X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=a10b037faaf1ba34497a33d318d1229c0565fcdd;hb=99830f5e58e49c6839c777b23aa6df200318064b;hp=f8bb9f929f497a61b34687b2ea7df726cb60a927;hpb=d579f105e3feca4b77ac93c52bb45f8cc39c39cd;p=jalview.git

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index f8bb9f9..a10b037 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -45,7 +45,6 @@ import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Comparator;
 import java.util.List;
-import java.util.Map;
 
 public class Dna
 {
@@ -69,7 +68,7 @@ public class Dna
 
   final private int dnaWidth;
 
-  final private Alignment dataset;
+  final private AlignmentI dataset;
 
   /*
    * Working variables for the translation.
@@ -134,7 +133,8 @@ public class Dna
    * @param ac2
    * @return
    */
-  private static int jalview_2_8_2compare(AlignedCodon ac1, AlignedCodon ac2)
+  private static int jalview_2_8_2compare(AlignedCodon ac1,
+          AlignedCodon ac2)
   {
     if (ac1 == null || ac2 == null || (ac1.equals(ac2)))
     {
@@ -208,13 +208,13 @@ public class Dna
     for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
-      DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+      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
@@ -435,7 +435,8 @@ public class Dna
         /*
          * Filled up a reading frame...
          */
-        AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
+        AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
+                cdp[2]);
         String aa = ResidueProperties.codonTranslate(new String(codon));
         rf = 0;
         final String gapString = String.valueOf(gapChar);
@@ -444,10 +445,11 @@ 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];
         }
@@ -502,8 +504,8 @@ public class Dna
                       }
                       if (vc + 2 < t.length)
                       {
-                        System.arraycopy(scontigs, vc + 2, t, vc, t.length
-                                - vc + 2);
+                        System.arraycopy(scontigs, vc + 2, t, vc,
+                                t.length - vc + 2);
                       }
                       scontigs = t;
                     }
@@ -596,9 +598,9 @@ public class Dna
         }
         else if (!alignedCodons[aspos].equals(alignedCodon))
         {
-          throw new IllegalStateException("Tried to coalign "
-                  + alignedCodons[aspos].toString() + " with "
-                  + alignedCodon.toString());
+          throw new IllegalStateException(
+                  "Tried to coalign " + alignedCodons[aspos].toString()
+                          + " with " + alignedCodon.toString());
         }
         if (aspos >= aaWidth)
         {
@@ -685,7 +687,7 @@ public class Dna
          */
         MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
 
-        transferCodedFeatures(selection, newseq, map, null, null);
+        transferCodedFeatures(selection, newseq, map);
 
         /*
          * Construct a dataset sequence for our new peptide.
@@ -754,26 +756,16 @@ public class Dna
 
   /**
    * Given a peptide newly translated from a dna sequence, copy over and set any
-   * features on the peptide from the DNA. If featureTypes is null, all features
-   * on the dna sequence are searched (rather than just the displayed ones), and
-   * similarly for featureGroups.
+   * features on the peptide from the DNA.
    * 
    * @param dna
    * @param pep
    * @param map
-   * @param featureTypes
-   *          hash whose keys are the displayed feature type strings
-   * @param featureGroups
-   *          hash where keys are feature groups and values are Boolean objects
-   *          indicating if they are displayed.
    */
   private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
-          MapList map, Map<String, Object> featureTypes,
-          Map<String, Boolean> featureGroups)
+          MapList map)
   {
-    SequenceFeature[] sfs = dna.getSequenceFeatures();
-    Boolean fgstate;
-    DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+    DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
             DBRefSource.DNACODINGDBS);
     if (dnarefs != null)
     {
@@ -786,24 +778,15 @@ public class Dna
         }
       }
     }
-    if (sfs != null)
+    for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
     {
-      for (SequenceFeature sf : sfs)
-      {
-        fgstate = (featureGroups == null) ? null : featureGroups
-                .get(sf.featureGroup);
-        if ((featureTypes == null || featureTypes.containsKey(sf.getType()))
-                && (fgstate == null || fgstate.booleanValue()))
+        if (FeatureProperties.isCodingFeature(null, sf.getType()))
         {
-          if (FeatureProperties.isCodingFeature(null, sf.getType()))
+          // if (map.intersectsFrom(sf[f].begin, sf[f].end))
           {
-            // if (map.intersectsFrom(sf[f].begin, sf[f].end))
-            {
 
-            }
           }
         }
-      }
     }
   }
 
@@ -852,13 +835,18 @@ public class Dna
     char[] originalSequence = sequence.toCharArray();
     int length = originalSequence.length;
     char[] reversedSequence = new char[length];
-
+    int bases = 0;
     for (int i = 0; i < length; i++)
     {
-      reversedSequence[length - i - 1] = complement ? getComplement(originalSequence[i])
+      char c = complement ? getComplement(originalSequence[i])
               : originalSequence[i];
+      reversedSequence[length - i - 1] = c;
+      if (!Comparison.isGap(c))
+      {
+        bases++;
+      }
     }
-    SequenceI reversed = new Sequence(newName, reversedSequence, 1, length);
+    SequenceI reversed = new Sequence(newName, reversedSequence, 1, bases);
     return reversed;
   }
 
@@ -873,7 +861,12 @@ public class Dna
   public static char getComplement(char c)
   {
     char result = c;
-    switch (c) {
+    switch (c)
+    {
+    case '-':
+    case '.':
+    case ' ':
+      break;
     case 'a':
       result = 't';
       break;