAlignment(), bySequence ? alignViewport.getSelectionGroup() : null);
   
       if (seqs == null)
       {
@@ -349,19 +370,24 @@ public abstract class JabawsCalcWorker extends AlignCalcWorker
   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
-            // || (alignedSeqs && !alignment.isAligned() && !submitGaps)
             || 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>();
-  
+
     int minlen = 10;
     int ln = -1;
     if (bySequence)
@@ -369,9 +395,13 @@ public abstract class JabawsCalcWorker 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 (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
@@ -403,7 +433,7 @@ public abstract class JabawsCalcWorker 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)
         {