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JAL-2933 pass viewport in Finder constructor, find acts on viewport selection if any
bug/JAL-2839findWithHidden
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 14 Mar 2018 13:52:41 +0000
(13:52 +0000)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Wed, 14 Mar 2018 13:52:41 +0000
(13:52 +0000)
src/jalview/analysis/Finder.java
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src/jalview/api/FinderI.java
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src/jalview/appletgui/Finder.java
patch
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src/jalview/gui/Finder.java
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test/jalview/analysis/FinderTest.java
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test/jalview/controller/AlignViewControllerTest.java
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diff --git
a/src/jalview/analysis/Finder.java
b/src/jalview/analysis/Finder.java
index
0996830
..
3cbef6d
100644
(file)
--- a/
src/jalview/analysis/Finder.java
+++ b/
src/jalview/analysis/Finder.java
@@
-20,6
+20,7
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
+import jalview.api.AlignViewportI;
import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Range;
import jalview.api.FinderI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Range;
@@
-52,14
+53,9
@@
public class Finder implements FinderI
private Vector<SequenceI> idMatches;
/*
private Vector<SequenceI> idMatches;
/*
- * the alignment to search over
+ * the viewport to search over
*/
*/
- private AlignmentI alignment;
-
- /*
- * (optional) selection to restrict search to
- */
- private SequenceGroup selection;
+ private AlignViewportI viewport;
/*
* sequence index in alignment to search from
/*
* sequence index in alignment to search from
@@
-74,20
+70,20
@@
public class Finder implements FinderI
private int columnIndex;
/**
private int columnIndex;
/**
- * Constructor for searching an alignment
+ * Constructor for searching a viewport
*
*
- * @param al
+ * @param av
*/
*/
- public Finder(AlignmentI al)
+ public Finder(AlignViewportI av)
{
{
- this.alignment = al;
+ this.viewport = av;
this.sequenceIndex = 0;
this.columnIndex = -1;
}
@Override
this.sequenceIndex = 0;
this.columnIndex = -1;
}
@Override
- public void findAll(String theSearchString, SequenceGroup sg,
- boolean matchCase, boolean searchDescription)
+ public void findAll(String theSearchString, boolean matchCase,
+ boolean searchDescription)
{
/*
* search from the start
{
/*
* search from the start
@@
-95,7
+91,7
@@
public class Finder implements FinderI
sequenceIndex = 0;
columnIndex = -1;
sequenceIndex = 0;
columnIndex = -1;
- doFind(theSearchString, sg, matchCase, searchDescription, true);
+ doFind(theSearchString, matchCase, searchDescription, true);
/*
* reset to start for next search
/*
* reset to start for next search
@@
-105,10
+101,10
@@
public class Finder implements FinderI
}
@Override
}
@Override
- public void findNext(String theSearchString, SequenceGroup sg,
- boolean matchCase, boolean searchDescription)
+ public void findNext(String theSearchString, boolean matchCase,
+ boolean searchDescription)
{
{
- doFind(theSearchString, sg, matchCase, searchDescription, false);
+ doFind(theSearchString, matchCase, searchDescription, false);
if (searchResults.isEmpty() && idMatches.isEmpty())
{
if (searchResults.isEmpty() && idMatches.isEmpty())
{
@@
-121,19
+117,16
@@
public class Finder implements FinderI
}
/**
}
/**
- * Performs a 'find next' or 'find all', optionally restricted to the
- * specified selection region
+ * Performs a 'find next' or 'find all'
*
* @param theSearchString
*
* @param theSearchString
- * @param selectionRegion
* @param matchCase
* @param searchDescription
* @param findAll
*/
* @param matchCase
* @param searchDescription
* @param findAll
*/
- protected void doFind(String theSearchString, SequenceGroup selectionRegion,
- boolean matchCase, boolean searchDescription, boolean findAll)
+ protected void doFind(String theSearchString, boolean matchCase,
+ boolean searchDescription, boolean findAll)
{
{
- this.selection = selectionRegion;
String searchString = matchCase ? theSearchString
: theSearchString.toUpperCase();
Regex searchPattern = new Regex(searchString);
String searchString = matchCase ? theSearchString
: theSearchString.toUpperCase();
Regex searchPattern = new Regex(searchString);
@@
-142,11
+135,13
@@
public class Finder implements FinderI
