JAL-3499 process motifs in features file to create features

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

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 090de6f..5c7bf15 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -23,6 +23,7 @@ package jalview.io;
 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;
@@ -62,6 +63,7 @@ import org.testng.annotations.Test;
 
 public class FeaturesFileTest
 {
+  private static final String TAB = "\t";
   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
 
   @AfterClass(alwaysRun = true)
@@ -899,4 +901,145 @@ public class FeaturesFileTest
             + "ENDGROUP\tgrp2\n";
     assertEquals(expected, exported);
   }
+
+  /**
+   * Test parsing a features file with Jalview format features, including
+   * STARTMOTIFS/ENDMOTIFS lines with motifs to be matched to create features
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" })
+  public void testParse_jalviewFeaturesWithMotifs() throws IOException
+  {
+    File f = new File("examples/uniref50.fa");
+    AlignmentI al = readAlignmentFile(f);
+    AlignFrame af = new AlignFrame(al, 500, 500);
+    Map<String, FeatureColourI> colours = af.getFeatureRenderer()
+            .getFeatureColours();
+
+    /*
+     * hide columns with YKV motif; these should not get
+     * matched by the Finder
+     */
+    al.getHiddenColumns().hideColumns(62, 64);
+
+    // @formatter:off
+    String featureData = 
+            /*
+             * features in the null grup
+             */
+            "HELIX" + TAB + "blue\n" +
+            "MOTIF1" + TAB + "green\n" +
+            "MOTIF2" + TAB + "250,200,150|100,50,0|-3.9|4.5|above|-2.0\n" +
+            "adescription" + TAB + "FER_CAPAN" + TAB + "-1" + TAB + "42" + TAB + "45" + TAB + "HELIX\n" +
+            "STARTMOTIFS\n" +
+            "FLP" + TAB + "MOTIF1" + TAB + "flxMotifP\n" +
+            "F[LR]N" + TAB + "MOTIF1" + TAB + "flxMotifN\n" +
+            "fld" + TAB + "MOTIF1" + TAB + "flxMotifD\n" +
+            "YKV" + TAB + "MOTIF1" + TAB + "ykvMotif\n" +
+            "ENDMOTIFS\n" +
+            /*
+             * features in group uniprot
+             */
+            "STARTGROUP" + TAB + "uniprot\n" +
+            "bdescription" + TAB + "FER_CAPAN" + TAB + "-1" + TAB + "47" + TAB + "48" + TAB + "HELIX\n" +
+            "STARTMOTIFS\n" +
+            "FLG" + TAB + "MOTIF1" + TAB + "flxMotifG\n" +
+            "VTT" + TAB + "MOTIF2" + TAB + "vxtMotifT" + TAB + "-3.21\n" +
+            "VRT" + TAB + "MOTIF2" + TAB + "vxtMotifR\n" +
+            "ENDMOTIFS\n" +
+            "ENDGROUP"; 
+            // @formatter:on
+    FeaturesFile featuresFile = new FeaturesFile(featureData,
+            DataSourceType.PASTE);
+    assertTrue("Failed to parse features file",
+            featuresFile.parse(al, colours, true));
+
+    // verify HELIX features were parsed as normal
+    List<SequenceFeature> sfs = al.getSequenceAt(1).findFeatures(0, 999,
+            "HELIX");
+    assertEquals(2, sfs.size());
+    SequenceFeature sf = sfs.get(0);
+    assertNull(sf.getFeatureGroup());
+    assertEquals(42, sf.getBegin());
+    assertEquals(45, sf.getEnd());
+    assertEquals("adescription", sf.getDescription());
+    sf = sfs.get(1);
+    assertEquals("uniprot", sf.getFeatureGroup());
+    assertEquals(47, sf.getBegin());
+    assertEquals(48, sf.getEnd());
+    assertEquals("bdescription", sf.getDescription());
+
+    /*
+     * feature type MOTIF1
+     * FLP motif should match FER1_SOLLC/13-15 and Q93XJ9_SOLTU/13-15
+     * F[LR]N should match O80429_MAIZE/107-109
+     * fld should match nothing (as case sensitive)
+     * feature group should be null for the above
+     * FLG should match FER1_PEA/36-38, feature group uniprot
+     * YKV should match nothing as entirely within hidden columns
+     */
+    for (SequenceI seq : al.getSequences())
+    {
+      List<SequenceFeature> features = seq.findFeatures(0, 9999, "MOTIF1");
+      String name = seq.getName();
+      if (name.equals("FER1_SOLLC") || name.equals("Q93XJ9_SOLTU"))
+      {
+        assertEquals(1, features.size());
+        sf = features.get(0);
+        assertNull(sf.getFeatureGroup());
+        assertEquals(13, sf.getBegin());
+        assertEquals(15, sf.getEnd());
+        assertEquals("flxMotifP", sf.getDescription());
+      }
+      else if (name.equals("O80429_MAIZE"))
+      {
+        assertEquals(1, features.size());
+        sf = features.get(0);
+        assertNull(sf.getFeatureGroup());
+        assertEquals(107, sf.getBegin());
+        assertEquals(109, sf.getEnd());
+        assertEquals("flxMotifN", sf.getDescription());
+      }
+      else if (name.equals("FER1_PEA"))
+      {
+        assertEquals(1, features.size());
+        sf = features.get(0);
+        assertEquals("uniprot", sf.getFeatureGroup());
+        assertEquals(36, sf.getBegin());
+        assertEquals(38, sf.getEnd());
+        assertEquals("flxMotifG", sf.getDescription());
+      }
+      else
+      {
+        assertTrue("MOTIF1 features found for " + name, features.isEmpty());
+      }
+    }
+
+    /*
+     * feature type MOTIF2
+     * VTT motif should match FER1_PEA/26-28
+     * VRT should match nothing
+     */
+    for (SequenceI seq : al.getSequences())
+    {
+      List<SequenceFeature> features = seq.findFeatures(0, 9999, "MOTIF2");
+      String name = seq.getName();
+      if (name.equals("FER1_PEA"))
+      {
+        assertEquals(1, features.size());
+        sf = features.get(0);
+        assertEquals("uniprot", sf.getFeatureGroup());
+        assertEquals(26, sf.getBegin());
+        assertEquals(28, sf.getEnd());
+        assertEquals("vxtMotifT", sf.getDescription());
+        assertEquals(-3.21f, sf.getScore());
+      }
+      else
+      {
+        assertTrue("MOTIF2 features found for " + name, features.isEmpty());
+        assertTrue(features.isEmpty());
+      }
+    }
+  }
 }