From e97e48617663304146a91d18e54fc23aa1b9e4b0 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 1 Nov 2016 17:52:58 +0000
Subject: [PATCH] JAL-1738 JAL-345 failing test for mark columns  - fail
 actually due to jalview.analysis.Finder creating more than
 expected SearchResultMatch objects for a given pattern

---
 .../controller/AlignViewControllerTest.java        |   57 ++++++++++++++++++++
 1 file changed, 57 insertions(+)

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index 7fd8965..b1af507 100644
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -23,11 +23,19 @@ 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;
@@ -116,4 +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",
+            f.getSearchResults(), sr);
+
+    /*
+     * now check simple mark columns from find operation
+     */
+    af.getViewport().setSearchResults(sr);
+    AlignViewControllerI avc = af.avc;
+
+    avc.markHighlightedColumns(false, false, false);
+    assertEquals("Didn't select highlighted columns", af.getViewport()
+            .getColumnSelection().getSelectedRanges(),
+            Arrays.asList(new int[][] { { 1, 13 } }));
+  }
 }
-- 
1.7.10.2