gff utilities

uk/ac/sanger/artemis/io/GFFUtils.java

+/* GFFUtils.java
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2013  Genome Research Limited
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ * 
+ */
+package uk.ac.sanger.artemis.io;
+
+import java.util.Vector;
+
+import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
+
+
+public class GFFUtils
+{
+  /**
+   * Test if this is feature is marked as having a stop codon
+   * redefined as selenocysteine
+   * @param f
+   * @return
+   */
+  public static boolean isSelenocysteine(Feature f)
+  {
+    if(!(f instanceof GFFStreamFeature))
+      return false;
+    try
+    {
+      ChadoCanonicalGene gffGene = ((GFFStreamFeature)f).getChadoGene();
+      if(gffGene == null)
+        return false;
+      String transcript = gffGene.getTranscriptFromName(
+          GeneUtils.getUniqueName(f));
+      if(transcript == null)
+        return false;
+      Feature pep = gffGene.getProteinOfTranscript(transcript);
+      if(pep == null)
+        return false;
+      if(pep.getQualifierByName("stop_codon_redefined_as_selenocysteine") != null)
+        return true;
+    }
+    catch (Exception e){}
+
+    return false;
+  }
+  
+  /**
+   * Update the segment range store for GFFStreamFeature with a new location
+   * @param gff
+   * @param oldLocation
+   * @param newLocation
+   */
+  public static void updateSegmentRangeStore(final GFFStreamFeature gff,
+                                             final Location oldLocation, 
+                                             final Location newLocation)
+  {
+    final RangeVector rv_new = newLocation.getRanges();
+    final RangeVector rv_old = oldLocation.getRanges();
+    if(rv_new.size() != rv_old.size())
+    {
+      final RangeVector rangesToAdd = new RangeVector();
+      for(Range r: rv_new)
+        if(!rv_old.containsRange(r))
+          rangesToAdd.add(r);
+      
+      final Vector<Integer> deleted = new Vector<Integer>();
+      for(int ideleted = 0; ideleted < rv_old.size(); ideleted++)
+        if(!rv_new.containsRange(rv_old.get(ideleted)))
+          deleted.add(ideleted);
+
+      try
+      {
+        if(gff.getQualifierByName("Parent") != null)
+          GeneUtils.addSegment(gff, rangesToAdd, 
+             gff.getQualifierByName("Parent").getValues().get(0));
+      }
+      catch(Exception e)
+      {
+        e.printStackTrace();
+      }
+      
+      for(Integer d: deleted)
+        gff.getSegmentRangeStore().remove(
+            gff.getSegmentID(rv_old.elementAt(d)));
+    }
+    else if(gff.getSegmentRangeStore() != null)
+    {
+      Vector<Integer> changes = new Vector<Integer>();
+      for(int i=0; i<rv_old.size(); i++)
+      {
+        Range rnew = rv_new.elementAt(i);
+        Range rold = rv_old.elementAt(i);
+
+        if(rnew.getStart() != rold.getStart() ||
+           rnew.getEnd()   != rold.getEnd() ||
+           (oldLocation.isComplement(rold) !=
+            newLocation.isComplement(rnew)))
+          changes.add(i);
+      }
+
+      for(Integer c: changes)
+      {
+        Range rnew = rv_new.elementAt(c);
+        String segId = gff.getSegmentID(rnew);
+        if(segId == null)
+          segId = gff.getSegmentID(rv_old.elementAt(c));
+        gff.getSegmentRangeStore().put(segId, rnew);
+      }
+    }
+  }
+  
+}
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