X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FFeaturesFileTest.java;h=506ee91dcf1248a9506fe6592a3a3e799a8ec9e4;hb=2acdd7fdaa575dd5238585ad86597f808b30d281;hp=ed388a5f1aecae14f188fe16961174411d5c7cca;hpb=ab9351a591e5295be9e41bfa86238ccc2a8024f8;p=jalview.git

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index ed388a5..506ee91 100644
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -24,10 +24,14 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
+import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
+import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
@@ -38,16 +42,16 @@ import jalview.schemes.GraduatedColor;
 import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
+import java.util.Iterator;
 import java.util.Map;
+import java.util.Set;
 
 import org.testng.annotations.Test;
 
 public class FeaturesFileTest
 {
 
-  private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
-          exonerateOutput = "examples/testdata/exonerateoutput.gff",
-          simpleGffFile = "examples/testdata/simpleGff3.gff";
+  private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
 
   @Test(groups = { "Functional" })
   public void testParse() throws Exception
@@ -144,8 +148,9 @@ public class FeaturesFileTest
     AlignFrame af = new AlignFrame(al, 500, 500);
     Map<String, Object> colours = af.getFeatureRenderer()
             .getFeatureColours();
+    // GFF2 uses space as name/value separator in column 9
     String gffData = "METAL\tcc9900\n" + "GFF\n"
-            + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\n"
+            + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
     FeaturesFile featuresFile = new FeaturesFile(gffData,
             FormatAdapter.PASTE);
@@ -162,7 +167,7 @@ public class FeaturesFileTest
             .getSequenceFeatures();
     assertEquals(1, sfs.length);
     SequenceFeature sf = sfs[0];
-    assertEquals("uniprot", sf.description);
+    assertEquals("Iron-sulfur; 2Fe-2S", sf.description);
     assertEquals(44, sf.begin);
     assertEquals(45, sf.end);
     assertEquals("uniprot", sf.featureGroup);
@@ -240,14 +245,15 @@ public class FeaturesFileTest
    * @throws Exception
    */
   @Test(groups = { "Functional" })
-  public void testParse_pureGff() throws Exception
+  public void testParse_pureGff3() throws Exception
   {
     File f = new File("examples/uniref50.fa");
     AlignmentI al = readAlignmentFile(f);
     AlignFrame af = new AlignFrame(al, 500, 500);
     Map<String, Object> colours = af.getFeatureRenderer()
             .getFeatureColours();
-    String gffData = "##gff-version 2\n"
+    // GFF3 uses '=' separator for name/value pairs in colum 9
+    String gffData = "##gff-version 3\n"
             + "FER_CAPAA\tuniprot\tMETAL\t39\t39\t0.0\t.\t.\t"
             + "Note=Iron-sulfur (2Fe-2S);Note=another note;evidence=ECO:0000255|PROSITE-ProRule:PRU00465\n"
             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.";
@@ -389,14 +395,6 @@ public class FeaturesFileTest
   }
 
   @Test(groups = { "Functional" })
-  public void simpleGff3FileIdentify()
-  {
-    assertEquals("Didn't recognise file correctly.",
-            IdentifyFile.FeaturesFile,
-            new IdentifyFile().identify(simpleGffFile, FormatAdapter.FILE));
-  }
-
-  @Test(groups = { "Functional" })
   public void simpleGff3FileLoader() throws IOException
   {
     AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
@@ -421,24 +419,63 @@ public class FeaturesFileTest
     checkDatasetfromSimpleGff3(dataset);
   }
 
+  /**
+   * Tests loading exonerate GFF2 output, including 'similarity' alignment
+   * feature, on to sequences
+   */
   @Test(groups = { "Functional" })
   public void testExonerateImport()
   {
-    // exonerate does not tag sequences after features, so we have a more
-    // conventional annotation import test here
-  
     FileLoader loader = new FileLoader(false);
-  
-    AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
+    AlignFrame af = loader.LoadFileWaitTillLoaded(
+            "examples/testdata/exonerateseqs.fa",
             FormatAdapter.FILE);
   
-    assertEquals("Unexpected number of DNA protein associations", 0, af
-            .getViewport().getAlignment().getCodonFrames().size());
+    af.loadJalviewDataFile("examples/testdata/exonerateoutput.gff",
+            FormatAdapter.FILE, null, null);
   
-    af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
-  
-    assertTrue("Expected at least one DNA protein association", 0 != af
-            .getViewport().getAlignment().getDataset().getCodonFrames()
-            .size());
+    /*
+     * verify one mapping to a dummy sequence, one to a real one
+     */
+    Set<AlignedCodonFrame> mappings = af
+            .getViewport().getAlignment().getDataset().getCodonFrames();
+    assertEquals(2, mappings.size());
+    Iterator<AlignedCodonFrame> iter = mappings.iterator();
+
+    // first mapping is to dummy sequence
+    AlignedCodonFrame mapping = iter.next();
+    Mapping[] mapList = mapping.getProtMappings();
+    assertEquals(1, mapList.length);
+    assertTrue(mapList[0].getTo() instanceof SequenceDummy);
+    assertEquals("DDB_G0269124", mapList[0].getTo().getName());
+
+    // second mapping is to a sequence in the alignment
+    mapping = iter.next();
+    mapList = mapping.getProtMappings();
+    assertEquals(1, mapList.length);
+    SequenceI proteinSeq = af.getViewport().getAlignment()
+            .findName("DDB_G0280897");
+    assertSame(proteinSeq.getDatasetSequence(), mapList[0].getTo());
+    assertEquals(1, mapping.getdnaToProt().length);
+
+    // 143 in protein should map to codon [11270, 11269, 11268] in dna
+    int[] mappedRegion = mapList[0].getMap().locateInFrom(143, 143);
+    assertArrayEquals(new int[] { 11270, 11268 }, mappedRegion);
+
+    // 182 in protein should map to codon [11153, 11152, 11151] in dna
+    mappedRegion = mapList[0].getMap().locateInFrom(182, 182);
+    assertArrayEquals(new int[] { 11153, 11151 }, mappedRegion);
+
+    // and the reverse mapping:
+    mappedRegion = mapList[0].getMap().locateInTo(11151, 11153);
+    assertArrayEquals(new int[] { 182, 182 }, mappedRegion);
+
+    // 11150 in dna should _not_ map to protein
+    mappedRegion = mapList[0].getMap().locateInTo(11150, 11150);
+    assertNull(mappedRegion);
+
+    // similarly 183 in protein should _not_ map to dna
+    mappedRegion = mapList[0].getMap().locateInFrom(183, 183);
+    assertNull(mappedRegion);
   }
 }