X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=0220c36effdc8f951b2c3f6e7d20368731cd3127;hb=404d5b51a7a7781ad6924df6a7ce63c754370f16;hp=42225e89c1dcd332867a54263a12d298361f8b17;hpb=fae891ea08e5ceb278a0ff91313a2f50cbc017f0;p=jalview.git

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 42225e8..0220c36 100644
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -40,7 +40,9 @@ 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;
@@ -81,6 +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)
@@ -925,4 +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());
+
+  }
 }