searchResults = new SearchResults();
idMatches = new Vector<>();
searchResults = new SearchResults();
idMatches = new Vector<>();
+ SequenceGroup selection = viewport.getSelectionGroup();
if (selection != null && selection.getSize() < 1)
{
selection = null; // ? ignore column-only selection
}
if (selection != null && selection.getSize() < 1)
{
selection = null; // ? ignore column-only selection
}
+ AlignmentI alignment = viewport.getAlignment();
int end = alignment.getHeight();
while (sequenceIndex < end)
int end = alignment.getHeight();
while (sequenceIndex < end)
@@
-184,6
+179,7
@@
public class Finder implements FinderI
* restrict search to (next) visible column region,
* in case there are hidden columns
*/
* restrict search to (next) visible column region,
* in case there are hidden columns
*/
+ AlignmentI alignment = viewport.getAlignment();
VisibleContigsIterator visibleRegions = alignment.getHiddenColumns()
.getVisContigsIterator(column, alignment.getWidth(),
false);
VisibleContigsIterator visibleRegions = alignment.getHiddenColumns()
.getVisContigsIterator(column, alignment.getWidth(),
false);
@@
-199,6
+195,7
@@
public class Finder implements FinderI
/*
* restrict search to selected region if there is one
*/
/*
* restrict search to selected region if there is one
*/
+ SequenceGroup selection = viewport.getSelectionGroup();
if (selection != null)
{
int selectionStart = selection.getStartRes();
if (selection != null)
{
int selectionStart = selection.getStartRes();
@@
-233,6
+230,7
@@
public class Finder implements FinderI
protected boolean findNextMatch(SequenceI seq, String searchString,
Regex searchPattern, boolean matchDescription)
{
protected boolean findNextMatch(SequenceI seq, String searchString,
Regex searchPattern, boolean matchDescription)
{
+ SequenceGroup selection = viewport.getSelectionGroup();
if (selection != null && !selection.contains(seq))
{
/*
if (selection != null && !selection.contains(seq))
{
/*
diff --git
a/src/jalview/api/FinderI.java
b/src/jalview/api/FinderI.java
index
a1a3efd
..
19f6136
100644
(file)
--- a/
src/jalview/api/FinderI.java
+++ b/
src/jalview/api/FinderI.java
@@
-1,7
+1,6
@@
package jalview.api;
import jalview.datamodel.SearchResultsI;
package jalview.api;
import jalview.datamodel.SearchResultsI;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import java.util.List;
import jalview.datamodel.SequenceI;
import java.util.List;
@@
-16,7
+15,7
@@
public interface FinderI
* Performs a find for the given search string (interpreted as a regular
* expression). Search may optionally be case-sensitive, and may optionally
* including match in sequence description (sequence id is always searched).
* Performs a find for the given search string (interpreted as a regular
* expression). Search may optionally be case-sensitive, and may optionally
* including match in sequence description (sequence id is always searched).
- * If <code>selection</code> is not null, then the find is restricted to the
+ * If the viewport has an active selection, then the find is restricted to the
* selection region. Sequences matched by id or description can be retrieved
* by getIdMatches(), and matched residue patterns by getSearchResults().
*
* selection region. Sequences matched by id or description can be retrieved
* by getIdMatches(), and matched residue patterns by getSearchResults().
*
@@
-25,26
+24,25
@@
public interface FinderI
* @param searchDescription
* @return
*/
* @param searchDescription
* @return
*/
- void findAll(String theSearchString, SequenceGroup selection,
- boolean caseSensitive, boolean searchDescription);
+ void findAll(String theSearchString, boolean caseSensitive,
+ boolean searchDescription);
/**
* Finds the next match for the given search string (interpreted as a regular
* expression), starting from the position after the last match found. Search
* may optionally be case-sensitive, and may optionally including match in
/**
* Finds the next match for the given search string (interpreted as a regular
* expression), starting from the position after the last match found. Search
* may optionally be case-sensitive, and may optionally including match in
- * sequence description (sequence id is always searched). If
- * <code>selection</code> is not null, then the find is restricted to the
- * selection region. Sequences matched by id or description can be retrieved
- * by getIdMatches(), and matched residue patterns by getSearchResults().
