feature offset in GFF with multiple sequences

test/uk/ac/sanger/artemis/io/GFFTest.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 static org.junit.Assert.assertTrue;
+import junit.framework.Assert;
+
+import org.junit.Test;
+
+import uk.ac.sanger.artemis.EntryGroup;
+import uk.ac.sanger.artemis.Feature;
+import uk.ac.sanger.artemis.FeatureVector;
+import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.SimpleEntryGroup;
+import uk.ac.sanger.artemis.io.Entry;
+import uk.ac.sanger.artemis.io.Qualifier;
+import uk.ac.sanger.artemis.io.InvalidRelationException;
+import uk.ac.sanger.artemis.sequence.NoSequenceException;
+import uk.ac.sanger.artemis.util.OutOfRangeException;
+import uk.ac.sanger.artemis.util.StringVector;
+
+public class GFFTest
+{
+  @Test
+  /**
+   * For a GFF with multiple sequences check the offset position 
+   * of a gene is correctly set.
+   */
+  public void testGFFMultipleFastaOffset()
+  {
+    try
+    {
+      final Entry entry = Utils.getEntry("/data/Pf3D7_01_02_v3.gff.gz");
+      final EntryGroup egrp = new SimpleEntryGroup();
+      egrp.add(new uk.ac.sanger.artemis.Entry(entry));
+      final FeatureVector features = egrp.getAllFeatures();
+
+      // change the translation table did cause a problem
+      // with the offset that has now been fixed in GFFDocumentEntry
+      Utils.changeTranslationTable("11");
+
+      for (int i=0; i<features.size(); i++)
+      {
+        Feature f = features.elementAt(i);
+        try
+        {
+          final Qualifier q = f.getQualifierByName("ID");
+          if (q != null)
+          {
+            final String id = q.getValues().get(0);
+            if (id.equals("PF3D7_0200100"))
+            {
+              assertTrue("Offset check first base: " + id + 
+                  " " +f.getFirstBase() + " != 666083",
+                  f.getFirstBase() == 666083);
+
+              assertTrue("Offset check location: " + id+ 
+                  " " +f.getEmblFeature().getLocation().getFirstBase() + " != 666083", 
+                  f.getEmblFeature().getLocation().getFirstBase() == 666083);
+            }
+          }
+        }
+        catch(InvalidRelationException e)
+        {
+          Assert.fail(e.getMessage());
+        }
+      }
+    }
+    catch (OutOfRangeException e)
+    {
+      Assert.fail(e.getMessage());
+    }
+    catch (NoSequenceException e)
+    {
+      Assert.fail(e.getMessage());
+    }
+  }
+
+}
\ No newline at end of file

test/uk/ac/sanger/artemis/io/Utils.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.io.IOException;
+import java.net.URL;
+
+import junit.framework.Assert;
+import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.io.DocumentEntryFactory;
+import uk.ac.sanger.artemis.io.Entry;
+import uk.ac.sanger.artemis.io.EntryInformationException;
+import uk.ac.sanger.artemis.sequence.AminoAcidSequence;
+import uk.ac.sanger.artemis.sequence.Bases;
+import uk.ac.sanger.artemis.util.Document;
+import uk.ac.sanger.artemis.util.DocumentFactory;
+import uk.ac.sanger.artemis.util.StringVector;
+
+public class Utils
+{
+  protected static Entry getEntry(final String fileName)
+  {
+    try
+    {
+      URL entryFile = ValidateFeatureTest.class.getResource(fileName);
+      final Document doc = DocumentFactory.makeDocument(entryFile.getFile());
+      return DocumentEntryFactory.makeDocumentEntry(
+          Options.getArtemisEntryInformation(),doc,null);
+    }
+    catch(EntryInformationException e) 
+    {
+      Assert.fail(e.getMessage());
+    }
+    catch(IOException e) 
+    {
+      Assert.fail(e.getMessage());
+    }
+    return null;
+  }
+  
+  /**
+   * Method to change the translation table being used
+   * @param n - genetic code table number
+   */
+  protected static void changeTranslationTable(String n)
+  {
+    StringVector options_file_table =
+                 Options.getOptions().getOptionValues("translation_table_"+n);
+    StringVector table = Options.getOptions().getOptionValues("translation_table_1");
+    for(String cod_plus_aa: options_file_table)
+    {
+      final int codon_index = Bases.getIndexOfBase(cod_plus_aa.charAt(0)) * 16 +
+                              Bases.getIndexOfBase(cod_plus_aa.charAt(1)) * 4 +
+                              Bases.getIndexOfBase(cod_plus_aa.charAt(2));
+      table.setElementAt(cod_plus_aa.substring(3), codon_index);
+    }
+        
+    StringBuffer sbuff = new StringBuffer();
+    for(int i = 0; i < 64; ++i)
+      sbuff.append(table.elementAt(i)+" ");
+    Options.getOptions().setGeneticCode(sbuff.toString());
+      
+    options_file_table =
+          Options.getOptions().getOptionValues("start_codons_"+n);
+    sbuff = new StringBuffer();
+    for(String start: options_file_table)
+      sbuff.append(start+" ");
+        
+    Options.getOptions().setProperty("start_codons",sbuff.toString());   
+    AminoAcidSequence.setGeneCode();
+  }
+}
\ No newline at end of file

