X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fcontroller%2FAlignViewControllerTest.java;h=f037599f7044a8d06bac6146a704169220509918;hb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;hp=d85b68fd0efc4728610b2c5b63fcbcbf1864c63d;hpb=3828a47f3ee9549412e04d91cbc1455cada45d01;p=jalview.git
diff --git a/test/jalview/controller/AlignViewControllerTest.java b/test/jalview/controller/AlignViewControllerTest.java
index d85b68f..f037599 100644
--- a/test/jalview/controller/AlignViewControllerTest.java
+++ b/test/jalview/controller/AlignViewControllerTest.java
@@ -1,16 +1,42 @@
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.controller;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
-import jalview.datamodel.ColumnSelection;
+import jalview.analysis.Finder;
+import jalview.api.AlignViewControllerI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.io.DataSourceType;
+import jalview.io.FileLoader;
+import java.util.Arrays;
import java.util.BitSet;
-import java.util.List;
import org.testng.annotations.Test;
@@ -19,10 +45,10 @@ public class AlignViewControllerTest
@Test(groups = "Functional")
public void testFindColumnsWithFeature()
{
- SequenceI seq1 = new Sequence("seq1", "aMMMaaaaaaaaaaaaaaaa");
- SequenceI seq2 = new Sequence("seq2", "aaaMMMMMMMaaaaaaaaaa");
- SequenceI seq3 = new Sequence("seq3", "aaaaaaaaaaMMMMMaaaaa");
- SequenceI seq4 = new Sequence("seq3", "aaaaaaaaaaaaaaaaaaaa");
+ SequenceI seq1 = new Sequence("seq1", "-a-MMMaaaaaaaaaaaaaaaa");
+ SequenceI seq2 = new Sequence("seq2", "aa--aMM-MMMMMaaaaaaaaaa");
+ SequenceI seq3 = new Sequence("seq3", "abcab-caD-aaMMMMMaaaaa");
+ SequenceI seq4 = new Sequence("seq4", "abc--abcaaaaaaaaaaaaaa");
/*
* features start/end are base 1
@@ -35,13 +61,16 @@ public class AlignViewControllerTest
null));
seq3.addSequenceFeature(new SequenceFeature("Metal", "desc", 11, 15,
0f, null));
+ // disulfide bond is a 'contact feature' - only select its 'start' and 'end'
+ seq3.addSequenceFeature(new SequenceFeature("disulfide bond", "desc", 8, 12,
+ 0f, null));
/*
- * select the first three columns --> seq1 2-3
+ * select the first five columns --> Metal in seq1 cols 4-5
*/
SequenceGroup sg = new SequenceGroup();
sg.setStartRes(0); // base 0
- sg.setEndRes(2);
+ sg.setEndRes(4);
sg.addSequence(seq1, false);
sg.addSequence(seq2, false);
sg.addSequence(seq3, false);
@@ -52,37 +81,37 @@ public class AlignViewControllerTest
bs);
assertEquals(1, seqCount);
assertEquals(2, bs.cardinality());
- assertTrue(bs.get(1));
- assertTrue(bs.get(2));
-
+ assertTrue(bs.get(3)); // base 0
+ assertTrue(bs.get(4));
+
/*
- * select the first four columns: seq1 2:4, seq2 4:4
+ * select the first seven columns: Metal in seq1 cols 4-6, seq2 cols 6-7
*/
- sg.setEndRes(3);
+ sg.setEndRes(6);
bs.clear();
- seqCount = AlignViewController.findColumnsWithFeature("Metal", sg,
- bs);
+ seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
assertEquals(2, seqCount);
- assertEquals(3, bs.cardinality());
- assertTrue(bs.get(1));
- assertTrue(bs.get(2));
+ assertEquals(4, bs.cardinality());
assertTrue(bs.get(3));
+ assertTrue(bs.get(4));
+ assertTrue(bs.get(5));
+ assertTrue(bs.get(6));
/*
- * select column 11: seq3 only
+ * select column 14: Metal in seq3 only
*/
- sg.setStartRes(10);
- sg.setEndRes(10);
+ sg.setStartRes(13);
+ sg.setEndRes(13);
bs.clear();
seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
assertEquals(1, seqCount);
assertEquals(1, bs.cardinality());
- assertTrue(bs.get(10));
+ assertTrue(bs.get(13));
/*
- * select columns 16-20: no Metal feature
+ * select columns 18-20: no Metal feature
*/
- sg.setStartRes(15);
+ sg.setStartRes(17);
sg.setEndRes(19);
bs.clear();
seqCount = AlignViewController.findColumnsWithFeature("Metal", sg, bs);
@@ -90,6 +119,30 @@ public class AlignViewControllerTest
assertEquals(0, bs.cardinality());
/*
+ * columns 11-13 should not match disulfide bond at 8/12
+ */
+ sg.setStartRes(10);
+ sg.setEndRes(12);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
+ sg, bs);
+ assertEquals(0, seqCount);
+ assertEquals(0, bs.cardinality());
