JAL-2933 gui and applet Finder hold a FinderI per viewport

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

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index f05bfb3..e453dd3 100644 (file)
--- 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.FinderI;
 import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -43,6 +44,8 @@ import java.util.List;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class FinderTest
 {
   @BeforeClass(alwaysRun = true)
@@ -79,8 +82,8 @@ public class FinderTest
     /*
      * find next match only
      */
-    Finder f = new Finder(al, null);
-    f.find("E.H"); // 'E, any character, H'
+    Finder f = new Finder(al);
+    f.findNext("E.H", null, false, false); // 'E, any character, H'
     // should match seq2 efH only
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getSize(), 1);
@@ -89,9 +92,8 @@ public class FinderTest
     assertEquals(matches.get(0).getStart(), 5);
     assertEquals(matches.get(0).getEnd(), 7);
 
-    f = new Finder(al, null);
-    f.setFindAll(true);
-    f.find("E.H"); // 'E, any character, H'
+    f = new Finder(al);
+    f.findAll("E.H", null, false, false); // 'E, any character, H'
     // should match seq2 efH and seq3 EFH
     sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
@@ -110,12 +112,12 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_residueNumber()
   {
-    Finder f = new Finder(al, null);
+    Finder f = new Finder(al);
 
     /*
      * find first match should return seq1 residue 9
      */
-    f.find("9");
+    f.findNext("9", null, false, false);
     SearchResultsI sr = f.getSearchResults();
     assertEquals(sr.getSize(), 1);
     List<SearchResultMatchI> matches = sr.getResults();
@@ -126,9 +128,8 @@ public class FinderTest
     /*
      * find all matches should return seq1 and seq4 (others are too short)
      */
-    f = new Finder(al, null);
-    f.setFindAll(true);
-    f.find("9");
+    f = new Finder(al);
+    f.findAll("9", null, false, false);
     sr = f.getSearchResults();
     assertEquals(sr.getSize(), 2);
     matches = sr.getResults();
@@ -142,8 +143,8 @@ public class FinderTest
     /*
      * parsing of search string as integer is strict
      */
-    f = new Finder(al, null);
-    f.find(" 9");
+    f = new Finder(al);
+    f.findNext(" 9", null, false, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -157,34 +158,40 @@ public class FinderTest
      * start at second sequence; colIndex of -1
      * means sequence id / description is searched
      */
-    Finder f = new Finder(al, null, 1, -1);
-    f.find("e"); // matches id
+    Finder f = new Finder(al);
+    PA.setValue(f, "sequenceIndex", 1);
+    PA.setValue(f, "columnIndex", -1);
+    f.findNext("e", null, false, false); // matches id
 
     assertTrue(f.getSearchResults().isEmpty());
-    assertEquals(f.getIdMatch().size(), 1);
-    assertSame(f.getIdMatch().get(0), al.getSequenceAt(1));
+    assertEquals(f.getIdMatches().size(), 1);
+    assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
 
     // colIndex is now 0 - for use in next find next
     // searching A--BCDefHI
-    assertEquals(f.getColumnIndex(), 0);
-    f = new Finder(al, null, 1, 0);
-    f.find("e"); // matches in sequence
-    assertTrue(f.getIdMatch().isEmpty());
+    assertEquals(PA.getValue(f, "columnIndex"), 0);
+    f = new Finder(al);
+    PA.setValue(f, "sequenceIndex", 1);
+    PA.setValue(f, "columnIndex", 0);
+    f.findNext("e", null, false, false); // matches in sequence
+    assertTrue(f.getIdMatches().isEmpty());
     assertEquals(f.getSearchResults().getSize(), 1);
     List<SearchResultMatchI> matches = f.getSearchResults().getResults();
     assertEquals(matches.get(0).getStart(), 5);
     assertEquals(matches.get(0).getEnd(), 5);
     assertSame(matches.get(0).getSequence(), al.getSequenceAt(1));
     // still in the second sequence
-    assertEquals(f.getSequenceIndex(), 1);
+    assertEquals(PA.getValue(f, "sequenceIndex"), 1);
     // next column position to search from is 7
-    assertEquals(f.getColumnIndex(), 7);
+    assertEquals(PA.getValue(f, "columnIndex"), 7);
 
