X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fdatamodel%2FSearchResultsTest.java;h=a08c57732e963cdc6f534a8d6927aff020b9e281;hb=bdc5ecb2b1d6021d235c633112990cbacd072c4a;hp=46228b825cc7e0df5da56fe90f6cf0bbb7380f4b;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index 46228b8..a08c577 100644
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -25,7 +25,7 @@ import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertSame;
 import static org.testng.AssertJUnit.assertTrue;
 
-import jalview.datamodel.SearchResults.Match;
+import java.util.BitSet;
 
 import org.testng.annotations.Test;
 
@@ -36,7 +36,7 @@ public class SearchResultsTest
   public void testToString()
   {
     SequenceI seq = new Sequence("", "abcdefghijklm");
-    SearchResults sr = new SearchResults();
+    SearchResultsI sr = new SearchResults();
     sr.addResult(seq, 1, 1);
     assertEquals("0a", sr.toString());
     sr.addResult(seq, 3, 5);
@@ -66,8 +66,8 @@ public class SearchResultsTest
   public void testEquals()
   {
     SequenceI seq1 = new Sequence("", "abcdefghijklm");
-    SearchResults sr1 = new SearchResults();
-    SearchResults sr2 = new SearchResults();
+    SearchResultsI sr1 = new SearchResults();
+    SearchResultsI sr2 = new SearchResults();
 
     assertFalse(sr1.equals(null)); // null object
     assertFalse(sr1.equals(seq1)); // wrong type
@@ -111,8 +111,8 @@ public class SearchResultsTest
   {
     SequenceI seq1 = new Sequence("", "abcdefghijklm");
     SequenceI seq2 = new Sequence("", "abcdefghijklm");
-    SearchResults sr1 = new SearchResults();
-    SearchResults sr2 = new SearchResults();
+    SearchResultsI sr1 = new SearchResults();
+    SearchResultsI sr2 = new SearchResults();
 
     sr1.addResult(seq1, 1, 1);
     sr2.addResult(seq2, 1, 1);
@@ -127,8 +127,8 @@ public class SearchResultsTest
   public void testEquals_orderDiffers()
   {
     SequenceI seq1 = new Sequence("", "abcdefghijklm");
-    SearchResults sr1 = new SearchResults();
-    SearchResults sr2 = new SearchResults();
+    SearchResultsI sr1 = new SearchResults();
+    SearchResultsI sr2 = new SearchResults();
 
     sr1.addResult(seq1, 1, 1);
     sr1.addResult(seq1, 2, 2);
@@ -145,8 +145,8 @@ public class SearchResultsTest
   public void testHashcode()
   {
     SequenceI seq1 = new Sequence("", "abcdefghijklm");
-    SearchResults sr1 = new SearchResults();
-    SearchResults sr2 = new SearchResults();
+    SearchResultsI sr1 = new SearchResults();
+    SearchResultsI sr2 = new SearchResults();
 
     /*
      * both empty
@@ -178,7 +178,7 @@ public class SearchResultsTest
   public void testMatchConstructor()
   {
     SequenceI seq1 = new Sequence("", "abcdefghijklm");
-    Match m = new SearchResults().new Match(seq1, 2, 5);
+    SearchResultMatchI m = new SearchResults().new Match(seq1, 2, 5);
     assertSame(seq1, m.getSequence());
     assertEquals(2, m.getStart());
     assertEquals(5, m.getEnd());
@@ -189,4 +189,82 @@ public class SearchResultsTest
     assertEquals(2, m.getStart());
     assertEquals(5, m.getEnd());
   }
+
+  /**
+   * test markColumns for creating column selections
+   */
+  @Test(groups = { "Functional" })
+  public void testMarkColumns()
+  {
+    int marked = 0;
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SequenceI seq2 = new Sequence("", "abcdefghijklm");
+    SequenceGroup s1g=new SequenceGroup(), s2g=new SequenceGroup(), sallg=new SequenceGroup();
+    s1g.addSequence(seq1, false);
+    s2g.addSequence(seq2, false);
+    sallg.addSequence(seq1, false);
+    sallg.addSequence(seq2, false);
+    
+    SearchResultsI sr = new SearchResults();
+    BitSet bs = new BitSet();
+    
+    sr.addResult(seq1, 1,1);
+    sr.addResult(seq2, 1,2);
+    
+    // set start/end range for groups to cover matches
+
+    s1g.setStartRes(0);
+    s1g.setEndRes(5);
+    s2g.setStartRes(0);
+    s2g.setEndRes(5);
+    sallg.setStartRes(0);
+    sallg.setEndRes(5);
+
+    /*
+     * just seq1
+     */
+    marked = sr.markColumns(s1g, bs);
+    // check the bitset cardinality before checking the return value
+    assertEquals("Didn't mark expected number", 1, bs.cardinality());
+    assertEquals("Didn't return count of number of bits marked", 1, marked);
+    assertTrue("Didn't mark expected position", bs.get(0));
+    // now check return value for marking the same again
+    assertEquals(
+            "Didn't count number of bits marked for existing marked set",
+            0,
+            sr.markColumns(s1g, bs));
+    bs.clear();
+    
+    /*
+     * just seq2
+     */
+    marked = sr.markColumns(s2g, bs);
+    assertEquals("Didn't mark expected number", 2, bs.cardinality());
+    assertEquals("Didn't return count of number of bits marked", 2, marked);
+    assertTrue("Didn't mark expected position (1)", bs.get(0));
+    assertTrue("Didn't mark expected position (2)", bs.get(0));
+    
+    /*
+     * both seq1 and seq2 
+     * should be same as seq2
+     */
+    BitSet allbs = new BitSet();
+    assertEquals(2, sr.markColumns(sallg, allbs));
+    assertEquals(bs, allbs);
+
+    // now check range selection
+
+    /*
+     * limit s2g to just the second column, sallg to the first column
+     */
+    s2g.setStartRes(1);
+    s2g.setEndRes(1);
+    sallg.setEndRes(0);
+    BitSet tbs = new BitSet();
+    assertEquals("Group start/end didn't select columns to mark",1, sr.markColumns(s2g, tbs));
+    assertEquals("Group start/end didn't select columns to mark", 1, sr.markColumns(sallg, tbs));
+    assertEquals(
+            "Didn't set expected number of columns in total for two successive marks",
+            2, tbs.cardinality());
+  }
 }