--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.analysis;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertSame;
+import static org.testng.Assert.assertTrue;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.Sequence;
+import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+
+import java.util.List;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class FinderTest
+{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ private AlignFrame af;
+
+ private AlignmentI al;
+
+ @BeforeClass(groups = "Functional")
+ public void setUp()
+ {
+ String seqData = "seq1 ABCD--EF-GHI\n" + "seq2 A--BCDefHI\n"
+ + "seq3 --bcdEFH\n" + "seq4 aa---aMMMMMaaa\n";
+ af = new FileLoader().LoadFileWaitTillLoaded(seqData,
+ DataSourceType.PASTE);
+ al = af.getViewport().getAlignment();
+ }
+
+ /**
+ * Test for find all matches of a regular expression
+ */
+ @Test(groups = "Functional")
+ public void testFindAll_regex()
+ {
+ Finder f = new Finder(al, null);
+ f.setFindAll(true);
+ f.find("E.H"); // 'E, any character, H'
+
+ // should match seq2 efH and seq3 EFH
+ SearchResultsI sr = f.getSearchResults();
+ assertEquals(sr.getSize(), 2);
+ List<SearchResultMatchI> matches = sr.getResults();
+ assertSame(al.getSequenceAt(1), matches.get(0).getSequence());
+ assertSame(al.getSequenceAt(2), matches.get(1).getSequence());
+ assertEquals(matches.get(0).getStart(), 5);
+ assertEquals(matches.get(0).getEnd(), 7);
+ assertEquals(matches.get(1).getStart(), 4);
+ assertEquals(matches.get(1).getEnd(), 6);
+ }
+
+ /**
+ * Test for (undocumented) find residue by position
+ */
+ @Test(groups = "Functional")
+ public void testFind_residueNumber()
+ {
+ Finder f = new Finder(al, null);
+ f.setFindAll(true);
+ f.find("9");
+
+ // seq1 and seq4 have 9 residues; no match in other sequences
+ SearchResultsI sr = f.getSearchResults();
+ assertEquals(sr.getSize(), 2);
+ List<SearchResultMatchI> matches = sr.getResults();
+ assertSame(al.getSequenceAt(0), matches.get(0).getSequence());
+ assertSame(al.getSequenceAt(3), matches.get(1).getSequence());
+ assertEquals(matches.get(0).getStart(), 9);
+ assertEquals(matches.get(0).getEnd(), 9);
+ assertEquals(matches.get(1).getStart(), 9);
+ assertEquals(matches.get(1).getEnd(), 9);
+ }
+
+ /**
+ * Test for find next action
+ */
+ @Test(groups = "Functional")
+ public void testFindNext()
+ {
+ /*
+ * start at second sequence; resIndex of -1
+ * means sequence id / description is searched
+ */
+ Finder f = new Finder(al, null, 1, -1);
+ f.find("e"); // matches id
+
+ assertTrue(f.getSearchResults().isEmpty());
+ assertEquals(f.getIdMatch().size(), 1);
+ assertSame(f.getIdMatch().get(0), al.getSequenceAt(1));
+
+ // resIndex is now 0 - for use in next find next
+ assertEquals(f.getResIndex(), 0);
+ f = new Finder(al, null, 1, 0);
+ f.find("e"); // matches in sequence
+ assertTrue(f.getIdMatch().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.getSeqIndex(), 1);
+ // next residue position to search from is 5
+ // (used as base 0 by RegEx so the same as 6 if base 1)
+ assertEquals(f.getResIndex(), 5);
+
+ // find next from end of sequence - finds next sequence id
+ f = new Finder(al, null, 1, 5);
+ f.find("e");
+ assertEquals(f.getIdMatch().size(), 1);
+ assertSame(f.getIdMatch().get(0), al.getSequenceAt(2));
+ }
+
+ /**
+ * Test for matching within sequence descriptions
+ */
+ @Test(groups = "Functional")
+ public void testFindAll_inDescription()
+ {
+ AlignmentI al2 = new Alignment(al);
+ al2.getSequenceAt(0).setDescription("BRAF");
+ al2.getSequenceAt(1).setDescription("braf");
+ Finder 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));
+ 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));
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * match sequence id, description and sequence!
