X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FFinderTest.java;h=42225e89c1dcd332867a54263a12d298361f8b17;hb=fae891ea08e5ceb278a0ff91313a2f50cbc017f0;hp=7e3bd86f2e341cc9ffd2e50396d3d5b2631defa1;hpb=6912e5c1ada266cbd4c66922c2f73583ce0489b9;p=jalview.git

diff --git a/test/jalview/analysis/FinderTest.java b/test/jalview/analysis/FinderTest.java
index 7e3bd86..42225e8 100644
--- 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;
@@ -40,13 +46,6 @@ 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
@@ -100,7 +99,7 @@ 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 +109,7 @@ 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 +130,7 @@ 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 +147,7 @@ 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 +162,7 @@ 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 +178,7 @@ 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 +195,7 @@ 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 +207,7 @@ 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 +223,7 @@ 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 +245,7 @@ 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 +254,7 @@ 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 +264,7 @@ 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 +280,7 @@ 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 +308,7 @@ 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 +318,7 @@ 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 +329,7 @@ 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 +358,7 @@ 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 +370,7 @@ 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 +378,7 @@ 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 +386,7 @@ 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 +394,13 @@ 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 +417,7 @@ 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 +433,7 @@ 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 +448,7 @@ 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 +476,7 @@ 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 +492,7 @@ 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 +500,7 @@ 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 +523,7 @@ 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 +535,12 @@ 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 +548,7 @@ 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 +580,7 @@ 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 +595,7 @@ 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 +626,7 @@ 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 +663,7 @@ 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 +685,7 @@ 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 +698,7 @@ 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 +707,7 @@ 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 +726,7 @@ 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 +741,7 @@ 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 +751,7 @@ 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 +794,7 @@ 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 +831,7 @@ 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 +850,7 @@ 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 +863,7 @@ 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 +880,7 @@ 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 +907,7 @@ 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);