Merge branch 'develop' into feature/JAL-1713_overviewInProject

[jalview.git] / test / jalview / analysis / FinderTest.java

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 7e3bd86..0220c36 100644 (file)
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -24,6 +24,12 @@ import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import java.util.List;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.api.AlignViewportI;
 import jalview.api.FinderI;
 import jalview.bin.Cache;
@@ -34,19 +40,14 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultMatchI;
 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.AlignViewport;
 import jalview.gui.JvOptionPane;
 import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-
-import java.util.List;
-
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 import junit.extensions.PA;
 
 public class FinderTest
@@ -82,6 +83,12 @@ public class FinderTest
             DataSourceType.PASTE);
     av = af.getViewport();
     al = av.getAlignment();
+    al.getSequenceAt(0).addSequenceFeature(
+            new SequenceFeature("BBBB", "FeatureB", 9, 11, ""));
+    al.getSequenceAt(3).addSequenceFeature(
+            new SequenceFeature("BBAB", "FeatureA", 1, 3, ""));
+    al.getSequenceAt(3).addSequenceFeature(
+            new SequenceFeature("AAAA", "FeatureA", 9, 11, ""));
   }
 
   @AfterMethod(alwaysRun = true)
@@ -100,7 +107,7 @@ public class FinderTest
      * find next match only
      */
     Finder f = new Finder(av);
-    f.findNext("E.H", false, false, false); // 'E, any character, H'
+    f.findNext("E.H", false, false, false, false); // 'E, any character, H'
     // should match seq2 efH only
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getCount(), 1);
@@ -110,7 +117,7 @@ public class FinderTest
     assertEquals(matches.get(0).getEnd(), 7);
 
     f = new Finder(av);
-    f.findAll("E.H", false, false, false); // 'E, any character, H'
+    f.findAll("E.H", false, false, false, false); // 'E, any character, H'
     // should match seq2 efH and seq3 EFH
     sr = f.getSearchResults();
     assertEquals(sr.getCount(), 2);
@@ -131,7 +138,7 @@ public class FinderTest
      * single symbol should find *all* matching symbols 
      */
     Finder f = new Finder(av);
-    f.findAll("M", false, false, false);
+    f.findAll("M", false, false, false, false);
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getCount(), 5);
 
@@ -148,7 +155,7 @@ public class FinderTest
     /*
      * find first match should return seq1 residue 9
      */
-    f.findNext("9", false, false, false);
+    f.findNext("9", false, false, false, false);
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getCount(), 1);
     List<SearchResultMatchI> matches = sr.getResults();
@@ -163,7 +170,7 @@ public class FinderTest
     f = new Finder(av);
     String name = al.getSequenceAt(0).getName();
     al.getSequenceAt(0).setName("Q9XA0");
-    f.findAll("9", false, false, false);
+    f.findAll("9", false, false, false, false);
     sr = f.getSearchResults();
     assertEquals(sr.getCount(), 2);
     matches = sr.getResults();
@@ -179,7 +186,7 @@ public class FinderTest
      * parsing of search string as integer is strict
      */
     f = new Finder(av);
-    f.findNext(" 9", false, false, false);
+    f.findNext(" 9", false, false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -196,7 +203,7 @@ public class FinderTest
     Finder f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
     PA.setValue(f, "residueIndex", -1);
-    f.findNext("e", false, false, false); // matches id
+    f.findNext("e", false, false, false, false); // matches id
 
