X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcontroller%2FAlignViewControllerTest.java;h=fde4da174b25d2298f1568382637d353b15a664f;hb=490bea038483dcc853766de08a8971668930f43a;hp=8c81d5166eb2ee7b705fd5c89cffd3aedf33182c;hpb=a2fe8b63324a2907943cab8e5d4de2c81107b793;p=jalview.git

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index 8c81d51..fde4da1 100644
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -23,17 +23,40 @@ 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.api.FeatureColourI;
+import jalview.api.FinderI;
+import jalview.datamodel.Alignment;
+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 jalview.schemes.FeatureColour;
 
+import java.awt.Color;
+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()
   {
@@ -49,13 +72,14 @@ public class AlignViewControllerTest
             null));
     seq1.addSequenceFeature(new SequenceFeature("Helix", "desc", 1, 15, 0f,
             null));
-    seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10, 0f,
+    seq2.addSequenceFeature(new SequenceFeature("Metal", "desc", 4, 10,
+            10f,
             null));
     seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
-            0f, null));
+            10f, null));
     // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
-    seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", 8, 12,
-            0f, null));
+    seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc",
+            8, 12, 0f, null));
 
     /*
      * select the first five columns --> Metal in seq1 cols 4-5
@@ -68,9 +92,18 @@ public class AlignViewControllerTest
     sg.addSequence(seq3, false);
     sg.addSequence(seq4, false);
 
+    /*
+     * set features visible on a viewport as only visible features are selected
+     */
+    AlignFrame af = new AlignFrame(new Alignment(new SequenceI[] { seq1,
+        seq2, seq3, seq4 }), 100, 100);
+    af.getFeatureRenderer().findAllFeatures(true);
+
+    AlignViewController avc = new AlignViewController(af, af.getViewport(),
+            af.alignPanel);
+
     BitSet bs = new BitSet();
-    int seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
-            bs);
+    int seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(1, seqCount);
     assertEquals(2, bs.cardinality());
     assertTrue(bs.get(3)); // base 0
@@ -81,7 +114,7 @@ public class AlignViewControllerTest
      */
     sg.setEndRes(6);
     bs.clear();
-    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+    seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(2, seqCount);
     assertEquals(4, bs.cardinality());
     assertTrue(bs.get(3));
@@ -95,7 +128,7 @@ public class AlignViewControllerTest
     sg.setStartRes(13);
     sg.setEndRes(13);
     bs.clear();
-    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+    seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(1, seqCount);
     assertEquals(1, bs.cardinality());
     assertTrue(bs.get(13));
@@ -106,18 +139,36 @@ public class AlignViewControllerTest
     sg.setStartRes(17);
     sg.setEndRes(19);
     bs.clear();
-    seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
+    seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
     assertEquals(0, seqCount);
     assertEquals(0, bs.cardinality());
 
     /*
+     * threshold Metal to hide where score < 5
+     * seq1 feature in columns 4-6 is hidden
+     * seq2 feature in columns 6-7 is shown
+     */
+    FeatureColourI fc = new FeatureColour(null, Color.red, Color.blue, null,
+            0f, 10f);
+    fc.setAboveThreshold(true);
+    fc.setThreshold(5f);
+    af.getFeatureRenderer().setColour("Metal", fc);
+    sg.setStartRes(0);
+    sg.setEndRes(6);
+    bs.clear();
+    seqCount = avc.findColumnsWithFeature("Metal", sg, bs);
+    assertEquals(1, seqCount);
+    assertEquals(2, bs.cardinality());
+    assertTrue(bs.get(5));
+    assertTrue(bs.get(6));
+
+    /*
      * columns 11-13 should not match disulfide bond at 8/12
      */
     sg.setStartRes(10);
     sg.setEndRes(12);
     bs.clear();
-    seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
-            sg, bs);
+    seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
     assertEquals(0, seqCount);
     assertEquals(0, bs.cardinality());
 
@@ -127,8 +178,7 @@ public class AlignViewControllerTest
     sg.setStartRes(5);
     sg.setEndRes(17);
     bs.clear();
-    seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
-            sg, bs);
+    seqCount = avc.findColumnsWithFeature("disulfide bond", sg, bs);
     assertEquals(1, seqCount);
     assertEquals(2, bs.cardinality());
     assertTrue(bs.get(8));
@@ -140,8 +190,55 @@ public class AlignViewControllerTest
     sg.setStartRes(0);
     sg.setEndRes(19);
     bs.clear();
-    seqCount = AlignViewController.findColumnsWithFeature("Pfam", sg, bs);
+    seqCount = avc.findColumnsWithFeature("Pfam", sg, bs);
     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
+     */
+    FinderI f = new Finder(af.getViewport());
+    f.findAll("M+", true, false, false);
+    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 } }));
+  }
 }