X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcontroller%2FAlignViewControllerTest.java;h=2e89b0ecd6d95dc5a8e0c24c8fd2204b570e1e3b;hb=818aa3cd6fb2d07b54e3b4c283f8580c74bc4b58;hp=d7f7acbfe5fe5bfc653e9c24452519af8b283f7d;hpb=095f0d92cb343875bd0f76f833c1eaa8614c22cd;p=jalview.git

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index d7f7acb..2e89b0e 100644
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -23,24 +23,42 @@ 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()
   {
-    SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
-    SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
-    SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
-    SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+    SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
+    SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
+    SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
+    SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
 
     /*
      * features start/end are base 1
@@ -58,11 +76,11 @@ public class AlignViewControllerTest
             0f, null));
 
     /*
-     * select the first three columns --> Metal in seq1 2-3
+     * select the first five columns --> Metal in seq1 cols 4-5
      */
     SequenceGroup sg = new SequenceGroup();
     sg.setStartRes(0); // base 0
-    sg.setEndRes(2);
+    sg.setEndRes(4);
     sg.addSequence(seq1, false);
     sg.addSequence(seq2, false);
     sg.addSequence(seq3, false);
@@ -73,36 +91,37 @@ public class AlignViewControllerTest
             bs);
     assertEquals(1, seqCount);
     assertEquals(2, bs.cardinality());
-    assertTrue(bs.get(1));
-    assertTrue(bs.get(2));
+    assertTrue(bs.get(3)); // base 0
+    assertTrue(bs.get(4));
 
     /*
-     * select the first four columns: Metal in seq1 2:4, seq2 4:4
+     * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7 
      */
-    sg.setEndRes(3);
+    sg.setEndRes(6);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(2, seqCount);
-    assertEquals(3, bs.cardinality());
-    assertTrue(bs.get(1));
-    assertTrue(bs.get(2));
+    assertEquals(4, bs.cardinality());
     assertTrue(bs.get(3));
+    assertTrue(bs.get(4));
+    assertTrue(bs.get(5));
+    assertTrue(bs.get(6));
 
     /*
-     * select column 11: Metal in seq3 only
+     * select column 14: Metal in seq3 only
      */
-    sg.setStartRes(10);
-    sg.setEndRes(10);
+    sg.setStartRes(13);
+    sg.setEndRes(13);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(1, seqCount);
     assertEquals(1, bs.cardinality());
-    assertTrue(bs.get(10));
+    assertTrue(bs.get(13));
 
     /*
-     * select columns 16-20: no Metal feature
+     * select columns 18-20: no Metal feature
      */
-    sg.setStartRes(15);
+    sg.setStartRes(17);
     sg.setEndRes(19);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
@@ -110,10 +129,10 @@ public class AlignViewControllerTest
     assertEquals(0, bs.cardinality());
 
     /*
-     * columns 9-11 should not match disulfide bond at 8/12
+     * columns 11-13 should not match disulfide bond at 8/12
      */
-    sg.setStartRes(8);
-    sg.setEndRes(10);
+    sg.setStartRes(10);
+    sg.setEndRes(12);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
             sg, bs);
@@ -121,17 +140,17 @@ public class AlignViewControllerTest
     assertEquals(0, bs.cardinality());
 
     /*
-     * columns 6-14 should match disulfide bond at 8/12
+     * columns 6-18 should match disulfide bond at columns 9, 14
      */
     sg.setStartRes(5);
-    sg.setEndRes(13);
+    sg.setEndRes(17);
     bs.clear();
     seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
             sg, bs);
     assertEquals(1, seqCount);
     assertEquals(2, bs.cardinality());
-    assertTrue(bs.get(7));
-    assertTrue(bs.get(11));
+    assertTrue(bs.get(8));
+    assertTrue(bs.get(13));
 
     /*
      * look for a feature that isn't there
@@ -143,4 +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 } }));
+  }
 }