     assertTrue(f.getSearchResults().isEmpty());
     assertEquals(f.getIdMatches().size(), 1);
@@ -208,7 +215,7 @@ public class FinderTest
     f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
     PA.setValue(f, "residueIndex", 0);
-    f.findNext("e", false, false, false); // matches in sequence
+    f.findNext("e", false, false, false, false); // matches in sequence
     assertTrue(f.getIdMatches().isEmpty());
     assertEquals(f.getSearchResults().getCount(), 1);
     List<SearchResultMatchI> matches = f.getSearchResults().getResults();
@@ -224,7 +231,7 @@ public class FinderTest
     f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
     PA.setValue(f, "residueIndex", 7);
-    f.findNext("e", false, false, false);
+    f.findNext("e", false, false, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
     assertTrue(f.getSearchResults().isEmpty());
@@ -246,7 +253,7 @@ public class FinderTest
      * find first match only
      */
     Finder f = new Finder(av2);
-    f.findNext("rAF", false, true, false);
+    f.findNext("rAF", false, true, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
@@ -255,7 +262,7 @@ public class FinderTest
      * find all matches
      */
     f = new Finder(av2);
-    f.findAll("rAF", false, true, false);
+    f.findAll("rAF", false, true, false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -265,7 +272,7 @@ public class FinderTest
      * case sensitive
      */
     f = new Finder(av2);
-    f.findAll("RAF", true, true, false);
+    f.findAll("RAF", true, true, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
@@ -281,7 +288,7 @@ public class FinderTest
     /*
      * sequence matches should have no duplicates
      */
-    f.findAll("EFH", false, true, false);
+    f.findAll("EFH", false, true, false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -309,7 +316,7 @@ public class FinderTest
      * case insensitive; seq1 occurs twice in sequence id but
      * only one match should be returned
      */
-    f.findAll("SEQ1", false, false, false);
+    f.findAll("SEQ1", false, false, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(0));
     SearchResultsI searchResults = f.getSearchResults();
@@ -319,7 +326,7 @@ public class FinderTest
      * case sensitive
      */
     f = new Finder(av);
-    f.findAll("SEQ1", true, false, false);
+    f.findAll("SEQ1", true, false, false, false);
     searchResults = f.getSearchResults();
     assertTrue(searchResults.isEmpty());
 
@@ -330,7 +337,7 @@ public class FinderTest
     AlignViewportI av2 = new AlignViewport(al2);
     al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
     f = new Finder(av2);
-    f.findAll("ABZ", false, false, false);
+    f.findAll("ABZ", false, false, false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
     searchResults = f.getSearchResults();
@@ -359,7 +366,7 @@ public class FinderTest
      * efh should be matched in seq2 only
      */
     FinderI f = new Finder(av);
-    f.findNext("EfH", false, false, false);
+    f.findNext("EfH", false, false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -371,7 +378,7 @@ public class FinderTest
      * I should be found in seq1 (twice) and seq2 (once)
      */
     f = new Finder(av);
-    f.findNext("I", false, false, false); // find next: seq1/16
+    f.findNext("I", false, false, false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -379,7 +386,7 @@ public class FinderTest
     assertEquals(match.getStart(), 16);
     assertEquals(match.getEnd(), 16);
 
-    f.findNext("I", false, false, false); // find next: seq1/18
+    f.findNext("I", false, false, false, false); // find next: seq1/18
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -387,7 +394,7 @@ public class FinderTest
     assertEquals(match.getStart(), 18);
     assertEquals(match.getEnd(), 18);
 
-    f.findNext("I", false, false, false); // find next: seq2/8
+    f.findNext("I", false, false, false, false); // find next: seq2/8
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -395,13 +402,13 @@ public class FinderTest
     assertEquals(match.getStart(), 8);
     assertEquals(match.getEnd(), 8);
 
-    f.findNext("I", false, false, false);
+    f.findNext("I", false, false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
      * find should reset to start of alignment after a failed search
      */
-    f.findNext("I", false, false, false); // find next: seq1/16
+    f.findNext("I", false, false, false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -418,7 +425,7 @@ public class FinderTest
   public void testFindAll_maximalResultOnly()
   {
     Finder f = new Finder(av);
-    f.findAll("M+", false, false, false);
+    f.findAll("M+", false, false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -434,7 +441,7 @@ public class FinderTest
   public void testFindAll()
   {
     Finder f = new Finder(av);
-    f.findAll("EfH", false, false, false);
+    f.findAll("EfH", false, false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -449,7 +456,7 @@ public class FinderTest
     /*
      * find all I should find 2 positions in seq1, 1 in seq2
      */
-    f.findAll("I", false, false, false);
+    f.findAll("I", false, false, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 3);
     match = searchResults.getResults().get(0);
@@ -477,7 +484,7 @@ public class FinderTest
     /*
      * BC should match seq1/9-10 and seq2/2-3
      */
-    f.findAll("BC", true, false, false);
+    f.findAll("BC", true, false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -493,7 +500,7 @@ public class FinderTest
      * bc should match seq3/1-2
      */
     f = new Finder(av);
-    f.findAll("bc", true, false, false);
+    f.findAll("bc", true, false, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -501,7 +508,7 @@ public class FinderTest
     assertEquals(match.getStart(), 1);
     assertEquals(match.getEnd(), 2);
 
