JAl-1705 ENSEMBL cDNA type cannot be queried with peptide IDs

[jalview.git] / src / jalview / io / FeaturesFile.java

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 4085fc1..57f6384 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -70,27 +70,48 @@ public class FeaturesFile extends AlignFile
   }
 
   /**
-   * Creates a new FeaturesFile object.
-   * 
    * @param inFile
-   *          DOCUMENT ME!
    * @param type
-   *          DOCUMENT ME!
-   * 
    * @throws IOException
-   *           DOCUMENT ME!
    */
   public FeaturesFile(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
 
+  /**
+   * @param source
+   * @throws IOException
+   */
   public FeaturesFile(FileParse source) throws IOException
   {
     super(source);
   }
 
   /**
+   * @param parseImmediately
+   * @param source
+   * @throws IOException
+   */
+  public FeaturesFile(boolean parseImmediately, FileParse source)
+          throws IOException
+  {
+    super(parseImmediately, source);
+  }
+
+  /**
+   * @param parseImmediately
+   * @param inFile
+   * @param type
+   * @throws IOException
+   */
+  public FeaturesFile(boolean parseImmediately, String inFile, String type)
+          throws IOException
+  {
+    super(parseImmediately, inFile, type);
+  }
+
+  /**
    * Parse GFF or sequence features file using case-independent matching,
    * discarding URLs
    * 
@@ -148,6 +169,27 @@ public class FeaturesFile extends AlignFile
     return parse(align, colours, featureLink, removeHTML, false);
   }
 
+  @Override
+  public void addAnnotations(AlignmentI al)
+  {
+    // TODO Auto-generated method stub
+    super.addAnnotations(al);
+  }
+
+  @Override
+  public void addProperties(AlignmentI al)
+  {
+    // TODO Auto-generated method stub
+    super.addProperties(al);
+  }
+
+  @Override
+  public void addSeqGroups(AlignmentI al)
+  {
+    // TODO Auto-generated method stub
+    super.addSeqGroups(al);
+  }
+
   /**
    * Parse GFF or sequence features file
    * 
@@ -1082,6 +1124,16 @@ public class FeaturesFile extends AlignFile
     else
     {
       match = align.findName(seqId, true);
+      if (match == null && newseqs != null)
+      {
+        for (SequenceI m : newseqs)
+        {
+          if (seqId.equals(m.getName()))
+          {
+            return m;
+          }
+        }
+      }
       
     }
     if (match==null && newseqs!=null)
@@ -1092,6 +1144,8 @@ public class FeaturesFile extends AlignFile
         matcher.addAll(Arrays.asList(new SequenceI[]
         { match }));
       }
+      // add dummy sequence to the newseqs list
+      newseqs.add(match);
     }
     return match;
   }