+/*
+ * 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()
{
*/
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);
+ 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";
// 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);
+ 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);
+ 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);
+ 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);
+ 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);
+ 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);
+ 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);
+ 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);
+ assertTrue(GffHelperFactory
+ .getHelper(gff.split(tabRegex)) instanceof InterProScanHelper);
/*
* nothing specific - return the generic GFF3 class if Name=Value is present in col9