+ * sequence description (sequence id is always searched). If the viewport has
+ * an active selection, then the find is restricted to the selection region.
+ * Sequences matched by id or description can be retrieved by getIdMatches(),
+ * and matched residue patterns by getSearchResults().
*
* @param theSearchString
*
* @param theSearchString
- * @param selection
* @param caseSensitive
* @param searchDescription
* @return
*/
* @param caseSensitive
* @param searchDescription
* @return
*/
- void findNext(String theSearchString, SequenceGroup selection,
- boolean caseSensitive, boolean searchDescription);
+ void findNext(String theSearchString, boolean caseSensitive,
+ boolean searchDescription);
/**
* Returns the (possibly empty) list of sequences matched on sequence name or
/**
* Returns the (possibly empty) list of sequences matched on sequence name or
diff --git
a/src/jalview/appletgui/Finder.java
b/src/jalview/appletgui/Finder.java
index
4b55574
..
2fc3441
100644
(file)
--- a/
src/jalview/appletgui/Finder.java
+++ b/
src/jalview/appletgui/Finder.java
@@
-25,7
+25,6
@@
import jalview.api.FinderI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
@@
-163,23
+162,20
@@
public class Finder extends Panel implements ActionListener
/*
* first time we searched this viewport
*/
/*
* first time we searched this viewport
*/
- finder = new jalview.analysis.Finder(av.getAlignment());
+ finder = new jalview.analysis.Finder(av);
finders.put(av, finder);
}
String searchString = textfield.getText();
finders.put(av, finder);
}
String searchString = textfield.getText();
- SequenceGroup selectionGroup = av.getSelectionGroup();
boolean isCaseSensitive = caseSensitive.getState();
boolean doSearchDescription = searchDescription.getState();
if (doFindAll)
{
boolean isCaseSensitive = caseSensitive.getState();
boolean doSearchDescription = searchDescription.getState();
if (doFindAll)
{
- finder.findAll(searchString, selectionGroup, isCaseSensitive,
- doSearchDescription);
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription);
}
else
{
}
else
{
- finder.findNext(searchString, selectionGroup, isCaseSensitive,
- doSearchDescription);
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription);
}
searchResults = finder.getSearchResults();
}
searchResults = finder.getSearchResults();
diff --git
a/src/jalview/gui/Finder.java
b/src/jalview/gui/Finder.java
index
dcc3518
..
a4d7ad0
100755
(executable)
--- a/
src/jalview/gui/Finder.java
+++ b/
src/jalview/gui/Finder.java
@@
-25,7
+25,6
@@
import jalview.api.FinderI;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GFinder;
import jalview.util.MessageManager;
import jalview.datamodel.SequenceI;
import jalview.jbgui.GFinder;
import jalview.util.MessageManager;
@@
-269,22
+268,19
@@
public class Finder extends GFinder
/*
* first time we've searched this viewport
*/
/*
* first time we've searched this viewport
*/
- finder = new jalview.analysis.Finder(av.getAlignment());
+ finder = new jalview.analysis.Finder(av);
finders.put(av, finder);
}
finders.put(av, finder);
}
- SequenceGroup selectionGroup = av.getSelectionGroup();
boolean isCaseSensitive = caseSensitive.isSelected();
boolean doSearchDescription = searchDescription.isSelected();
if (doFindAll)
{
boolean isCaseSensitive = caseSensitive.isSelected();
boolean doSearchDescription = searchDescription.isSelected();
if (doFindAll)
{
- finder.findAll(searchString, selectionGroup, isCaseSensitive,
- doSearchDescription);
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription);
}
else
{
}
else
{
- finder.findNext(searchString, selectionGroup, isCaseSensitive,
- doSearchDescription);
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription);
}
searchResults = finder.getSearchResults();
}
searchResults = finder.getSearchResults();
diff --git
a/test/jalview/analysis/FinderTest.java
b/test/jalview/analysis/FinderTest.java
index
e453dd3
..
