X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=2feeb919a3d7791c74584018f69e26b493371ec0;hb=d8ddf2968124b3518e567a91411357b1d291ff77;hp=5659d19f5267e1e150ad6c6c605563e259d22e7a;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 5659d19..2feeb91 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -27,16 +27,19 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.AlignmentI;
 
 /**
- * grab bag of useful alignment manipulation operations
- * Expect these to be refactored elsewhere at some point.
+ * grab bag of useful alignment manipulation operations Expect these to be
+ * refactored elsewhere at some point.
+ * 
  * @author jimp
- *
+ * 
  */
 public class AlignmentUtils
 {
 
   /**
-   * given an existing alignment, create a new alignment including all, or up to flankSize additional symbols from each sequence's dataset sequence
+   * given an existing alignment, create a new alignment including all, or up to
+   * flankSize additional symbols from each sequence's dataset sequence
+   * 
    * @param core
    * @param flankSize
    * @return AlignmentI
@@ -45,67 +48,79 @@ public class AlignmentUtils
   {
     List<SequenceI> sq = new ArrayList<SequenceI>();
     int maxoffset = 0;
-    for (SequenceI s:core.getSequences())
+    for (SequenceI s : core.getSequences())
     {
       SequenceI newSeq = s.deriveSequence();
-      if (newSeq.getStart()>maxoffset && newSeq.getDatasetSequence().getStart()<s.getStart())
+      if (newSeq.getStart() > maxoffset
+              && newSeq.getDatasetSequence().getStart() < s.getStart())
       {
         maxoffset = newSeq.getStart();
       }
       sq.add(newSeq);
     }
-    if (flankSize>-1) {
+    if (flankSize > -1)
+    {
       maxoffset = flankSize;
     }
     // now add offset to create a new expanded alignment
-    for (SequenceI s:sq)
+    for (SequenceI s : sq)
     {
       SequenceI ds = s;
-      while (ds.getDatasetSequence()!=null) {
-        ds=ds.getDatasetSequence();
+      while (ds.getDatasetSequence() != null)
+      {
+        ds = ds.getDatasetSequence();
       }
-      int s_end = s.findPosition(s.getStart()+s.getLength());
+      int s_end = s.findPosition(s.getStart() + s.getLength());
       // find available flanking residues for sequence
-      int ustream_ds=s.getStart()-ds.getStart(),dstream_ds=ds.getEnd()-s_end;
-      
+      int ustream_ds = s.getStart() - ds.getStart(), dstream_ds = ds
+              .getEnd() - s_end;
+
       // build new flanked sequence
-      
+
       // compute gap padding to start of flanking sequence
-      int offset=maxoffset - ustream_ds;
-      
+      int offset = maxoffset - ustream_ds;
+
       // padding is gapChar x ( maxoffset - min(ustream_ds, flank)
-      if (flankSize>=0) {
-        if (flankSize<ustream_ds)
+      if (flankSize >= 0)
+      {
+        if (flankSize < ustream_ds)
         {
-        // take up to flankSize residues
-        offset = maxoffset-flankSize;
-        ustream_ds = flankSize;
-      }
-        if (flankSize<dstream_ds)
+          // take up to flankSize residues
+          offset = maxoffset - flankSize;
+          ustream_ds = flankSize;
+        }
+        if (flankSize < dstream_ds)
         {
-          dstream_ds=flankSize;
+          dstream_ds = flankSize;
         }
       }
-      char[] upstream = new String(ds.getSequence(s.getStart()-1-ustream_ds, s.getStart()-1)).toLowerCase().toCharArray();
-      char[] downstream = new String(ds.getSequence(s_end-1,s_end+1+dstream_ds)).toLowerCase().toCharArray();
-      char[] coreseq=s.getSequence();
-      char[] nseq = new char[offset+upstream.length+downstream.length+coreseq.length]; 
+      char[] upstream = new String(ds.getSequence(s.getStart() - 1
+              - ustream_ds, s.getStart() - 1)).toLowerCase().toCharArray();
+      char[] downstream = new String(ds.getSequence(s_end - 1, s_end + 1
+              + dstream_ds)).toLowerCase().toCharArray();
+      char[] coreseq = s.getSequence();
+      char[] nseq = new char[offset + upstream.length + downstream.length
+              + coreseq.length];
       char c = core.getGapCharacter();
       // TODO could lowercase the flanking regions
-      int p=0;
-      for (; p<offset;p++)
+      int p = 0;
+      for (; p < offset; p++)
       {
         nseq[p] = c;
       }
-//      s.setSequence(new String(upstream).toLowerCase()+new String(coreseq) + new String(downstream).toLowerCase());
+      // s.setSequence(new String(upstream).toLowerCase()+new String(coreseq) +
+      // new String(downstream).toLowerCase());
       System.arraycopy(upstream, 0, nseq, p, upstream.length);
-      System.arraycopy(coreseq, 0, nseq, p+upstream.length, coreseq.length);
-      System.arraycopy(downstream, 0, nseq, p+coreseq.length+upstream.length, downstream.length);
+      System.arraycopy(coreseq, 0, nseq, p + upstream.length,
+              coreseq.length);
+      System.arraycopy(downstream, 0, nseq, p + coreseq.length
+              + upstream.length, downstream.length);
       s.setSequence(new String(nseq));
-      s.setStart(s.getStart()-ustream_ds);
-      s.setEnd(s_end+downstream.length);
+      s.setStart(s.getStart() - ustream_ds);
+      s.setEnd(s_end + downstream.length);
     }
-    AlignmentI newAl = new jalview.datamodel.Alignment(sq.toArray(new SequenceI[0]));
+    AlignmentI newAl = new jalview.datamodel.Alignment(
+            sq.toArray(new SequenceI[0]));
     newAl.setDataset(core.getDataset());
     return newAl;
   }