JAL-2446 merged to spike branch

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

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 0ec5d36..2106dc2 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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
 {
@@ -685,7 +684,7 @@ 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.
@@ -754,25 +753,15 @@ 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.getDBRefs(),
             DBRefSource.DNACODINGDBS);
     if (dnarefs != null)
@@ -786,24 +775,15 @@ 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))
-            {
 
-            }
           }
         }
-      }
     }
   }