X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=e2a94efa300daaf1a5fba2afdb2114316df42c34;hb=refs%2Fheads%2Fbug%2FJAL-2839findWithHidden;hp=e453dd38e3e9e4e0ae15b779a535e5b3483e21ed;hpb=24de2d6a6f3db1b9d55f367e2bf8ba112e202a8a;p=jalview.git

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index e453dd3..e2a94ef 100644
--- a/test/jalview/analysis/FinderTest.java
+++ b/test/jalview/analysis/FinderTest.java
@@ -24,6 +24,7 @@ import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import jalview.api.AlignViewportI;
 import jalview.api.FinderI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
@@ -35,12 +36,14 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 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;
 
@@ -59,6 +62,8 @@ public class FinderTest
 
   private AlignmentI al;
 
+  private AlignViewportI av;
+
   @BeforeClass(groups = "Functional")
   public void setUp()
   {
@@ -70,7 +75,14 @@ public class FinderTest
             + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
     af = new FileLoader().LoadFileWaitTillLoaded(seqData,
             DataSourceType.PASTE);
-    al = af.getViewport().getAlignment();
+    av = af.getViewport();
+    al = av.getAlignment();
+  }
+
+  @AfterMethod
+  public void tearDownAfterTest()
+  {
+    av.setSelectionGroup(null);
   }
 
   /**
@@ -82,8 +94,8 @@ public class FinderTest
     /*
      * find next match only
      */
-    Finder f = new Finder(al);
-    f.findNext("E.H", null, false, false); // 'E, any character, H'
+    Finder f = new Finder(av);
+    f.findNext("E.H", false, false); // 'E, any character, H'
     // should match seq2 efH only
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getSize(), 1);
@@ -92,8 +104,8 @@ public class FinderTest
     assertEquals(matches.get(0).getStart(), 5);
     assertEquals(matches.get(0).getEnd(), 7);
 
-    f = new Finder(al);
-    f.findAll("E.H", null, false, false); // 'E, any character, H'
+    f = new Finder(av);
+    f.findAll("E.H", false, false); // 'E, any character, H'
     // should match seq2 efH and seq3 EFH
     sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
@@ -112,12 +124,12 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_residueNumber()
   {
-    Finder f = new Finder(al);
+    Finder f = new Finder(av);
 
     /*
      * find first match should return seq1 residue 9
      */
-    f.findNext("9", null, false, false);
+    f.findNext("9", false, false);
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getSize(), 1);
     List<SearchResultMatchI> matches = sr.getResults();
@@ -128,8 +140,8 @@ public class FinderTest
     /*
      * find all matches should return seq1 and seq4 (others are too short)
      */
-    f = new Finder(al);
-    f.findAll("9", null, false, false);
+    f = new Finder(av);
+    f.findAll("9", false, false);
     sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
     matches = sr.getResults();
@@ -143,8 +155,8 @@ public class FinderTest
     /*
      * parsing of search string as integer is strict
      */
-    f = new Finder(al);
-    f.findNext(" 9", null, false, false);
+    f = new Finder(av);
+    f.findNext(" 9", false, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -158,10 +170,10 @@ public class FinderTest
      * start at second sequence; colIndex of -1
      * means sequence id / description is searched
      */
-    Finder f = new Finder(al);
+    Finder f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
     PA.setValue(f, "columnIndex", -1);
-    f.findNext("e", null, false, false); // matches id
+    f.findNext("e", false, false); // matches id
 
     assertTrue(f.getSearchResults().isEmpty());
     assertEquals(f.getIdMatches().size(), 1);
@@ -170,10 +182,10 @@ public class FinderTest
     // colIndex is now 0 - for use in next find next
     // searching A--BCDefHI
     assertEquals(PA.getValue(f, "columnIndex"), 0);
-    f = new Finder(al);
+    f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
     PA.setValue(f, "columnIndex", 0);
-    f.findNext("e", null, false, false); // matches in sequence
+    f.findNext("e", false, false); // matches in sequence
     assertTrue(f.getIdMatches().isEmpty());
     assertEquals(f.getSearchResults().getSize(), 1);
     List<SearchResultMatchI> matches = f.getSearchResults().getResults();
@@ -186,10 +198,10 @@ public class FinderTest
     assertEquals(PA.getValue(f, "columnIndex"), 7);
 
     // find next from end of sequence - finds next sequence id
-    f = new Finder(al);
+    f = new Finder(av);
     PA.setValue(f, "sequenceIndex", 1);
     PA.setValue(f, "columnIndex", 7);
-    f.findNext("e", null, false, false);
+    f.findNext("e", false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
     assertTrue(f.getSearchResults().isEmpty());
@@ -205,11 +217,13 @@ public class FinderTest
     al2.getSequenceAt(0).setDescription("BRAF");
     al2.getSequenceAt(1).setDescription("braf");
 