e2a94ef
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 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;
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.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 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 org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@@
-59,6
+62,8
@@
public class FinderTest
private AlignmentI al;
private AlignmentI al;
+ private AlignViewportI av;
+
@BeforeClass(groups = "Functional")
public void setUp()
{
@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);
+ "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
*/
/*
* 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);
// 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);
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);
// 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()
{
@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
*/
/*
* 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();
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)
*/
/*
* 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();
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
*/
/*
* 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());
}
assertTrue(f.getSearchResults().isEmpty());
}
@@
-158,10
+170,10
@@
public class FinderTest
* start at second sequence; colIndex of -1
* means sequence id / description is searched
*/
* 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);
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);
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);
// 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);
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();
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
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);
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());
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");
al2.getSequenceAt(0).setDescription("BRAF");
al2.getSequenceAt(1).setDescription("braf");
+ AlignViewportI av2 = new AlignViewport(al2);
+
/*
* find first match only
*/
/*
* 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());
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
*/
/*
* 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));
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
*/
/*
* 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());
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");
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
*/
/*
* 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));
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()
{
@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
*/
/*
* 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();
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
*/
/*
* 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());
searchResults = f.getSearchResults();
assertTrue(searchResults.isEmpty());
@@
-290,9
+304,10
@@
public class FinderTest
* match both sequence id and sequence
*/
AlignmentI al2 = new Alignment(al);
* match both sequence id and sequence
*/
AlignmentI al2 = new Alignment(al);
+ AlignViewportI av2 = new AlignViewport(al2);
al2.addSequence(new Sequence("aBz", "xyzabZpqrAbZ"));
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();
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
*/
/*
* 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);
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)
*/
/*
* 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);
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);
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);
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);
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);
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);
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
*/
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);
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()
{
@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);
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()
{
@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);
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
*/
/*
* 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);
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()
{
@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
*/
/*
* 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);
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
*/
/*
* 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);
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);
assertEquals(match.getStart(), 1);
assertEquals(match.getEnd(), 2);
- f.findAll("bC", null, true, false);
+ f.findAll("bC", true, false);
assertTrue(f.getSearchResults().isEmpty());
}
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);
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);
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
*/
/*
* 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());
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);
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);
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);
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);
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
*/
/*
* 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));
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
*/
/*
* 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));
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);
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
*/
/*
* 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);
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
*/
* 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);
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);
* 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);
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
*/
/*
* 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());
/*
assertTrue(f.getSearchResults().isEmpty());
/*
@@
-656,8
+674,8
@@
public class FinderTest
*/
hc.revealAllHiddenColumns(new ColumnSelection());
hc.hideColumns(8, 13);
*/
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);
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);
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
*/
/*
* 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);
SearchResultsI searchResults = f.getSearchResults();
assertEquals(searchResults.getSize(), 2);
SearchResultMatchI match = searchResults.getResults().get(0);
diff --git
a/test/jalview/controller/AlignViewControllerTest.java
b/test/jalview/controller/AlignViewControllerTest.java
index
ad86f32
..
2669c99
100644
(file)
--- a/
test/jalview/controller/AlignViewControllerTest.java
+++ b/
test/jalview/controller/AlignViewControllerTest.java
@@
-223,8
+223,8
@@
public class AlignViewControllerTest
/*
* test Match/Find works first
*/
/*
* test Match/Find works first
*/
- FinderI f = new Finder(af.getViewport().getAlignment());
- f.findAll("M+", null, true, false);
+ FinderI f = new Finder(af.getViewport());
+ f.findAll("M+", true, false);
assertEquals(
"Finder found different set of results to manually created SearchResults",
sr, f.getSearchResults());
assertEquals(
"Finder found different set of results to manually created SearchResults",
sr, f.getSearchResults());