X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcontroller%2FAlignViewControllerTest.java;h=2e89b0ecd6d95dc5a8e0c24c8fd2204b570e1e3b;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=8c81d5166eb2ee7b705fd5c89cffd3aedf33182c;hpb=a2fe8b63324a2907943cab8e5d4de2c81107b793;p=jalview.git

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index 8c81d51..2e89b0e 100644
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -23,17 +23,35 @@ package jalview.controller;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.analysis.Finder;
+import jalview.api.AlignViewControllerI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
 
+import java.util.Arrays;
 import java.util.BitSet;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class AlignViewControllerTest
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @Test(groups = "Functional")
   public void testFindColumnsWithFeature()
   {
@@ -144,4 +162,53 @@ public class AlignViewControllerTest
     assertEquals(0, seqCount);
     assertEquals(0, bs.cardinality());
   }
+
+  /**
+   * shameless copy of test data from findFeature for testing mark columns from
+   * highlight
+   */
+  @Test(groups = "Functional")
+  public void testSelectColumnsWithHighlight()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
+                    + "seq3 aaaaaaaaaaMMMMMaaaaa\n"
+                    + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
+
+    SearchResultsI sr = new SearchResults();
+    SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
+    SequenceI seq1 = sqs[0];
+    SequenceI seq2 = sqs[1];
+    SequenceI seq3 = sqs[2];
+    SequenceI seq4 = sqs[3];
+
+    /*
+     * features start/end are base 1
+     */
+    sr.addResult(seq1, 2, 4);
+    sr.addResult(seq2, 4, 10);
+    sr.addResult(seq3, 11, 15);
+
+    /*
+     *  test Match/Find works first
+     */
+    Finder f = new Finder(af.getViewport().getAlignment(), null);
+    f.setFindAll(true);
+    f.setCaseSensitive(true);
+    f.find("M+");
+    assertEquals(
+            "Finder found different set of results to manually created SearchResults",
+            sr, f.getSearchResults());
+
+    /*
+     * now check simple mark columns from find operation
+     */
+    af.getViewport().setSearchResults(sr);
+    AlignViewControllerI avc = af.avc;
+
+    avc.markHighlightedColumns(false, false, false);
+    assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
+            .getViewport().getColumnSelection().getSelectedRanges()
+            .toArray(), new int[][] { { 1, 14 } }));
+  }
 }