Merge branch 'develop' into features/JAL-2446NCList

[jalview.git] / src / jalview / io / gff / ExonerateHelper.java

diff --git a/src/jalview/io/gff/ExonerateHelper.java b/src/jalview/io/gff/ExonerateHelper.java
index e373861..da0c245 100644 (file)
--- a/src/jalview/io/gff/ExonerateHelper.java
+++ b/src/jalview/io/gff/ExonerateHelper.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io.gff;
 
 import jalview.datamodel.AlignedCodonFrame;
@@ -41,7 +61,7 @@ public class ExonerateHelper extends Gff2Helper
    * 
    * @param seq
    *          the sequence with which this feature is associated
-   * @param sf
+   * @param gffColumns
    *          the sequence feature with ATTRIBUTES property containing any
    *          additional attributes
    * @param align
@@ -64,8 +84,8 @@ public class ExonerateHelper extends Gff2Helper
 
     try
     {
-      processGffSimilarity(set, seq, gffColumns,
-              align, newseqs, relaxedIdMatching);
+      processGffSimilarity(set, seq, gffColumns, align, newseqs,
+              relaxedIdMatching);
     } catch (IOException ivfe)
     {
       System.err.println(ivfe);
@@ -98,8 +118,7 @@ public class ExonerateHelper extends Gff2Helper
    *          if true allow fuzzy search for a matching target sequence
    * @throws IOException
    */
-  protected void processGffSimilarity(
-          Map<String, List<String>> set,
+  protected void processGffSimilarity(Map<String, List<String>> set,
           SequenceI seq, String[] gff, AlignmentI align,
           List<SequenceI> newseqs, boolean relaxedIdMatching)
           throws IOException
@@ -146,7 +165,8 @@ public class ExonerateHelper extends Gff2Helper
     SequenceI mapFromSequence = seq;
     SequenceI mapToSequence = mappedSequence;
     if ((type == MappingType.NucleotideToPeptide && featureIsOnTarget)
-            || (type == MappingType.PeptideToNucleotide && !featureIsOnTarget))
+            || (type == MappingType.PeptideToNucleotide
+                    && !featureIsOnTarget))
     {
       mapFromSequence = mappedSequence;
       mapToSequence = seq;
@@ -167,7 +187,7 @@ public class ExonerateHelper extends Gff2Helper
             mapToSequence);
 
     /*
-     * exonerate GFF has the strand of the target in column 7 rather
+     * exonerate GFF has the strand of the target in column 7
      * (differs from GFF3 which has it in the Target descriptor)
      */
     String strand = gff[STRAND_COL];
@@ -228,15 +248,17 @@ public class ExonerateHelper extends Gff2Helper
     int alignFromStart;
     int alignToStart;
     int alignCount;
-    try {
+    try
+    {
       alignFromStart = Integer.parseInt(tokens[0]);
       alignToStart = Integer.parseInt(tokens[1]);
       alignCount = Integer.parseInt(tokens[2]);
-    } catch (NumberFormatException nfe) {
+    } catch (NumberFormatException nfe)
+    {
       System.err.println(nfe.toString());
       return null;
     }
-    
+
     int fromStart;
     int fromEnd;
     int toStart;
@@ -246,8 +268,8 @@ public class ExonerateHelper extends Gff2Helper
     {
       fromStart = alignToStart;
       toStart = alignFromStart;
-      toEnd = forwardStrand ? toStart + alignCount - 1 : toStart
-              - (alignCount - 1);
+      toEnd = forwardStrand ? toStart + alignCount - 1
+              : toStart - (alignCount - 1);
       int toLength = Math.abs(toEnd - toStart) + 1;
       int fromLength = toLength * type.getFromRatio() / type.getToRatio();
       fromEnd = fromStart + fromLength - 1;
@@ -290,10 +312,8 @@ public class ExonerateHelper extends Gff2Helper
     {
       result = MappingType.PeptideToNucleotide;
     }
-    else if (model.contains(CODING2CODING)
-            || model.contains(CODING2GENOME)
-            || model.contains(CDNA2GENOME)
-            || model.contains(GENOME2GENOME))
+    else if (model.contains(CODING2CODING) || model.contains(CODING2GENOME)
+            || model.contains(CDNA2GENOME) || model.contains(GENOME2GENOME))
     {
       result = MappingType.NucleotideToNucleotide;
     }
@@ -304,7 +324,7 @@ public class ExonerateHelper extends Gff2Helper
    * Tests whether the GFF data looks like it was generated by exonerate, and is
    * a format we are willing to handle
    * 
-   * @param sf
+   * @param columns
    * @return
    */
   public static boolean recognises(String[] columns)
@@ -323,10 +343,8 @@ public class ExonerateHelper extends Gff2Helper
     {
       String mdl = model.toLowerCase();
       if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
-              || mdl.contains(CODING2CODING)
-              || mdl.contains(CODING2GENOME)
-              || mdl.contains(CDNA2GENOME)
-              || mdl.contains(GENOME2GENOME))
+              || mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
+              || mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
       {
         return true;
       }
@@ -335,12 +353,16 @@ public class ExonerateHelper extends Gff2Helper
     return false;
   }
 
+  /**
+   * An override to set feature group to "exonerate" instead of the default GFF
+   * source value (column 2)
+   */
   @Override
   protected SequenceFeature buildSequenceFeature(String[] gff,
           Map<String, List<String>> set)
   {
-    SequenceFeature sf = super.buildSequenceFeature(gff, set);
-    sf.setFeatureGroup("exonerate");
+    SequenceFeature sf = super.buildSequenceFeature(gff, TYPE_COL,
+            "exonerate", set);
 
     return sf;
   }