-    f.findAll("bC", true, false, false);
+    f.findAll("bC", true, false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -524,7 +531,7 @@ public class FinderTest
     av.setSelectionGroup(sg);
 
     FinderI f = new Finder(av);
-    f.findNext("b", false, false, false);
+    f.findNext("b", false, false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
@@ -536,12 +543,12 @@ public class FinderTest
     /*
      * a second Find should not return the 'b' in seq3 as outside the selection
      */
-    f.findNext("b", false, false, false);
+    f.findNext("b", false, false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
     assertTrue(f.getIdMatches().isEmpty());
 
     f = new Finder(av);
-    f.findNext("d", false, false, false);
+    f.findNext("d", false, false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
@@ -549,7 +556,7 @@ public class FinderTest
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 4);
     assertEquals(match.getEnd(), 4);
-    f.findNext("d", false, false, false);
+    f.findNext("d", false, false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
@@ -581,7 +588,7 @@ public class FinderTest
      * search for 'e' should match two sequence ids and one residue
      */
     Finder f = new Finder(av);
-    f.findAll("e", false, false, false);
+    f.findAll("e", false, false, false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -596,7 +603,7 @@ public class FinderTest
      * search for 'Q' should match two sequence ids only
      */
     f = new Finder(av);
-    f.findAll("Q", false, false, false);
+    f.findAll("Q", false, false, false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -627,7 +634,7 @@ public class FinderTest
      * search for 'I' should match two sequence positions
      */
     Finder f = new Finder(av);
-    f.findAll("I", false, false, false);
+    f.findAll("I", false, false, false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 2);
@@ -664,7 +671,7 @@ public class FinderTest
     hc.hideColumns(3, 3);
     al.setHiddenColumns(hc);
     Finder f = new Finder(av);
-    f.findAll("aaa", false, false, false);
+    f.findAll("aaa", false, false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -686,7 +693,7 @@ public class FinderTest
      * find the visible D in seq2
      */
     f = new Finder(av);
-    f.findAll("D", false, false, false);
+    f.findAll("D", false, false, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -699,7 +706,7 @@ public class FinderTest
      * consecutive in the visible columns
      */
     f = new Finder(av);
-    f.findAll("AD", false, false, false);
+    f.findAll("AD", false, false, false, false);
     searchResults = f.getSearchResults();
     assertTrue(searchResults.isEmpty());
 
@@ -708,7 +715,7 @@ public class FinderTest
      * (first run includes hidden gaps)
      */
     f = new Finder(av);
-    f.findAll("aaa", false, false, false);
+    f.findAll("aaa", false, false, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 2);
     match = searchResults.getResults().get(0);
@@ -727,7 +734,7 @@ public class FinderTest
      */
     hc.hideColumns(2, 5);
     f = new Finder(av);
-    f.findAll("aaa", false, false, false);
+    f.findAll("aaa", false, false, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 2);
     match = searchResults.getResults().get(0);
@@ -742,7 +749,7 @@ public class FinderTest
     /*
      * find all 'BE' should not match across hidden columns in seq1
      */
-    f.findAll("BE", false, false, false);
+    f.findAll("BE", false, false, false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
@@ -752,7 +759,7 @@ public class FinderTest
     hc.revealAllHiddenColumns(new ColumnSelection());
     hc.hideColumns(8, 13);
     f = new Finder(av);
-    f.findNext("H", false, false, false);
+    f.findNext("H", false, false, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     match = searchResults.getResults().get(0);
@@ -795,7 +802,7 @@ public class FinderTest
      * should match seq2/1, seq2/7, not seq3/6
      */
     Finder f = new Finder(av);
-    f.findAll("[AH]", false, false, false);
+    f.findAll("[AH]", false, false, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -832,7 +839,7 @@ public class FinderTest
      * aaaMMMMaaa
      */
     Finder f = new Finder(av);
-    f.findAll("abe", false, false, true); // true = ignore hidden
+    f.findAll("abe", false, false, false, true); // true = ignore hidden
     SearchResultsI searchResults = f.getSearchResults();
 