     // find next from end of sequence - finds next sequence id
-    f = new Finder(al, null, 1, 7);
-    f.find("e");
-    assertEquals(f.getIdMatch().size(), 1);
-    assertSame(f.getIdMatch().get(0), al.getSequenceAt(2));
+    f = new Finder(al);
+    PA.setValue(f, "sequenceIndex", 1);
+    PA.setValue(f, "columnIndex", 7);
+    f.findNext("e", null, false, false);
+    assertEquals(f.getIdMatches().size(), 1);
+    assertSame(f.getIdMatches().get(0), al.getSequenceAt(2));
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -201,36 +208,29 @@ public class FinderTest
     /*
      * find first match only
      */
-    Finder f = new Finder(al2, null);
-    f.setIncludeDescription(true);
-    f.find("rAF");
-    assertEquals(f.getIdMatch().size(), 1);
-    assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
+    Finder f = new Finder(al2);
+    f.findNext("rAF", null, false, true);
+    assertEquals(f.getIdMatches().size(), 1);
+    assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
      * find all matches
      */
-    f = new Finder(al2, null);
-    f.setFindAll(true);
-    f.setIncludeDescription(true);
-    f.find("rAF");
-    assertEquals(f.getIdMatch().size(), 2);
-    assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
-    assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1));
+    f = new Finder(al2);
+    f.findAll("rAF", null, false, true);
+    assertEquals(f.getIdMatches().size(), 2);
+    assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
+    assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
      * case sensitive
      */
-    f = new Finder(al2, null);
-    f.setFindAll(true);
-    f.setCaseSensitive(true);
-    f.setIncludeDescription(true);
-
-    f.find("RAF");
-    assertEquals(f.getIdMatch().size(), 1);
-    assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
+    f = new Finder(al2);
+    f.findAll("RAF", null, true, true);
+    assertEquals(f.getIdMatches().size(), 1);
+    assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
@@ -239,17 +239,15 @@ public class FinderTest
     al2.getSequenceAt(0).setDescription("the efh sequence");
     al2.getSequenceAt(0).setName("mouseEFHkinase");
     al2.getSequenceAt(1).setName("humanEFHkinase");
-    f = new Finder(al2, null);
-    f.setFindAll(true);
-    f.setIncludeDescription(true);
+    f = new Finder(al2);
 
     /*
      * sequence matches should have no duplicates
      */
-    f.find("EFH");
-    assertEquals(f.getIdMatch().size(), 2);
-    assertSame(f.getIdMatch().get(0), al2.getSequenceAt(0));
-    assertSame(f.getIdMatch().get(1), al2.getSequenceAt(1));
+    f.findAll("EFH", null, false, true);
+    assertEquals(f.getIdMatches().size(), 2);
+    assertSame(f.getIdMatches().get(0), al2.getSequenceAt(0));
+    assertSame(f.getIdMatches().get(1), al2.getSequenceAt(1));
 
     assertEquals(f.getSearchResults().getSize(), 2);
     SearchResultMatchI match = f.getSearchResults().getResults().get(0);
@@ -268,26 +266,23 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFindAll_sequenceIds()
   {
-    Finder f = new Finder(al, null);
-    f.setFindAll(true);
+    Finder f = new Finder(al);
 
     /*
      * case insensitive; seq1 occurs twice in sequence id but
      * only one match should be returned
      */
-    f.find("SEQ1");
-    assertEquals(f.getIdMatch().size(), 1);
-    assertSame(f.getIdMatch().get(0), al.getSequenceAt(0));
+    f.findAll("SEQ1", null, false, false);
+    assertEquals(f.getIdMatches().size(), 1);
+    assertSame(f.getIdMatches().get(0), al.getSequenceAt(0));
     SearchResultsI searchResults = f.getSearchResults();
     assertTrue(searchResults.isEmpty());
 
     /*
      * case sensitive
      */
-    f = new Finder(al, null);
-    f.setFindAll(true);
-    f.setCaseSensitive(true);
-    f.find("SEQ1");
+    f = new Finder(al);
+    f.findAll("SEQ1", null, true, false);
     searchResults = f.getSearchResults();
     assertTrue(searchResults.isEmpty());
 