+    AlignViewportI av2 = new AlignViewport(al2);
+
     /*
      * find first match only
      */
-    Finder f = new Finder(al2);
-    f.findNext("rAF", null, false, true);
+    Finder f = new Finder(av2);
+    f.findNext("rAF", false, true);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
@@ -217,8 +231,8 @@ public class FinderTest
     /*
      * find all matches
      */
-    f = new Finder(al2);
-    f.findAll("rAF", null, false, true);
+    f = new Finder(av2);
+    f.findAll("rAF", false, true);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -227,8 +241,8 @@ public class FinderTest
     /*
      * case sensitive
      */
-    f = new Finder(al2);
-    f.findAll("RAF", null, true, true);
+    f = new Finder(av2);
+    f.findAll("RAF", true, true);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
@@ -239,12 +253,12 @@ public class FinderTest
     al2.getSequenceAt(0).setDescription("the efh sequence");
     al2.getSequenceAt(0).setName("mouseEFHkinase");
     al2.getSequenceAt(1).setName("humanEFHkinase");
-    f = new Finder(al2);
+    f = new Finder(av2);
 
     /*
      * sequence matches should have no duplicates
      */
-    f.findAll("EFH", null, false, true);
+    f.findAll("EFH", false, true);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
@@ -266,13 +280,13 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFindAll_sequenceIds()
   {
-    Finder f = new Finder(al);
+    Finder f = new Finder(av);
 
     /*
      * case insensitive; seq1 occurs twice in sequence id but
      * only one match should be returned
      */
-    f.findAll("SEQ1", null, false, false);
+    f.findAll("SEQ1", false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(0));
     SearchResultsI searchResults = f.getSearchResults();
@@ -281,8 +295,8 @@ public class FinderTest
     /*
      * case sensitive
      */
-    f = new Finder(al);
-    f.findAll("SEQ1", null, true, false);
+    f = new Finder(av);
+    f.findAll("SEQ1", true, false);
     searchResults = f.getSearchResults();
     assertTrue(searchResults.isEmpty());
 
@@ -290,9 +304,10 @@ public class FinderTest
      * match both sequence id and sequence
      */
     AlignmentI al2 = new Alignment(al);
+    AlignViewportI av2 = new AlignViewport(al2);
     al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
-    f = new Finder(al2);
-    f.findAll("ABZ", null, false, false);
+    f = new Finder(av2);
+    f.findAll("ABZ", false, false);
     assertEquals(f.getIdMatches().size(), 1);
     assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
     searchResults = f.getSearchResults();
@@ -316,8 +331,8 @@ public class FinderTest
     /*
      * efh should be matched in seq2 only
      */
-    FinderI f = new Finder(al);
-    f.findNext("EfH", null, false, false);
+    FinderI f = new Finder(av);
+    f.findNext("EfH", false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -328,8 +343,8 @@ public class FinderTest
     /*
      * I should be found in seq1 (twice) and seq2 (once)
      */
-    f = new Finder(al);
-    f.findNext("I", null, false, false); // find next: seq1/16
+    f = new Finder(av);
+    f.findNext("I", false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -337,7 +352,7 @@ public class FinderTest
     assertEquals(match.getStart(), 16);
     assertEquals(match.getEnd(), 16);
 
-    f.findNext("I", null, false, false); // find next: seq1/18
+    f.findNext("I", false, false); // find next: seq1/18
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -345,7 +360,7 @@ public class FinderTest
     assertEquals(match.getStart(), 18);
     assertEquals(match.getEnd(), 18);
 
-    f.findNext("I", null, false, false); // find next: seq2/8
+    f.findNext("I", false, false); // find next: seq2/8
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -353,13 +368,13 @@ public class FinderTest
     assertEquals(match.getStart(), 8);
     assertEquals(match.getEnd(), 8);
 
-    f.findNext("I", null, false, false);
+    f.findNext("I", false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
      * find should reset to start of alignment after a failed search
      */
-    f.findNext("I", null, false, false); // find next: seq1/16
+    f.findNext("I", false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -375,8 +390,8 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_maximalResultOnly()
   {
-    Finder f = new Finder(al);
-    f.findAll("M+", null, false, false);
+    Finder f = new Finder(av);
+    f.findAll("M+", false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -391,8 +406,8 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_findAll()
   {
-    Finder f = new Finder(al);
-    f.findAll("EfH", null, false, false);
+    Finder f = new Finder(av);
+    f.findAll("EfH", false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -407,7 +422,7 @@ public class FinderTest
     /*
      * find all I should find 2 positions in seq1, 1 in seq2
      */
-    f.findAll("I", null, false, false);
+    f.findAll("I", false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 3);
     match = searchResults.getResults().get(0);
@@ -430,12 +445,12 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_findAllCaseSensitive()
   {
-    Finder f = new Finder(al);
+    Finder f = new Finder(av);
 