+ */
+ 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);
+
+ /*
+ * 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));
+
+ assertEquals(f.getSearchResults().getSize(), 2);
+ SearchResultMatchI match = f.getSearchResults().getResults().get(0);
+ assertSame(al2.getSequenceAt(1), match.getSequence());
+ assertEquals(5, match.getStart());
+ assertEquals(7, match.getEnd());
+ match = f.getSearchResults().getResults().get(1);
+ assertSame(al2.getSequenceAt(2), match.getSequence());
+ assertEquals(4, match.getStart());
+ assertEquals(6, match.getEnd());
+ }
+
+ /**
+ * Test for matching within sequence ids
+ */
+ @Test(groups = "Functional")
+ public void testFindAll_sequenceIds()
+ {
+ Finder f = new Finder(al, null);
+ f.setFindAll(true);
+
+ /*
+ * case insensitive
+ */
+ f.find("SEQ1");
+ assertEquals(f.getIdMatch().size(), 1);
+ assertSame(f.getIdMatch().get(0), al.getSequenceAt(0));
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * case sensitive
+ */
+ f = new Finder(al, null);
+ f.setFindAll(true);
+ f.setCaseSensitive(true);
+ f.find("SEQ1");
+ assertTrue(f.getSearchResults().isEmpty());
+
+ /*
+ * match both sequence id and sequence
+ */
+ 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));
+ assertEquals(f.getSearchResults().getSize(), 2);
+ SearchResultMatchI match = f.getSearchResults().getResults().get(0);
+ assertSame(al2.getSequenceAt(4), match.getSequence());
+ assertEquals(4, match.getStart());
+ assertEquals(6, match.getEnd());
+ match = f.getSearchResults().getResults().get(1);
+ assertSame(al2.getSequenceAt(4), match.getSequence());
+ assertEquals(10, match.getStart());
+ assertEquals(12, match.getEnd());
+ }
+
+ /**
+ * Test finding all matches of a sequence pattern in an alignment
+ */
+ @Test(groups = "Functional")
+ public void testFindAll_simpleMatch()
+ {
+ Finder f = new Finder(al, null);
+ f.setFindAll(true);
+
+ /*
+ * case insensitive first
+ */
+ f.find("EfH");
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(al.getSequenceAt(1), match.getSequence());
+ assertEquals(5, match.getStart());
+ assertEquals(7, match.getEnd());
+ match = searchResults.getResults().get(1);
+ assertSame(al.getSequenceAt(2), match.getSequence());
+ assertEquals(4, match.getStart());
+ assertEquals(6, match.getEnd());
+
+ /*
+ * case sensitive
+ */
+ f = new Finder(al, null);
+ f.setFindAll(true);
+ f.setCaseSensitive(true);
+ f.find("BC");
+ searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 2);
+ match = searchResults.getResults().get(0);
+ assertSame(al.getSequenceAt(0), match.getSequence());
+ assertEquals(2, match.getStart());
+ assertEquals(3, match.getEnd());
+ match = searchResults.getResults().get(1);
+ assertSame(al.getSequenceAt(1), match.getSequence());
+ assertEquals(2, match.getStart());
+ assertEquals(3, match.getEnd());
+ }
+
+ /**
+ * Test for JAL-2302 to verify that sub-matches are not included in a find all
+ * result
+ */
+ @Test(groups = "Functional")
+ public void testFind_maximalResultOnly()
+ {
+ Finder f = new Finder(al, null);
+ f.setFindAll(true);
+ f.find("M+");
+ SearchResultsI searchResults = f.getSearchResults();
+ assertEquals(searchResults.getSize(), 1);
+ SearchResultMatchI match = searchResults.getResults().get(0);
+ assertSame(al.getSequenceAt(3), match.getSequence());
+ assertEquals(4, match.getStart()); // dataset sequence positions
+ assertEquals(8, match.getEnd()); // base 1
+ }
+}
git://source.jalview.org / jalview.git / blobdiff