diff --git a/test/uk/ac/sanger/artemis/io/GFFTest.java b/test/uk/ac/sanger/artemis/io/GFFTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..fd4b41cb42fedfa9610bb796da2b8349d3946d7a
--- /dev/null
+++ b/test/uk/ac/sanger/artemis/io/GFFTest.java
@@ -0,0 +1,97 @@
+/*
+ * 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
diff --git a/test/uk/ac/sanger/artemis/io/Utils.java b/test/uk/ac/sanger/artemis/io/Utils.java
new file mode 100644
index 0000000000000000000000000000000000000000..6395e94b028be31ecac37fab1d7ab89039db8c1a
--- /dev/null
+++ b/test/uk/ac/sanger/artemis/io/Utils.java
@@ -0,0 +1,90 @@
+/*
+ * 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
diff --git a/test/uk/ac/sanger/artemis/io/ValidateFeatureTest.java b/test/uk/ac/sanger/artemis/io/ValidateFeatureTest.java
index bbafa43ff7ac0d57f6c0d1be92e4e0b6c4974c67..676c92cd822543b4bd418649a4f28179135a6108 100644
--- a/test/uk/ac/sanger/artemis/io/ValidateFeatureTest.java
+++ b/test/uk/ac/sanger/artemis/io/ValidateFeatureTest.java
@@ -1,3 +1,23 @@
+/*
+ * 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