X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FGff3tests.java;fp=test%2Fjalview%2Fio%2FGff3tests.java;h=0000000000000000000000000000000000000000;hb=4da7d6ec8ef5ff030c6d06d37a099da2d92d7246;hp=b78a0049a6d072ec8d7306126f9037c14727f135;hpb=43ee8686fab13cd6952335ade1382adf3226f7a1;p=jalview.git

diff --git a/test/jalview/io/Gff3tests.java b/test/jalview/io/Gff3tests.java
deleted file mode 100644
index b78a004..0000000
--- a/test/jalview/io/Gff3tests.java
+++ /dev/null
@@ -1,171 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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 java.io.IOException;
-
-import org.testng.annotations.Test;
-
-public class Gff3tests
-{
-
-  private static String exonerateSeqs = "examples/testdata/exonerateseqs.fa",
-          exonerateOutput = "examples/testdata/exonerateoutput.gff",
-          simpleGff3file = "examples/testdata/simpleGff3.gff";
-
-  @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", 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(groups ={ "Functional" })
-  // public final void testPrintGFFFormatSequenceIArrayMapOfStringObject()
-  // {
-  // fail("Not yet implemented");
-  // }
-  //
-  // @Test(groups ={ "Functional" })
-  // public final void testAlignFileBooleanStringString()
-  // {
-  // fail("Not yet implemented");
-  // }
-
-}