merge

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 7dec4ec..f9d4c08 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -20,19 +20,6 @@
  */
 package jalview.analysis;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.TreeMap;
-
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
@@ -51,6 +38,20 @@ import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeMap;
+
 /**
  * grab bag of useful alignment manipulation operations Expect these to be
  * refactored elsewhere at some point.
@@ -76,18 +77,22 @@ public class AlignmentUtils
     for (SequenceI s : core.getSequences())
     {
       SequenceI newSeq = s.deriveSequence();
-      if (newSeq.getStart() > maxoffset
+      final int newSeqStart = newSeq.getStart() - 1;
+      if (newSeqStart > maxoffset
               && newSeq.getDatasetSequence().getStart() < s.getStart())
       {
-        maxoffset = newSeq.getStart();
+        maxoffset = newSeqStart;
       }
       sq.add(newSeq);
     }
     if (flankSize > -1)
     {
-      maxoffset = flankSize;
+      maxoffset = Math.min(maxoffset, flankSize);
     }
-    // now add offset to create a new expanded alignment
+
+    /*
+     * now add offset left and right to create an expanded alignment
+     */
     for (SequenceI s : sq)
     {
       SequenceI ds = s;
@@ -97,8 +102,8 @@ public class AlignmentUtils
       }
       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();
+      int dstream_ds = ds.getEnd() - s_end;
 
       // build new flanked sequence
 
@@ -114,27 +119,27 @@ public class AlignmentUtils
           offset = maxoffset - flankSize;
           ustream_ds = flankSize;
         }
-        if (flankSize < dstream_ds)
+        if (flankSize <= dstream_ds)
         {
-          dstream_ds = flankSize;
+          dstream_ds = flankSize - 1;
         }
       }
+      // TODO use Character.toLowerCase to avoid creating String objects?
       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
+      char[] downstream = new String(ds.getSequence(s_end - 1, s_end
               + 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++)
       {
         nseq[p] = c;
       }
-      // 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);
@@ -152,6 +157,7 @@ public class AlignmentUtils
       {
         for (AlignmentAnnotation aa : s.getAnnotation())
         {
+          aa.adjustForAlignment(); // JAL-1712 fix
           newAl.addAnnotation(aa);
         }
       }
@@ -442,6 +448,11 @@ public class AlignmentUtils
   protected static boolean translatesAs(char[] cdnaSeqChars, int cdnaStart,
           char[] aaSeqChars)
   {
+    if (cdnaSeqChars == null || aaSeqChars == null)
+    {
+      return false;
+    }
+
     int aaResidue = 0;
     for (int i = cdnaStart; i < cdnaSeqChars.length - 2
             && aaResidue < aaSeqChars.length; i += 3, aaResidue++)
@@ -856,7 +867,7 @@ public class AlignmentUtils
           {
             mapping.markMappedRegion(seq, pos, sr);
           }
-          newseq.append(sr.toString());
+          newseq.append(sr.getCharacters());
           if (first)
           {
             first = false;
@@ -1010,6 +1021,11 @@ public class AlignmentUtils
    */
   public static boolean isMappable(AlignmentI al1, AlignmentI al2)
   {
+    if (al1 == null || al2 == null)
+    {
+      return false;
+    }
+
     /*
      * Require one nucleotide and one protein
      */
@@ -1042,9 +1058,15 @@ public class AlignmentUtils
    * @param mappings
    * @return
    */
-  public static boolean isMappable(SequenceI dnaSeq, SequenceI proteinSeq,
+  protected static boolean isMappable(SequenceI dnaSeq,
+          SequenceI proteinSeq,
           Set<AlignedCodonFrame> mappings)
   {
+    if (dnaSeq == null || proteinSeq == null)
+    {
+      return false;
+    }
+
     SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq.getDatasetSequence();
     SequenceI proteinDs = proteinSeq.getDatasetSequence() == null ? proteinSeq
             : proteinSeq.getDatasetSequence();
@@ -1235,7 +1257,7 @@ public class AlignmentUtils
 
   /**
    * Returns true if seq1 has a cross-reference to seq2. Currently this assumes
-   * that sequence name is structured as Source|AccessId.
+   * that sequence name is structured as Source|AccessionId.
    * 
    * @param seq1
    * @param seq2
@@ -1278,7 +1300,7 @@ public class AlignmentUtils
   public static AlignmentI makeExonAlignment(SequenceI[] dna,
           Set<AlignedCodonFrame> mappings)
   {
-    Set<AlignedCodonFrame> newMappings = new HashSet<AlignedCodonFrame>();
+    Set<AlignedCodonFrame> newMappings = new LinkedHashSet<AlignedCodonFrame>();
     List<SequenceI> exonSequences = new ArrayList<SequenceI>();
     
     for (SequenceI dnaSeq : dna)
@@ -1346,8 +1368,8 @@ public class AlignmentUtils
       /*
        * Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
        */
-      List<int[]> exonRanges = seqMapping.getMap().getFromRanges();
-      for (int[] range : exonRanges)
+      final List<int[]> dnaExonRanges = seqMapping.getMap().getFromRanges();
+      for (int[] range : dnaExonRanges)
       {
         for (int pos = range[0]; pos <= range[1]; pos++)
         {
@@ -1389,6 +1411,8 @@ public class AlignmentUtils
               .getToRanges(),
               3, 1);
       newMapping.addMap(exon.getDatasetSequence(), seqMapping.getTo(), map);
+      MapList cdsToDnaMap = new MapList(dnaExonRanges, exonRange, 1, 1);
+      newMapping.addMap(dnaSeq, exon.getDatasetSequence(), cdsToDnaMap);
 
       exonSequences.add(exon);
     }