X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=be138f34da69af87153c5d4c6c5ed9e3a236761b;hb=205bbecbedfa28a3f4b3b4909c4f8be2a96b6579;hp=ab606f7d5194b3e6967d1d9eccad3913f0be05c6;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index ab606f7..be138f3 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -21,7 +21,6 @@
 package jalview.analysis;
 
 import jalview.api.AlignViewportI;
-import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
@@ -50,7 +49,7 @@ import java.util.Map;
 
 public class Dna
 {
-  private static final String STOP_X = "X";
+  private static final String STOP_ASTERIX = "*";
 
   private static final Comparator<AlignedCodon> comparator = new CodonComparator();
 
@@ -209,14 +208,13 @@ public class Dna
     for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
-      DBRefEntry[] dnarefs = DBRefUtils
-              .selectRefs(dna.getDBRef(),
-                      jalview.datamodel.DBRefSource.DNACODINGDBS);
+      DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
+              jalview.datamodel.DBRefSource.DNACODINGDBS);
       if (dnarefs != null)
       {
         // intersect with pep
         List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
-        DBRefEntry[] refs = dna.getDBRef();
+        DBRefEntry[] refs = dna.getDBRefs();
         for (int d = 0; d < refs.length; d++)
         {
           if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
@@ -301,8 +299,7 @@ public class Dna
         aa.graphHeight = annotation.graphHeight;
         if (annotation.getThreshold() != null)
         {
-          aa.setThreshold(new GraphLine(annotation
-                  .getThreshold()));
+          aa.setThreshold(new GraphLine(annotation.getThreshold()));
         }
         if (annotation.hasScore)
         {
@@ -447,8 +444,10 @@ public class Dna
           aa = gapString;
           if (skipint == null)
           {
-            skipint = new int[]
-            { alignedCodon.pos1, alignedCodon.pos3 /* cdp[0], cdp[2] */};
+            skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /*
+                                                                        * cdp[0],
+                                                                        * cdp[2]
+                                                                        */};
           }
           skipint[1] = alignedCodon.pos3; // cdp[2];
         }
@@ -545,7 +544,7 @@ public class Dna
           }
           if (aa.equals("STOP"))
           {
-            aa = STOP_X;
+            aa = STOP_ASTERIX;
           }
           resSize++;
         }
@@ -617,14 +616,7 @@ public class Dna
       if (rf != 0)
       {
         final String errMsg = "trimming contigs for incomplete terminal codon.";
-        if (Cache.log != null)
-        {
-          Cache.log.debug(errMsg);
-        }
-        else
-        {
-          System.err.println(errMsg);
-        }
+        System.err.println(errMsg);
         // map and trim contigs to ORF region
         vc = scontigs.length - 1;
         lastnpos = vismapping.shift(lastnpos); // place npos in context of
@@ -691,8 +683,7 @@ public class Dna
          * range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
          * iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
          */
-        MapList map = new MapList(scontigs, new int[]
-        { 1, resSize }, 3, 1);
+        MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
 
         transferCodedFeatures(selection, newseq, map, null, null);
 
@@ -722,8 +713,7 @@ public class Dna
    * @param proteinSeqs
    * @return
    */
-  protected void insertAAGap(int pos,
-          List<SequenceI> proteinSeqs)
+  protected void insertAAGap(int pos, List<SequenceI> proteinSeqs)
   {
     aaWidth++;
     for (SequenceI seq : proteinSeqs)
@@ -783,7 +773,7 @@ public class Dna
   {
     SequenceFeature[] sfs = dna.getSequenceFeatures();
     Boolean fgstate;
-    DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+    DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
             DBRefSource.DNACODINGDBS);
     if (dnarefs != null)
     {
@@ -816,4 +806,154 @@ public class Dna
       }
     }
   }
+
+  /**
+   * Returns an alignment consisting of the reversed (and optionally
+   * complemented) sequences set in this object's constructor
+   * 
+   * @param complement
+   * @return
+   */
+  public AlignmentI reverseCdna(boolean complement)
+  {
+    int sSize = selection.size();
+    List<SequenceI> reversed = new ArrayList<SequenceI>();
+    for (int s = 0; s < sSize; s++)
+    {
+      SequenceI newseq = reverseSequence(selection.get(s).getName(),
+              seqstring[s], complement);
+
+      if (newseq != null)
+      {
+        reversed.add(newseq);
+      }
+    }
+
+    SequenceI[] newseqs = reversed.toArray(new SequenceI[reversed.size()]);
+    AlignmentI al = new Alignment(newseqs);
+    ((Alignment) al).createDatasetAlignment();
+    return al;
+  }
+
+  /**
+   * Returns a reversed, and optionally complemented, sequence. The new
+   * sequence's name is the original name with "|rev" or "|revcomp" appended.
+   * aAcCgGtT and DNA ambiguity codes are complemented, any other characters are
+   * left unchanged.
+   * 
+   * @param seq
+   * @param complement
+   * @return
+   */
+  public static SequenceI reverseSequence(String seqName, String sequence,
+          boolean complement)
+  {
+    String newName = seqName + "|rev" + (complement ? "comp" : "");
+    char[] originalSequence = sequence.toCharArray();
+    int length = originalSequence.length;
+    char[] reversedSequence = new char[length];
+
+    for (int i = 0; i < length; i++)
+    {
+      reversedSequence[length - i - 1] = complement ? getComplement(originalSequence[i])
+              : originalSequence[i];
+    }
+    SequenceI reversed = new Sequence(newName, reversedSequence, 1, length);
+    return reversed;
+  }
+
+  /**
+   * Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
+   * are treated as on http://reverse-complement.com/. Anything else is left
+   * unchanged.
+   * 
+   * @param c
+   * @return
+   */
+  public static char getComplement(char c)
+  {
+    char result = c;
+    switch (c) {
+    case 'a':
+      result = 't';
+      break;
+    case 'A':
+      result = 'T';
+      break;
+    case 'c':
+      result = 'g';
+      break;
+    case 'C':
+      result = 'G';
+      break;
+    case 'g':
+      result = 'c';
+      break;
+    case 'G':
+      result = 'C';
+      break;
+    case 't':
+      result = 'a';
+      break;
+    case 'T':
+      result = 'A';
+      break;
+    case 'u':
+      result = 'a';
+      break;
+    case 'U':
+      result = 'A';
+      break;
+    case 'r':
+      result = 'y';
+      break;
+    case 'R':
+      result = 'Y';
+      break;
+    case 'y':
+      result = 'r';
+      break;
+    case 'Y':
+      result = 'R';
+      break;
+    case 'k':
+      result = 'm';
+      break;
+    case 'K':
+      result = 'M';
+      break;
+    case 'm':
+      result = 'k';
+      break;
+    case 'M':
+      result = 'K';
+      break;
+    case 'b':
+      result = 'v';
+      break;
+    case 'B':
+      result = 'V';
+      break;
+    case 'v':
+      result = 'b';
+      break;
+    case 'V':
+      result = 'B';
+      break;
+    case 'd':
+      result = 'h';
+      break;
+    case 'D':
+      result = 'H';
+      break;
+    case 'h':
+      result = 'd';
+      break;
+    case 'H':
+      result = 'D';
+      break;
+    }
+
+    return result;
+  }
 }