X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FGff3Helper.java;h=28941f57bc1c311c5861ed37098a5857786e7bb2;hb=d065bc916cb63af83cdab7319f5177a855724aba;hp=d878f64fb57dceeda2da5a9b79826cbafed27fe9;hpb=ecc50d775a514f9840cdcc10a9d5b1e49c60582c;p=jalview.git

diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index d878f64..28941f5 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.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;
@@ -69,15 +89,16 @@ public class Gff3Helper extends GffHelperBase
       String atts = gff[ATTRIBUTES_COL];
       Map<String, List<String>> attributes = parseNameValuePairs(atts);
 
-      if (SequenceOntology.getInstance().isProteinMatch(soTerm))
+      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      if (so.isA(soTerm, SequenceOntologyI.PROTEIN_MATCH))
       {
-        sf = processProteinMatch(attributes, seq, gff, align,
-                newseqs, relaxedIdMatching);
+        sf = processProteinMatch(attributes, seq, gff, align, newseqs,
+                relaxedIdMatching);
       }
-      else if (SequenceOntology.getInstance().isNucleotideMatch(soTerm))
+      else if (so.isA(soTerm, SequenceOntologyI.NUCLEOTIDE_MATCH))
       {
-        sf = processNucleotideMatch(attributes, seq, gff, align,
-                newseqs, relaxedIdMatching);
+        sf = processNucleotideMatch(attributes, seq, gff, align, newseqs,
+                relaxedIdMatching);
       }
       else
       {
@@ -91,7 +112,7 @@ public class Gff3Helper extends GffHelperBase
        */
       sf = buildSequenceFeature(gff, null);
     }
-  
+
     return sf;
   }
 
@@ -118,8 +139,7 @@ public class Gff3Helper extends GffHelperBase
   protected SequenceFeature processNucleotideMatch(
           Map<String, List<String>> attributes, SequenceI seq,
           String[] gffColumns, AlignmentI align, List<SequenceI> newseqs,
-          boolean relaxedIdMatching)
-          throws IOException
+          boolean relaxedIdMatching) throws IOException
   {
     String strand = gffColumns[STRAND_COL];
 
@@ -165,8 +185,8 @@ public class Gff3Helper extends GffHelperBase
        * (new or existing) virtual sequence in the newseqs list 
        */
       String targetId = findTargetId(tokens[0], attributes);
-      SequenceI mappedSequence1 = findSequence(targetId, align,
-      newseqs, relaxedIdMatching);
+      SequenceI mappedSequence1 = findSequence(targetId, align, newseqs,
+              relaxedIdMatching);
       SequenceI mappedSequence = mappedSequence1;
       if (mappedSequence == null)
       {
@@ -194,8 +214,7 @@ public class Gff3Helper extends GffHelperBase
         int fromStart = Integer.parseInt(gffColumns[START_COL]);
         int fromEnd = Integer.parseInt(gffColumns[END_COL]);
         MapList mapping = constructMappingFromAlign(fromStart, fromEnd,
-                toStart, toEnd,
-                MappingType.NucleotideToNucleotide);
+                toStart, toEnd, MappingType.NucleotideToNucleotide);
 
         if (mapping != null)
         {
@@ -279,8 +298,8 @@ public class Gff3Helper extends GffHelperBase
       for (String target : targets)
       {
 
-        SequenceI mappedSequence1 = findSequence(findTargetId(target, set), align,
-        newseqs, relaxedIdMatching);
+        SequenceI mappedSequence1 = findSequence(findTargetId(target, set),
+                align, newseqs, relaxedIdMatching);
         SequenceI mappedSequence = mappedSequence1;
         if (mappedSequence == null)
         {
@@ -291,10 +310,9 @@ public class Gff3Helper extends GffHelperBase
          * give the mapped sequence a copy of the sequence feature, with 
          * start/end range adjusted 
          */
-        SequenceFeature sf2 = new SequenceFeature(sf);
-        sf2.setBegin(1);
         int sequenceFeatureLength = 1 + sf.getEnd() - sf.getBegin();
-        sf2.setEnd(sequenceFeatureLength);
+        SequenceFeature sf2 = new SequenceFeature(sf, 1,
+                sequenceFeatureLength, sf.getFeatureGroup(), sf.getScore());
         mappedSequence.addSequenceFeature(sf2);
 
         /*
@@ -343,9 +361,11 @@ public class Gff3Helper extends GffHelperBase
    */
   @Override
   protected SequenceFeature buildSequenceFeature(String[] gff,
+          int typeColumn, String group,
           Map<String, List<String>> attributes)
   {
-    SequenceFeature sf = super.buildSequenceFeature(gff, attributes);
+    SequenceFeature sf = super.buildSequenceFeature(gff, typeColumn, group,
+            attributes);
     String desc = getDescription(sf, attributes);
     if (desc != null)
     {
@@ -371,14 +391,36 @@ public class Gff3Helper extends GffHelperBase
       desc = target.split(" ")[0];
     }
 
-    if (SequenceOntology.getInstance().isSequenceVariant(sf.getType()))
+    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    String type = sf.getType();
+    if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
     {
       /*
        * Ensembl returns dna variants as 'alleles'
        */
-      desc = StringUtils.listToDelimitedString(
-              attributes.get("alleles"), ",");
+      desc = StringUtils.listToDelimitedString(attributes.get("alleles"),
+              ",");
     }
+
+    /*
+     * extract 'Name' for a transcript (to show gene name)
+     * or an exon (so 'colour by label' shows exon boundaries) 
+     */
+    if (SequenceOntologyI.NMD_TRANSCRIPT_VARIANT.equals(type)
+            || so.isA(type, SequenceOntologyI.TRANSCRIPT)
+            || so.isA(type, SequenceOntologyI.EXON))
+    {
+      desc = StringUtils.listToDelimitedString(attributes.get("Name"), ",");
+    }
+
+    /*
+     * if the above fails, try ID
+     */
+    if (desc == null)
+    {
+      desc = (String) sf.getValue(ID);
+    }
+
     return desc;
   }
 }