@@ -296,11 +291,10 @@ public class FinderTest
      */
     AlignmentI al2 = new Alignment(al);
     al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
-    f = new Finder(al2, null);
-    f.setFindAll(true);
-    f.find("ABZ");
-    assertEquals(f.getIdMatch().size(), 1);
-    assertSame(f.getIdMatch().get(0), al2.getSequenceAt(4));
+    f = new Finder(al2);
+    f.findAll("ABZ", null, false, false);
+    assertEquals(f.getIdMatches().size(), 1);
+    assertSame(f.getIdMatches().get(0), al2.getSequenceAt(4));
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -322,8 +316,8 @@ public class FinderTest
     /*
      * efh should be matched in seq2 only
      */
-    Finder f = new Finder(al, null);
-    f.find("EfH");
+    FinderI f = new Finder(al);
+    f.findNext("EfH", null, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -334,8 +328,8 @@ public class FinderTest
     /*
      * I should be found in seq1 (twice) and seq2 (once)
      */
-    f = new Finder(al, null);
-    f.find("I"); // find next: seq1/16
+    f = new Finder(al);
+    f.findNext("I", null, false, false); // find next: seq1/16
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -343,7 +337,7 @@ public class FinderTest
     assertEquals(match.getStart(), 16);
     assertEquals(match.getEnd(), 16);
 
-    f.find("I"); // find next: seq1/18
+    f.findNext("I", null, false, false); // find next: seq1/18
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -351,7 +345,7 @@ public class FinderTest
     assertEquals(match.getStart(), 18);
     assertEquals(match.getEnd(), 18);
 
-    f.find("I"); // find next: seq2/8
+    f.findNext("I", null, false, false); // find next: seq2/8
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -359,8 +353,19 @@ public class FinderTest
     assertEquals(match.getStart(), 8);
     assertEquals(match.getEnd(), 8);
 
-    f.find("I");
+    f.findNext("I", null, 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
+    searchResults = f.getSearchResults();
+    assertEquals(searchResults.getSize(), 1);
+    match = searchResults.getResults().get(0);
+    assertSame(match.getSequence(), al.getSequenceAt(0));
+    assertEquals(match.getStart(), 16);
+    assertEquals(match.getEnd(), 16);
   }
 
   /**
@@ -370,9 +375,8 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_maximalResultOnly()
   {
-    Finder f = new Finder(al, null);
-    f.setFindAll(true);
-    f.find("M+");
+    Finder f = new Finder(al);
+    f.findAll("M+", null, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -387,9 +391,8 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_findAll()
   {
-    Finder f = new Finder(al, null);
-    f.setFindAll(true);
-    f.find("EfH");
+    Finder f = new Finder(al);
+    f.findAll("EfH", null, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -404,7 +407,7 @@ public class FinderTest
     /*
      * find all I should find 2 positions in seq1, 1 in seq2
      */
-    f.find("I");
+    f.findAll("I", null, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 3);
     match = searchResults.getResults().get(0);
@@ -427,14 +430,12 @@ public class FinderTest
   @Test(groups = "Functional")
   public void testFind_findAllCaseSensitive()
   {
-    Finder f = new Finder(al, null);
-    f.setCaseSensitive(true);
-    f.setFindAll(true);
+    Finder f = new Finder(al);
 
     /*
      * BC should match seq1/9-10 and seq2/2-3
      */
-    f.find("BC");
+    f.findAll("BC", null, true, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -449,10 +450,8 @@ public class FinderTest
     /*
      * bc should match seq3/1-2
      */
-    f = new Finder(al, null);
-    f.setCaseSensitive(true);
-    f.setFindAll(true);
-    f.find("bc");
+    f = new Finder(al);
+    f.findAll("bc", null, true, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -460,7 +459,7 @@ public class FinderTest
     assertEquals(match.getStart(), 1);
     assertEquals(match.getEnd(), 2);
 
-    f.find("bC");
+    f.findAll("bC", null, true, false);
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -481,9 +480,9 @@ public class FinderTest
     sg.addSequence(al.getSequenceAt(1), false);
     sg.addSequence(al.getSequenceAt(2), false);
 
-    Finder f = new Finder(al, sg);
-    f.find("b");
-    assertTrue(f.getIdMatch().isEmpty());
+    FinderI f = new Finder(al);
+    f.findNext("b", sg, false, false);
+    assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -494,21 +493,21 @@ public class FinderTest
     /*
      * a second Find should not return the 'b' in seq3 as outside the selection
      */
-    f.find("b");
+    f.findNext("b", sg, false, false);
     assertTrue(f.getSearchResults().isEmpty());
-    assertTrue(f.getIdMatch().isEmpty());
+    assertTrue(f.getIdMatches().isEmpty());
 