test/uk/ac/sanger/artemis/io/ValidateFeatureTest.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 static org.junit.Assert.assertEquals;
@@ -36,7 +56,7 @@ public class ValidateFeatureTest
   {
     try 
     {
-      final Entry entry = getEntry("/data/test.gff.gz");
+      final Entry entry = Utils.getEntry("/data/test.gff.gz");
       final EntryGroup egrp = new SimpleEntryGroup();
       egrp.add(new uk.ac.sanger.artemis.Entry(entry));
       ValidateFeature validate = new ValidateFeature(egrp);
@@ -82,7 +102,7 @@ public class ValidateFeatureTest
   @Test
   public void testGFFBoundary()
   {
-    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final Entry entry = Utils.getEntry("/data/test_boundary.gff.gz");
     final FeatureVector features = entry.getAllFeatures();
 
     for(uk.ac.sanger.artemis.io.Feature f: features)
@@ -105,7 +125,7 @@ public class ValidateFeatureTest
   @Test
   public void testGFFStrand()
   {
-    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final Entry entry = Utils.getEntry("/data/test_boundary.gff.gz");
     final FeatureVector features = entry.getAllFeatures();
 
     for(uk.ac.sanger.artemis.io.Feature f: features)
@@ -128,7 +148,7 @@ public class ValidateFeatureTest
   @Test
   public void testGFFPhase()
   {
-    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final Entry entry = Utils.getEntry("/data/test_boundary.gff.gz");
     final FeatureVector features = entry.getAllFeatures();
 
     for(uk.ac.sanger.artemis.io.Feature f: features)
@@ -151,7 +171,7 @@ public class ValidateFeatureTest
   @Test
   public void testGFFCompleteGeneModel()
   {
-    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final Entry entry = Utils.getEntry("/data/test_boundary.gff.gz");
     final FeatureVector features = entry.getAllFeatures();
 
     for(uk.ac.sanger.artemis.io.Feature f: features)
@@ -180,7 +200,7 @@ public class ValidateFeatureTest
   @Test
   public void testGFFId()
   {
-    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final Entry entry = Utils.getEntry("/data/test_boundary.gff.gz");
     final FeatureVector features = entry.getAllFeatures();
 
     for(uk.ac.sanger.artemis.io.Feature f: features)
@@ -205,7 +225,7 @@ public class ValidateFeatureTest
   @Test
   public void testGFFPartials()
   {
-    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final Entry entry = Utils.getEntry("/data/test_boundary.gff.gz");
     final FeatureVector features = entry.getAllFeatures();
 
     for(uk.ac.sanger.artemis.io.Feature f: features)
@@ -232,7 +252,7 @@ public class ValidateFeatureTest
   @Test
   public void testGFFAttributes()
   {
-    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final Entry entry = Utils.getEntry("/data/test_boundary.gff.gz");
     final FeatureVector features = entry.getAllFeatures();
 
     for(uk.ac.sanger.artemis.io.Feature f: features)
@@ -259,7 +279,7 @@ public class ValidateFeatureTest
   {
     try
     {
-      final Entry entry = getEntry("/data/test_boundary.gff.gz");
+      final Entry entry = Utils.getEntry("/data/test_boundary.gff.gz");
       final FeatureVector features = entry.getAllFeatures();
       final EntryGroup egrp = new SimpleEntryGroup();
       egrp.add(new uk.ac.sanger.artemis.Entry(entry));
@@ -294,7 +314,7 @@ public class ValidateFeatureTest
   {
     try
     {
-      final Entry entry = getEntry("/data/test_boundary.gff.gz");
+      final Entry entry = Utils.getEntry("/data/test_boundary.gff.gz");
       final FeatureVector features = entry.getAllFeatures();
       final EntryGroup egrp = new SimpleEntryGroup();
       egrp.add(new uk.ac.sanger.artemis.Entry(entry));
@@ -317,24 +337,4 @@ public class ValidateFeatureTest
     }
   }
   
-  
-  private Entry getEntry(final String gff)
-  {
-    try
-    {
-      URL gffFile = ValidateFeatureTest.class.getResource(gff);
-      final Document doc = DocumentFactory.makeDocument(gffFile.getFile());
-      return DocumentEntryFactory.makeDocumentEntry(
-          Options.getArtemisEntryInformation(),doc,null);
-    }
-    catch(EntryInformationException e) 
-    {
-      Assert.fail(e.getMessage());
-    }
-    catch(IOException e) 
-    {
-      Assert.fail(e.getMessage());
-    }
-    return null;
-  }
 }
\ No newline at end of file