     /*
@@ -851,7 +858,7 @@ public class FinderTest
     assertEquals(match.getEnd(), 12);
 
     f = new Finder(av);
-    f.findNext("a.E", false, false, true);
+    f.findNext("a.E", false, false, false, true);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     assertEquals(searchResults.getResults().size(), 2);
@@ -864,7 +871,7 @@ public class FinderTest
     assertEquals(match.getStart(), 12); // E
     assertEquals(match.getEnd(), 12);
 
-    f.findNext("a.E", false, false, true);
+    f.findNext("a.E", false, false, false, true);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     assertEquals(searchResults.getResults().size(), 2);
@@ -881,7 +888,7 @@ public class FinderTest
      * find all matching across two hidden column regions
      * note one 'match' is returned as three contiguous matches
      */
-    f.findAll("BEG", false, false, true);
+    f.findAll("BEG", false, false, false, true);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     assertEquals(searchResults.getResults().size(), 3);
@@ -908,7 +915,7 @@ public class FinderTest
     selection.setEndRes(9);
     al.getSequences().forEach(seq -> selection.addSequence(seq, false));
     av.setSelectionGroup(selection);
-    f.findAll("A.*H", false, false, true);
+    f.findAll("A.*H", false, false, false, true);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getCount(), 1);
     assertEquals(searchResults.getResults().size(), 3);
@@ -926,4 +933,60 @@ public class FinderTest
     assertEquals(match.getStart(), 7); // H (there is no G)
     assertEquals(match.getEnd(), 7);
   }
+
+  @Test(groups = "Functional")
+  public void testFind_featuresOnly()
+  {
+    Finder f = new Finder(av);
+    // no match when not searching feature descriptions
+    f.findAll("Feature", false, false, false, true);
+    assertEquals(f.getSearchResults().getCount(), 0);
+
+    // no match when case sensitive on feature descriptions
+    f.findAll("feature", true, false, true, true);
+    assertEquals(f.getSearchResults().getCount(), 0);
+
+    // search feature descriptions - all match
+    f.findAll("Feature", false, false, true, true);
+    assertEquals(f.getSearchResults().getCount(), 3);
+
+    List<SequenceI> seqs = f.getSearchResults().getMatchingSubSequences();
+    // assume order is preserved in results
+    assertEquals(al.getSequenceAt(0).getDatasetSequence(),
+            seqs.get(0).getDatasetSequence());
+    assertEquals(seqs.get(0).getStart(), 9);
+    assertEquals(seqs.get(0).getEnd(), 11);
+    assertEquals(al.getSequenceAt(3).getDatasetSequence(),
+            seqs.get(1).getDatasetSequence());
+    assertEquals(seqs.get(1).getStart(), 9);
+    assertEquals(seqs.get(1).getEnd(), 11);
+    assertEquals(al.getSequenceAt(3).getDatasetSequence(),
+            seqs.get(2).getDatasetSequence());
+    assertEquals(seqs.get(2).getStart(), 1);
+    assertEquals(seqs.get(2).getEnd(), 3);
+
+    SequenceI sq = null;
+    // search feature descriptions incrementally
+    // assume same order as before
+    f.findNext("Feature", false, false, true, true);
+    assertEquals(f.getSearchResults().getCount(), 1);
+    sq = f.getSearchResults().getMatchingSubSequences().get(0);
+    assertEquals(sq.getSequenceAsString(),
+            seqs.get(0).getSequenceAsString());
+
+    // ..
+    f.findNext("Feature", false, false, true, true);
+    assertEquals(f.getSearchResults().getCount(), 1);
+    sq = f.getSearchResults().getMatchingSubSequences().get(0);
+    assertEquals(sq.getSequenceAsString(),
+            seqs.get(1).getSequenceAsString());
+
+    // ..
+    f.findNext("Feature", false, false, true, true);
+    assertEquals(f.getSearchResults().getCount(), 1);
+    sq = f.getSearchResults().getMatchingSubSequences().get(0);
+    assertEquals(sq.getSequenceAsString(),
+            seqs.get(2).getSequenceAsString());
+
+  }
 }