-    f = new Finder(al, sg);
-    f.find("d");
-    assertTrue(f.getIdMatch().isEmpty());
+    f = new Finder(al);
+    f.findNext("d", sg, false, false);
+    assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
     assertSame(match.getSequence(), al.getSequenceAt(1));
     assertEquals(match.getStart(), 4);
     assertEquals(match.getEnd(), 4);
-    f.find("d");
-    assertTrue(f.getIdMatch().isEmpty());
+    f.findNext("d", sg, false, false);
+    assertTrue(f.getIdMatches().isEmpty());
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -537,12 +536,11 @@ public class FinderTest
     /*
      * search for 'e' should match two sequence ids and one residue
      */
-    Finder f = new Finder(al, sg);
-    f.setFindAll(true);
-    f.find("e");
-    assertEquals(f.getIdMatch().size(), 2);
-    assertSame(f.getIdMatch().get(0), al.getSequenceAt(1));
-    assertSame(f.getIdMatch().get(1), al.getSequenceAt(2));
+    Finder f = new Finder(al);
+    f.findAll("e", sg, false, false);
+    assertEquals(f.getIdMatches().size(), 2);
+    assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
+    assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -553,12 +551,11 @@ public class FinderTest
     /*
      * search for 'Q' should match two sequence ids only
      */
-    f = new Finder(al, sg);
-    f.setFindAll(true);
-    f.find("Q");
-    assertEquals(f.getIdMatch().size(), 2);
-    assertSame(f.getIdMatch().get(0), al.getSequenceAt(1));
-    assertSame(f.getIdMatch().get(1), al.getSequenceAt(2));
+    f = new Finder(al);
+    f.findAll("Q", sg, false, false);
+    assertEquals(f.getIdMatches().size(), 2);
+    assertSame(f.getIdMatches().get(0), al.getSequenceAt(1));
+    assertSame(f.getIdMatches().get(1), al.getSequenceAt(2));
     assertTrue(f.getSearchResults().isEmpty());
   }
 
@@ -584,10 +581,9 @@ public class FinderTest
     /*
      * search for 'I' should match two sequence positions
      */
-    Finder f = new Finder(al, sg);
-    f.setFindAll(true);
-    f.find("I");
-    assertTrue(f.getIdMatch().isEmpty());
+    Finder f = new Finder(al);
+    f.findAll("I", sg, false, false);
+    assertTrue(f.getIdMatches().isEmpty());
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -625,9 +621,8 @@ 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, null);
-    f.setFindAll(true);
-    f.find("D");
+    Finder f = new Finder(al);
+    f.findAll("D", null, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     SearchResultMatchI match = searchResults.getResults().get(0);
@@ -640,8 +635,8 @@ public class FinderTest
      * find all 'aaa' should find end of seq4 only
      */
     hc.hideColumns(2, 5);
-    f = new Finder(al, null);
-    f.find("aaa");
+    f = new Finder(al);
+    f.findAll("aaa", null, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -652,7 +647,7 @@ public class FinderTest
     /*
      * find all 'BE' should not match across hidden columns in seq1
      */
-    f.find("BE");
+    f.findAll("BE", null, false, false);
     assertTrue(f.getSearchResults().isEmpty());
 
     /*
@@ -661,8 +656,8 @@ public class FinderTest
      */
     hc.revealAllHiddenColumns(new ColumnSelection());
     hc.hideColumns(8, 13);
-    f = new Finder(al, null);
-    f.find("H");
+    f = new Finder(al);
+    f.findNext("H", null, false, false);
     searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 1);
     match = searchResults.getResults().get(0);
@@ -703,9 +698,8 @@ public class FinderTest
      * find all search for A or H
      * should match seq2/1, seq2/7, not seq3/6
      */
-    Finder f = new Finder(al, sg);
-    f.setFindAll(true);
-    f.find("[AH]");
+    Finder f = new Finder(al);
+    f.findAll("[AH]", sg, false, false);
     SearchResultsI searchResults = f.getSearchResults();
     assertEquals(searchResults.getSize(), 2);
     SearchResultMatchI match = searchResults.getResults().get(0);