JAL-1738 JAL-345 fix test - method appears to work

[jalview.git] / test / jalview / controller / AlignViewControllerTest.java

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index 3eefada..53eb171 100644 (file)
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -1,13 +1,41 @@
+/*
+ * 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.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.io.FileLoader;
+import jalview.io.FormatAdapter;
 
+import java.util.Arrays;
 import java.util.BitSet;
 
 import org.testng.annotations.Test;
@@ -52,14 +80,13 @@ public class AlignViewControllerTest
     assertEquals(2, bs.cardinality());
     assertTrue(bs.get(1));
     assertTrue(bs.get(2));
-    
+
     /*
      * select the first four columns: Metal in seq1 2:4, seq2 4:4
      */
     sg.setEndRes(3);
     bs.clear();
-    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
-            bs);
+    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(2, seqCount);
     assertEquals(3, bs.cardinality());
     assertTrue(bs.get(1));
@@ -97,4 +124,53 @@ 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", FormatAdapter.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 } }));
+  }
 }