Merge branch 'JAL-1956_featureStyles' into features/JAL-653_JAL-1766_htslib_refseqsupport

[jalview.git] / test / jalview / io / FeaturesFileTest.java

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index ed388a5..7112c77 100644 (file)
--- 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);
@@ -240,17 +245,18 @@ 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.";
+            + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t3.0\t.\t.\tID=$23";
     FeaturesFile featuresFile = new FeaturesFile(gffData,
             FormatAdapter.PASTE);
     assertTrue("Failed to parse features file",
@@ -333,8 +339,8 @@ public class FeaturesFileTest
     assertEquals("no sequences extracted from GFF3 file", 2,
             dataset.getHeight());
   
-    SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
-            .findName("seq2");
+    SequenceI seq1 = dataset.findName("seq1");
+    SequenceI seq2 = dataset.findName("seq2");
     assertNotNull(seq1);
     assertNotNull(seq2);
     assertFalse(
@@ -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(
@@ -404,8 +402,7 @@ public class FeaturesFileTest
     assertTrue(
             "Didn't read the alignment into an alignframe from Gff3 File",
             af != null);
-    // FIXME codon mappings are on the alignment but not on the dataset
-    checkDatasetfromSimpleGff3(af.getViewport().getAlignment()/* .getDataset() */);
+    checkDatasetfromSimpleGff3(af.getViewport().getAlignment());
   }
 
   @Test(groups = { "Functional" })
@@ -420,25 +417,4 @@ public class FeaturesFileTest
             parseResult);
     checkDatasetfromSimpleGff3(dataset);
   }
-
-  @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,
-            FormatAdapter.FILE);
-  
-    assertEquals("Unexpected number of DNA protein associations", 0, af
-            .getViewport().getAlignment().getCodonFrames().size());
-  
-    af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
-  
-    assertTrue("Expected at least one DNA protein association", 0 != af
-            .getViewport().getAlignment().getDataset().getCodonFrames()
-            .size());
-  }
 }