     /*
      * BC should match seq1/9-10 and seq2/2-3
      */
-    f.findAll("BC", null, true, false);
+    f.findAll("BC", true, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -450,8 +465,8 @@ public class FinderTest
     /*
      * bc should match seq3/1-2
      */
-    f = new Finder(al);
-    f.findAll("bc", null, true, false);
+    f = new Finder(av);
+    f.findAll("bc", true, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -459,7 +474,7 @@ public class FinderTest
     assertEquals(match.getStart(), 1);
     assertEquals(match.getEnd(), 2);
 
-    f.findAll("bC", null, true, false);
+    f.findAll("bC", true, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -479,9 +494,10 @@ public class FinderTest
     sg.setEndRes(5);
     sg.addSequence(al.getSequenceAt(1), false);
     sg.addSequence(al.getSequenceAt(2), false);
+    av.setSelectionGroup(sg);
 
-    FinderI f = new Finder(al);
-    f.findNext("b", sg, false, false);
+    FinderI f = new Finder(av);
+    f.findNext("b", false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
@@ -493,12 +509,12 @@ public class FinderTest
     /*
      * a second Find should not return the 'b' in seq3 as outside the selection
      */
-    f.findNext("b", sg, false, false);
+    f.findNext("b", false, false);
     assertTrue(f.getSearchResults().isEmpty());
     assertTrue(f.getIdMatches().isEmpty());
 
-    f = new Finder(al);
-    f.findNext("d", sg, false, false);
+    f = new Finder(av);
+    f.findNext("d", false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
@@ -506,7 +522,7 @@ public class FinderTest
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 4);
     assertEquals(match.getEnd(), 4);
-    f.findNext("d", sg, false, false);
+    f.findNext("d", false, false);
     assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
@@ -532,12 +548,13 @@ public class FinderTest
     sg.setEndRes(5);
     sg.addSequence(al.getSequenceAt(1), false);
     sg.addSequence(al.getSequenceAt(2), false);
+    av.setSelectionGroup(sg);
   
     /*
      * search for 'e' should match two sequence ids and one residue
      */
-    Finder f = new Finder(al);
-    f.findAll("e", sg, false, false);
+    Finder f = new Finder(av);
+    f.findAll("e", false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -551,8 +568,8 @@ public class FinderTest
     /*
      * search for 'Q' should match two sequence ids only
      */
-    f = new Finder(al);
-    f.findAll("Q", sg, false, false);
+    f = new Finder(av);
+    f.findAll("Q", false, false);
     assertEquals(f.getIdMatches().size(), 2);
     assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
     assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
@@ -577,12 +594,13 @@ public class FinderTest
     sg.addSequence(al.getSequenceAt(1), false);
     sg.addSequence(al.getSequenceAt(2), false);
     sg.addSequence(al.getSequenceAt(3), false);
-  
+    av.setSelectionGroup(sg);
+
     /*
      * search for 'I' should match two sequence positions
      */
-    Finder f = new Finder(al);
-    f.findAll("I", sg, false, false);
+    Finder f = new Finder(av);
+    f.findAll("I", false, false);
     assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
@@ -621,8 +639,8 @@ public class FinderTest
      * find all search for D should ignore hidden positions in seq1 and seq3,
      * find the visible D in seq2
      */
-    Finder f = new Finder(al);
-    f.findAll("D", null, false, false);
+    Finder f = new Finder(av);
+    f.findAll("D", false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -635,8 +653,8 @@ public class FinderTest
      * find all 'aaa' should find end of seq4 only
      */
     hc.hideColumns(2, 5);
-    f = new Finder(al);
-    f.findAll("aaa", null, false, false);
+    f = new Finder(av);
+    f.findAll("aaa", false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -647,7 +665,7 @@ public class FinderTest
     /*
      * find all 'BE' should not match across hidden columns in seq1
      */
-    f.findAll("BE", null, false, false);
+    f.findAll("BE", false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
@@ -656,8 +674,8 @@ public class FinderTest
      */
     hc.revealAllHiddenColumns(new ColumnSelection());
     hc.hideColumns(8, 13);
-    f = new Finder(al);
-    f.findNext("H", null, false, false);
+    f = new Finder(av);
+    f.findNext("H", false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -693,13 +711,14 @@ public class FinderTest
     sg.addSequence(al.getSequenceAt(2), false);
     sg.setStartRes(0);
     sg.setEndRes(13);
+    av.setSelectionGroup(sg);
 
     /*
      * find all search for A or H
      * should match seq2/1, seq2/7, not seq3/6
      */
-    Finder f = new Finder(al);
-    f.findAll("[AH]", sg, false, false);
+    Finder f = new Finder(av);
+    f.findAll("[AH]", false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);