JAL-3210 Barebones gradle/buildship/eclipse. See README

[jalview.git] / test / jalview / io / gff / GffHelperFactoryTest.java

diff --git a/test/jalview/io/gff/GffHelperFactoryTest.java b/test/jalview/io/gff/GffHelperFactoryTest.java
deleted file mode 100644 (file)
index 84725ff..0000000
--- a/test/jalview/io/gff/GffHelperFactoryTest.java
+++ /dev/null
@@ -1,102 +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.gff;
-
-import static org.testng.AssertJUnit.assertNull;
-import static org.testng.AssertJUnit.assertSame;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.gui.JvOptionPane;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class GffHelperFactoryTest
-{
-
-  @BeforeClass(alwaysRun = true)
-  public void setUpJvOptionPane()
-  {
-    JvOptionPane.setInteractiveMode(false);
-    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-  }
-
-  @Test(groups = "Functional")
-  public void testGetHelper()
-  {
-    assertNull(GffHelperFactory.getHelper(null));
-
-    String tabRegex = "\\t";
-
-    /*
-     * column 3 = 'similarity' indicates exonerate GFF alignment data
-     */
-    String gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\t";
-    // no attributes (column 9 data):
-    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof Gff2Helper);
-
-    // attributes set but unhandled featureGroup - get generic handler
-    gff = "submitted\taffine:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
-    assertSame(GffHelperFactory.getHelper(gff.split(tabRegex)).getClass(),
-            Gff3Helper.class);
-
-    // handled featureGroup (exonerate model) values
-    gff = "submitted\texonerate:protein2dna:local\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
-    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
-
-    gff = "submitted\tprotein2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
-    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
-
-    gff = "submitted\tcoding2coding\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
-    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
-
-    gff = "submitted\tcoding2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
-    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
-
-    gff = "submitted\tcdna2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
-    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
-
-    gff = "submitted\tgenome2genome\tsimilarity\t20\t30\t99\t+\t.\tID=$1";
-    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
-
-    // not case-sensitive:
-    gff = "submitted\tgenome2genome\tSIMILARITY\t20\t30\t99\t+\t.\tID=$1";
-    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof ExonerateHelper);
-
-    /*
-     * InterProScan has 'protein_match' in column 3
-     */
-    gff = "Submitted\tPANTHER\tprotein_match\t1\t1174\t0.0\t+\t.\tName=PTHR32154";
-    assertTrue(GffHelperFactory.getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
-
-    /*
-     * nothing specific - return the generic GFF3 class if Name=Value is present in col9
-     */
-    gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID=1";
-    GffHelperI helper = GffHelperFactory.getHelper(gff.split(tabRegex));
-    assertSame(helper.getClass(), Gff3Helper.class);
-
-    // return the generic GFF2 class if "Name Value" is present in col9
-    gff = "nothing\tinteresting\there\t20\t30\t99\t+\t.\tID 1";
-    helper = GffHelperFactory.getHelper(gff.split(tabRegex));
-    assertSame(helper.getClass(), Gff2Helper.class);
-  }
-}