X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FGff3Helper.java;h=031900d3c199d75b4f70e29b43abb07049ff7965;hb=55ea0e81c495953933370df9bb747120649e5274;hp=4c67caa7fb4db009038dd878c8f553d96e54a9cf;hpb=8f920d337154e092f5f9056ffde3cdf2735eca43;p=jalview.git

diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index 4c67caa..031900d 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -61,19 +61,6 @@ public class Gff3Helper extends GffHelperBase
           AlignmentI align, List<SequenceI> newseqs,
           boolean relaxedIdMatching) throws IOException
   {
-    /*
-     * (For now) we don't process mappings from reverse complement ; to do
-     * this would require (a) creating a virtual sequence placeholder for
-     * the reverse complement (b) resolving the sequence by its id from some
-     * source (GFF ##FASTA or other) (c) creating the reverse complement
-     * sequence (d) updating the mapping to be to the reverse complement
-     */
-    if ("-".equals(gff[STRAND_COL]))
-    {
-      System.err
-              .println("Skipping mapping from reverse complement as not yet supported");
-      return null;
-    }
     SequenceFeature sf = null;
 
     if (gff.length == 9)
@@ -82,12 +69,13 @@ 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);
@@ -135,10 +123,18 @@ public class Gff3Helper extends GffHelperBase
           throws IOException
   {
     String strand = gffColumns[STRAND_COL];
-    if ("-1".equals(strand))
+
+    /*
+     * (For now) we don't process mappings from reverse complement ; to do
+     * this would require (a) creating a virtual sequence placeholder for
+     * the reverse complement (b) resolving the sequence by its id from some
+     * source (GFF ##FASTA or other) (c) creating the reverse complement
+     * sequence (d) updating the mapping to be to the reverse complement
+     */
+    if ("-".equals(strand))
     {
       System.err
-              .println("Currently ignoring mappings from reverse complement");
+              .println("Skipping mapping from reverse complement as not yet supported");
       return null;
     }
 
@@ -351,11 +347,61 @@ public class Gff3Helper extends GffHelperBase
           Map<String, List<String>> attributes)
   {
     SequenceFeature sf = super.buildSequenceFeature(gff, attributes);
+    String desc = getDescription(sf, attributes);
+    if (desc != null)
+    {
+      sf.setDescription(desc);
+    }
+    return sf;
+  }
+
+  /**
+   * Apply heuristic rules to try to get the most useful feature description
+   * 
+   * @param sf
+   * @param attributes
+   * @return
+   */
+  protected String getDescription(SequenceFeature sf,
+          Map<String, List<String>> attributes)
+  {
+    String desc = null;
     String target = (String) sf.getValue(TARGET);
     if (target != null)
     {
-      sf.setDescription(target.split(" ")[0]);
+      desc = target.split(" ")[0];
     }
-    return sf;
+
+    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"), ",");
+    }
+
+    /*
+     * 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;
   }
 }