X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FDna.java;h=49c37df7f2d810881c0bc55e7a3a6b21c2f4f8ea;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=ce13665cdf2dfb60812c1f81695d5aa7490ce82d;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index ce13665..49c37df 100644
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program 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.
+ * 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.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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/>.
  */
 package jalview.analysis;
 
@@ -85,7 +84,7 @@ public class Dna
    * @param annotations
    * @param aWidth
    * @param dataset
-   *                destination dataset for translated sequences and mappings
+   *          destination dataset for translated sequences and mappings
    * @return
    */
   public static AlignmentI CdnaTranslate(SequenceI[] selection,
@@ -100,9 +99,9 @@ public class Dna
    * 
    * @param selection
    * @param seqstring
-   * @param product -
-   *                array of DbRefEntry objects from which exon map in seqstring
-   *                is derived
+   * @param product
+   *          - array of DbRefEntry objects from which exon map in seqstring is
+   *          derived
    * @param viscontigs
    * @param gapCharacter
    * @param annotations
@@ -128,7 +127,7 @@ public class Dna
       SequenceI newseq = translateCodingRegion(selection[s], seqstring[s],
               viscontigs, codons, gapCharacter,
               (product != null) ? product[s] : null); // possibly anonymous
-                                                      // product
+      // product
       if (newseq != null)
       {
         pepseqs.addElement(newseq);
@@ -215,7 +214,7 @@ public class Dna
    * @param viscontigs
    * @param gapCharacter
    * @param dataset
-   *                destination dataset for translated sequences
+   *          destination dataset for translated sequences
    * @param annotations
    * @param aWidth
    * @return
@@ -364,28 +363,60 @@ public class Dna
   {
     // Have a look at all the codon positions for annotation and put the first
     // one found into the translated annotation pos.
+    int contrib = 0;
+    Annotation annot = null;
     for (int p = 0; p < 3; p++)
     {
       if (annotations[is[p]] != null)
       {
-        return new Annotation(annotations[is[p]]);
+        if (annot == null)
+        {
+          annot = new Annotation(annotations[is[p]]);
+          contrib = 1;
+        }
+        else
+        {
+          // merge with last
+          Annotation cpy = new Annotation(annotations[is[p]]);
+          if (annot.colour == null)
+          {
+            annot.colour = cpy.colour;
+          }
+          if (annot.description == null || annot.description.length() == 0)
+          {
+            annot.description = cpy.description;
+          }
+          if (annot.displayCharacter == null)
+          {
+            annot.displayCharacter = cpy.displayCharacter;
+          }
+          if (annot.secondaryStructure == 0)
+          {
+            annot.secondaryStructure = cpy.secondaryStructure;
+          }
+          annot.value += cpy.value;
+          contrib++;
+        }
       }
     }
-    return null;
+    if (contrib > 1)
+    {
+      annot.value /= (float) contrib;
+    }
+    return annot;
   }
 
   /**
    * Translate a na sequence
    * 
    * @param selection
-   *                sequence displayed under viscontigs visible columns
+   *          sequence displayed under viscontigs visible columns
    * @param seqstring
-   *                ORF read in some global alignment reference frame
+   *          ORF read in some global alignment reference frame
    * @param viscontigs
-   *                mapping from global reference frame to visible seqstring ORF
-   *                read
+   *          mapping from global reference frame to visible seqstring ORF read
    * @param codons
-   *                Definition of global ORF alignment reference frame
+   *          Definition of global ORF alignment reference frame
    * @param gapCharacter
    * @param newSeq
    * @return sequence ready to be added to alignment.
@@ -517,8 +548,9 @@ public class Dna
         }
         if (aspos >= codons.aaWidth)
         {
-          // update maximum alignment width 
-          // (we can do this without calling checkCodonFrameWidth because it was already done above)
+          // update maximum alignment width
+          // (we can do this without calling checkCodonFrameWidth because it was
+          // already done above)
           codons.setAaWidth(aspos);
         }
         // ready for next translated reading frame alignment position (if any)
@@ -527,8 +559,8 @@ public class Dna
     }
     if (resSize > 0)
     {
-      SequenceI newseq = new Sequence(selection.getName(), protein
-              .toString());
+      SequenceI newseq = new Sequence(selection.getName(),
+              protein.toString());
       if (rf != 0)
       {
         jalview.bin.Cache.log
@@ -587,14 +619,13 @@ public class Dna
          * new ranges to exclude untranslated regions. if (skip.size()>0) {
          * Vector narange = new Vector(); for (vc=0; vc<scontigs.length; vc++) {
          * narange.addElement(new int[] {scontigs[vc]}); } int sint=0,iv[]; vc =
-         * 0; while (sint<skip.size()) { skipint = (int[])
-         * skip.elementAt(sint); do { iv = (int[]) narange.elementAt(vc); if
-         * (iv[0]>=skipint[0] && iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { //
-         * delete beginning of range } else { // truncate range and create new
-         * one if necessary iv = (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { //
-         * truncate range iv[0] = skipint[1]; } else {
-         *  } } } else if (iv[0]<skipint[0]) { iv = (int[])
-         * narange.elementAt(vc+1); } } while (iv[0]) } }
+         * 0; while (sint<skip.size()) { skipint = (int[]) skip.elementAt(sint);
+         * do { iv = (int[]) narange.elementAt(vc); if (iv[0]>=skipint[0] &&
+         * iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { // delete beginning of
+         * range } else { // truncate range and create new one if necessary iv =
+         * (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { // truncate
+         * 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);
@@ -624,7 +655,7 @@ public class Dna
       }
     }
     // register the mapping somehow
-    // 
+    //
     return null;
   }
 
@@ -638,10 +669,10 @@ public class Dna
    * @param pep
    * @param map
    * @param featureTypes
-   *                hash who's keys are the displayed feature type strings
+   *          hash who's 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.
+   *          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, Hashtable featureTypes, Hashtable featureGroups)
@@ -669,8 +700,7 @@ public class Dna
         fgstate = (featureGroups == null) ? null : ((Boolean) featureGroups
                 .get(sf[f].featureGroup));
         if ((featureTypes == null || featureTypes.containsKey(sf[f]
-                .getType()))
-                && (fgstate == null || fgstate.booleanValue()))
+                .getType())) && (fgstate == null || fgstate.booleanValue()))
         {
           if (FeatureProperties.isCodingFeature(null, sf[f].getType()))
           {