JAL-2189 apply license

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

diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index d85b68f..7fd8965 100644 (file)
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -1,16 +1,34 @@
+/*
+ * 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.datamodel.ColumnSelection;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 
 import java.util.BitSet;
-import java.util.List;
 
 import org.testng.annotations.Test;
 
@@ -37,7 +55,7 @@ public class AlignViewControllerTest
             0f, null));
 
     /*
-     * select the first three columns --> seq1 2-3
+     * select the first three columns --> Metal in seq1 2-3
      */
     SequenceGroup sg = new SequenceGroup();
     sg.setStartRes(0); // base 0
@@ -54,14 +72,13 @@ public class AlignViewControllerTest
     assertEquals(2, bs.cardinality());
     assertTrue(bs.get(1));
     assertTrue(bs.get(2));
-    
+
     /*
-     * select the first four columns: seq1 2:4, seq2 4:4
+     * 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));
@@ -69,7 +86,7 @@ public class AlignViewControllerTest
     assertTrue(bs.get(3));
 
     /*
-     * select column 11: seq3 only
+     * select column 11: Metal in seq3 only
      */
     sg.setStartRes(10);
     sg.setEndRes(10);
@@ -99,100 +116,4 @@ public class AlignViewControllerTest
     assertEquals(0, seqCount);
     assertEquals(0, bs.cardinality());
   }
-
-  @Test(groups = "Functional")
-  public void testSelectMarkedColumns_invert()
-  {
-    ColumnSelection cs = new ColumnSelection();
-    cs.addElement(5); // this will be cleared
-    BitSet toMark = new BitSet();
-    toMark.set(1);
-    toMark.set(3);
-    toMark.set(6);
-    toMark.set(9);
-
-    /*
-     * inverted selection of {3, 6} should select {4, 5, 7, 8}
-     */
-    assertTrue(AlignViewController.selectMarkedColumns(cs, true, false,
-            false, toMark, 3, 8));
-    List<Integer> selected = cs.getSelected();
-    assertEquals(4, selected.size());
-    assertTrue(selected.contains(4));
-    assertTrue(selected.contains(5));
-    assertTrue(selected.contains(7));
-    assertTrue(selected.contains(8));
-  }
-
-  @Test(groups = "Functional")
-  public void testSelectMarkedColumns()
-  {
-    ColumnSelection cs = new ColumnSelection();
-    cs.addElement(5); // this will be cleared
-    BitSet toMark = new BitSet();
-    toMark.set(1);
-    toMark.set(3);
-    toMark.set(6);
-    toMark.set(9);
-  
-    assertTrue(AlignViewController.selectMarkedColumns(cs, false, false,
-            false, toMark, 3, 8));
-    List<Integer> selected = cs.getSelected();
-    assertEquals(2, selected.size());
-    assertTrue(selected.contains(3));
-    assertTrue(selected.contains(6));
-  }
-
-  @Test(groups = "Functional")
-  public void testSelectMarkedColumns_extend()
-  {
-    ColumnSelection cs = new ColumnSelection();
-    cs.addElement(1);
-    cs.addElement(5);
-    BitSet toMark = new BitSet();
-    toMark.set(1);
-    toMark.set(3);
-    toMark.set(6);
-    toMark.set(9);
-  
-    /*
-     * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
-     */
-    assertTrue(AlignViewController.selectMarkedColumns(cs, false, true,
-            false, toMark, 3, 8));
-    List<Integer> selected = cs.getSelected();
-    assertEquals(4, selected.size());
-    assertTrue(selected.contains(1));
-    assertTrue(selected.contains(3));
-    assertTrue(selected.contains(5));
-    assertTrue(selected.contains(6));
-  }
-
-  @Test(groups = "Functional")
-  public void testSelectMarkedColumns_toggle()
-  {
-    ColumnSelection cs = new ColumnSelection();
-    cs.addElement(1); // outside change range
-    cs.addElement(3);
-    cs.addElement(4);
-    cs.addElement(10); // outside change range
-    BitSet toMark = new BitSet();
-    toMark.set(1);
-    toMark.set(3);
-    toMark.set(6);
-    toMark.set(9);
-  
-    /*
-     * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
-     */
-    assertTrue(AlignViewController.selectMarkedColumns(cs, false, false,
-            true, toMark, 3, 8));
-    List<Integer> selected = cs.getSelected();
-    assertEquals(4, selected.size());
-    assertTrue(selected.contains(1));
-    assertTrue(selected.contains(4));
-    assertTrue(selected.contains(6));
-    assertTrue(selected.contains(10));
-  }
-  // TODO testSelectMarkedColumns with combinations of invert/extend/toggle set
 }