JAL-4134 properly resolve positions in associated aligned sequence for matrix group...

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

diff --git a/test/jalview/io/gff/GffHelperFactoryTest.java b/test/jalview/io/gff/GffHelperFactoryTest.java
index cfe1d12..f607cd1 100644 (file)
--- a/test/jalview/io/gff/GffHelperFactoryTest.java
+++ b/test/jalview/io/gff/GffHelperFactoryTest.java
@@ -24,11 +24,21 @@ 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()
   {
@@ -41,7 +51,8 @@ public class GffHelperFactoryTest
      */
     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";
@@ -50,32 +61,40 @@ public class GffHelperFactoryTest
 
     // 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