X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FGff3tests.java;h=faa4d430d73538f769f2db6024e212cfdb2f459d;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=3a2e1ed47235fda440324d6d6822e6f94d43af6d;hpb=b032972727ddb48eb95e5f593603df57cd22d343;p=jalview.git

diff --git a/test/jalview/io/Gff3tests.java b/test/jalview/io/Gff3tests.java
index 3a2e1ed..faa4d43 100644
--- a/test/jalview/io/Gff3tests.java
+++ b/test/jalview/io/Gff3tests.java
@@ -1,17 +1,49 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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.assertTrue;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 
-import org.junit.Assert;
-import org.junit.Test;
+import java.io.IOException;
+
+import org.testng.annotations.Test;
 
 public class Gff3tests
 {
 
   private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
-          exonerateOutput = "examples/testdata/exonerateoutput.gff";
+          exonerateOutput = "examples/testdata/exonerateoutput.gff",
+          simpleGff3file = "examples/testdata/simpleGff3.gff";
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testExonerateImport()
   {
     // exonerate does not tag sequences after features, so we have a more
@@ -22,23 +54,115 @@ public class Gff3tests
     AlignFrame af = loader.LoadFileWaitTillLoaded(exonerateSeqs,
             FormatAdapter.FILE);
 
-    Assert.assertEquals("Unexpected number of DNA protein associations", 0,
-            af.getViewport().getAlignment().getCodonFrames().size());
+    assertEquals("Unexpected number of DNA protein associations", 0, af
+            .getViewport().getAlignment().getCodonFrames().size());
 
     af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
 
-    Assert.assertNotEquals("Expected at least one DNA protein association",
-            0, af.getViewport().getAlignment().getCodonFrames().size());
+    assertTrue("Expected at least one DNA protein association", af
+            .getViewport().getAlignment().getDataset().getCodonFrames()
+            .size() > 0);
+
+  }
+
+  @Test(groups = { "Functional" })
+  public void simpleGff3FileIdentify()
+  {
+    assertEquals("Didn't recognise file correctly.", IdentifyFile.GFF3File,
+            new IdentifyFile().Identify(simpleGff3file, FormatAdapter.FILE));
+  }
+
+  @Test(groups = { "Functional" })
+  public void simpleGff3FileClass() throws IOException
+  {
+    AlignmentI dataset = new Alignment(new SequenceI[] {});
+    FeaturesFile ffile = new FeaturesFile(simpleGff3file,
+            FormatAdapter.FILE);
+
+    boolean parseResult = ffile.parse(dataset, null, null, false, false);
+    assertTrue("return result should be true", parseResult);
+    checkDatasetfromSimpleGff3(dataset);
+  }
+
+  @Test(groups = { "Functional" })
+  public void simpleGff3FileLoader() throws IOException
+  {
+    AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+            simpleGff3file, FormatAdapter.FILE);
+    assertTrue(
+            "Didn't read the alignment into an alignframe from Gff3 File",
+            af != null);
+    checkDatasetfromSimpleGff3(af.getViewport().getAlignment().getDataset());
+  }
+
+  @Test(groups = { "Functional" })
+  public void simpleGff3RelaxedIdMatching() throws IOException
+  {
+    AlignmentI dataset = new Alignment(new SequenceI[] {});
+    FeaturesFile ffile = new FeaturesFile(simpleGff3file,
+            FormatAdapter.FILE);
+
+    boolean parseResult = ffile.parse(dataset, null, null, false, true);
+    assertTrue("return result (relaxedID matching) should be true",
+            parseResult);
+    checkDatasetfromSimpleGff3(dataset);
+  }
+
+  @Test(groups = { "Functional" })
+  public void readGff3File() throws IOException
+  {
+    Gff3File gff3reader = new Gff3File(simpleGff3file, FormatAdapter.FILE);
+    Alignment dataset = new Alignment(gff3reader.getSeqsAsArray());
+    gff3reader.addProperties(dataset);
+    checkDatasetfromSimpleGff3(dataset);
+
+  }
+
+  private void checkDatasetfromSimpleGff3(AlignmentI dataset)
+  {
+    assertEquals("no sequences extracted from GFF3 file", 2,
+            dataset.getHeight());
 
+    SequenceI seq1 = dataset.findName("seq1"), seq2 = dataset
+            .findName("seq2");
+    assertNotNull(seq1);
+    assertNotNull(seq2);
+    assertFalse(
+            "Failed to replace dummy seq1 with real sequence",
+            seq1 instanceof SequenceDummy
+                    && ((SequenceDummy) seq1).isDummy());
+    assertFalse(
+            "Failed to replace dummy seq2 with real sequence",
+            seq2 instanceof SequenceDummy
+                    && ((SequenceDummy) seq2).isDummy());
+    String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
+    assertFalse("dummy replacement buggy for seq1",
+            placeholderseq.equals(seq1.getSequenceAsString()));
+    assertFalse("dummy replacement buggy for seq2",
+            placeholderseq.equals(seq2.getSequenceAsString()));
+    assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// !=
+                                                                           // null);
+    assertEquals("Wrong number of features", 3,
+            seq1.getSequenceFeatures().length);
+    assertNull(seq2.getSequenceFeatures());
+    assertEquals(
+            "Wrong number of features",
+            0,
+            seq2.getSequenceFeatures() == null ? 0 : seq2
+                    .getSequenceFeatures().length);
+    assertTrue(
+            "Expected at least one CDNA/Protein mapping for seq1",
+            dataset.getCodonFrame(seq1) != null
+                    && dataset.getCodonFrame(seq1).size() > 0);
 
   }
-  // @Test
+  // @Test(groups ={ "Functional" })
   // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
   // {
   // fail("Not yet implemented");
   // }
   //
-  // @Test
+  // @Test(groups ={ "Functional" })
   // public final void testAlignFileBooleanStringString()
   // {
   // fail("Not yet implemented");