JAL-1705 align CDS and peptide products to transcripts

[jalview.git] / src / jalview / ext / ensembl / EnsemblGene.java

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 10841bd..6507ff5 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -1,14 +1,19 @@
 package jalview.ext.ensembl;
 
+import jalview.api.FeatureColourI;
+import jalview.api.FeatureSettingsI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
+import jalview.schemes.FeatureColourAdapter;
+import jalview.schemes.FeatureSettingsAdapter;
 import jalview.util.MapList;
 import jalview.util.StringUtils;
 
+import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -115,6 +120,9 @@ public class EnsemblGene extends EnsemblSeqProxy
       return getSequenceRecords(theIds);
     }
 
+    /*
+     * fetch the gene sequence(s) with features and xrefs
+     */
     AlignmentI al = super.getSequenceRecords(query);
 
     /*
@@ -171,6 +179,36 @@ public class EnsemblGene extends EnsemblSeqProxy
     {
       makeTranscript(transcriptFeature, al, gene);
     }
+
+    clearGeneFeatures(gene);
+  }
+
+  /**
+   * Remove unwanted features (transcript, exon, CDS) from the gene sequence
+   * after we have used them to derive transcripts and transfer features
+   * 
+   * @param gene
+   */
+  protected void clearGeneFeatures(SequenceI gene)
+  {
+    SequenceFeature[] sfs = gene.getSequenceFeatures();
+    if (sfs != null)
+    {
+      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      List<SequenceFeature> filtered = new ArrayList<SequenceFeature>();
+      for (SequenceFeature sf : sfs)
+      {
+        String type = sf.getType();
+        if (!isTranscript(type) && !so.isA(type, SequenceOntologyI.EXON)
+                && !so.isA(type, SequenceOntologyI.CDS))
+        {
+          filtered.add(sf);
+        }
+      }
+      gene.setSequenceFeatures(filtered
+              .toArray(new SequenceFeature[filtered
+              .size()]));
+    }
   }
 
   /**
@@ -360,13 +398,13 @@ public class EnsemblGene extends EnsemblSeqProxy
   @Override
   protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
-            SequenceOntologyI.GENE))
+    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    String type = sf.getType();
+    if (so.isA(type, SequenceOntologyI.GENE))
     {
       return false;
     }
-
-    if (isTranscript(sf.getType()))
+    if (isTranscript(type))
     {
       String parent = (String) sf.getValue(PARENT);
       if (!(GENE_PREFIX + accessionId).equals(parent))
@@ -412,4 +450,73 @@ public class EnsemblGene extends EnsemblSeqProxy
     return ACCESSION_REGEX;
   }
 
+  @Override
+  public FeatureSettingsI getFeatureColourScheme()
+  {
+    return new FeatureSettingsAdapter()
+    {
+      SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+      @Override
+      public boolean isFeatureDisplayed(String type)
+      {
+        return (so.isA(type, SequenceOntologyI.EXON) || so.isA(type,
+                SequenceOntologyI.SEQUENCE_VARIANT));
+      }
+
+      @Override
+      public FeatureColourI getFeatureColour(String type)
+      {
+        if (so.isA(type, SequenceOntologyI.EXON))
+        {
+          return new FeatureColourAdapter()
+          {
+            @Override
+            public boolean isColourByLabel()
+            {
+              return true;
+            }
+          };
+        }
+        if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
+        {
+          return new FeatureColourAdapter()
+          {
+
+            @Override
+            public Color getColour()
+            {
+              return Color.RED;
+            }
+          };
+        }
+        return null;
+      }
+
+      /**
+       * order to render sequence_variant after exon after the rest
+       */
+      @Override
+      public int compare(String feature1, String feature2)
+      {
+        if (so.isA(feature1, SequenceOntologyI.SEQUENCE_VARIANT))
+        {
+          return +1;
+        }
+        if (so.isA(feature2, SequenceOntologyI.SEQUENCE_VARIANT))
+        {
+          return -1;
+        }
+        if (so.isA(feature1, SequenceOntologyI.EXON))
+        {
+          return +1;
+        }
+        if (so.isA(feature2, SequenceOntologyI.EXON))
+        {
+          return -1;
+        }
+        return 0;
+      }
+    };
+  }
+
 }