X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FGff3Helper.java;h=c7e1d7a127f96a406b3819ff330fa220a26c169b;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;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..c7e1d7a 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;
@@ -61,19 +81,6 @@ 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)
@@ -82,15 +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
       {
@@ -104,7 +112,7 @@ public class Gff3Helper extends GffHelperBase
        */
       sf = buildSequenceFeature(gff, null);
     }
-  
+
     return sf;
   }
 
@@ -131,14 +139,21 @@ 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];
-    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");
+      System.err.println(
+              "Skipping mapping from reverse complement as not yet supported");
       return null;
     }
 
@@ -170,8 +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)
       {
@@ -199,8 +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)
         {
@@ -230,7 +244,8 @@ public class Gff3Helper extends GffHelperBase
    * @return
    */
   @SuppressWarnings("unused")
-  protected String findTargetId(String target, Map<String, List<String>> set)
+  protected String findTargetId(String target,
+          Map<String, List<String>> set)
   {
     return target;
   }
@@ -261,8 +276,8 @@ public class Gff3Helper extends GffHelperBase
    * @throws IOException
    */
   protected SequenceFeature processProteinMatch(
-          Map<String, List<String>> set, SequenceI seq,
-          String[] gffColumns, AlignmentI align, List<SequenceI> newseqs,
+          Map<String, List<String>> set, SequenceI seq, String[] gffColumns,
+          AlignmentI align, List<SequenceI> newseqs,
           boolean relaxedIdMatching)
   {
     // This is currently tailored to InterProScan GFF output:
@@ -284,8 +299,8 @@ 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)
         {
@@ -296,10 +311,9 @@ 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);
 
         /*
@@ -307,8 +321,8 @@ public class Gff3Helper extends GffHelperBase
          * renamed with its qualified accession id; renaming has to wait until
          * all sequence reference resolution is complete
          */
-        String accessionId = StringUtils.listToDelimitedString(
-                set.get(NAME), ",");
+        String accessionId = StringUtils
+                .listToDelimitedString(set.get(NAME), ",");
         if (accessionId.length() > 0)
         {
           String database = sf.getType(); // TODO InterProScan only??
@@ -348,14 +362,66 @@ 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, typeColumn, group,
+            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)
   {
-    SequenceFeature sf = super.buildSequenceFeature(gff, 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;
   }
 }