+
+ /*
+ * columns 6-18 should match disulfide bond at columns 9, 14
+ */
+ sg.setStartRes(5);
+ sg.setEndRes(17);
+ bs.clear();
+ seqCount = AlignViewController.findColumnsWithFeature("disulfide bond",
+ sg, bs);
+ assertEquals(1, seqCount);
+ assertEquals(2, bs.cardinality());
+ assertTrue(bs.get(8));
+ assertTrue(bs.get(13));
+
+ /*
* look for a feature that isn't there
*/
sg.setStartRes(0);
@@ -100,99 +153,52 @@ public class AlignViewControllerTest
assertEquals(0, bs.cardinality());
}
+ /**
+ * shameless copy of test data from findFeature for testing mark columns from
+ * highlight
+ */
@Test(groups = "Functional")
- public void testSelectMarkedColumns_invert()
+ public void testSelectColumnsWithHighlight()
{
- ColumnSelection cs = new ColumnSelection();
- cs.addElement(5); // this will be cleared
- BitSet toMark = new BitSet();
- toMark.set(1);
- toMark.set(3);
- toMark.set(6);
- toMark.set(9);
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "seq1 aMMMaaaaaaaaaaaaaaaa\n" + "seq2 aaaMMMMMMMaaaaaaaaaa\n"
+ + "seq3 aaaaaaaaaaMMMMMaaaaa\n"
+ + "seq4 aaaaaaaaaaaaaaaaaaaa\n", DataSourceType.PASTE);
+
+ SearchResultsI sr = new SearchResults();
+ SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
+ SequenceI seq1 = sqs[0];
+ SequenceI seq2 = sqs[1];
+ SequenceI seq3 = sqs[2];
+ SequenceI seq4 = sqs[3];
/*
- * inverted selection of {3, 6} should select {4, 5, 7, 8}
+ * features start/end are base 1
*/
- assertTrue(AlignViewController.selectMarkedColumns(cs, true, false,
- false, toMark, 3, 8));
- List selected = cs.getSelected();
- assertEquals(4, selected.size());
- assertTrue(selected.contains(4));
- assertTrue(selected.contains(5));
- assertTrue(selected.contains(7));
- assertTrue(selected.contains(8));
- }
+ sr.addResult(seq1, 2, 4);
+ sr.addResult(seq2, 4, 10);
+ sr.addResult(seq3, 11, 15);
- @Test(groups = "Functional")
- public void testSelectMarkedColumns()
- {
- ColumnSelection cs = new ColumnSelection();
- cs.addElement(5); // this will be cleared
- BitSet toMark = new BitSet();
- toMark.set(1);
- toMark.set(3);
- toMark.set(6);
- toMark.set(9);
-
- assertTrue(AlignViewController.selectMarkedColumns(cs, false, false,
- false, toMark, 3, 8));
- List selected = cs.getSelected();
- assertEquals(2, selected.size());
- assertTrue(selected.contains(3));
- assertTrue(selected.contains(6));
- }
-
- @Test(groups = "Functional")
- public void testSelectMarkedColumns_extend()
- {
- ColumnSelection cs = new ColumnSelection();
- cs.addElement(1);
- cs.addElement(5);
- BitSet toMark = new BitSet();
- toMark.set(1);
- toMark.set(3);
- toMark.set(6);
- toMark.set(9);
-
/*
- * extending selection of {3, 6} should leave {1, 3, 5, 6} selected
+ * test Match/Find works first
*/
- assertTrue(AlignViewController.selectMarkedColumns(cs, false, true,
- false, toMark, 3, 8));
- List selected = cs.getSelected();
- assertEquals(4, selected.size());
- assertTrue(selected.contains(1));
- assertTrue(selected.contains(3));
- assertTrue(selected.contains(5));
- assertTrue(selected.contains(6));
- }
+ Finder f = new Finder(af.getViewport().getAlignment(), null);
+ f.setFindAll(true);
+ f.setCaseSensitive(true);
+ f.find("M+");
+ assertEquals(
+ "Finder found different set of results to manually created SearchResults",
+ sr, f.getSearchResults());
- @Test(groups = "Functional")
- public void testSelectMarkedColumns_toggle()
- {
- ColumnSelection cs = new ColumnSelection();
- cs.addElement(1); // outside change range
- cs.addElement(3);
- cs.addElement(4);
- cs.addElement(10); // outside change range
- BitSet toMark = new BitSet();
- toMark.set(1);
- toMark.set(3);
- toMark.set(6);
- toMark.set(9);
-
/*
- * toggling state of {3, 6} should leave {1, 4, 6, 10} selected
+ * now check simple mark columns from find operation
*/
- assertTrue(AlignViewController.selectMarkedColumns(cs, false, false,
- true, toMark, 3, 8));
- List selected = cs.getSelected();
- assertEquals(4, selected.size());
- assertTrue(selected.contains(1));
- assertTrue(selected.contains(4));
- assertTrue(selected.contains(6));
- assertTrue(selected.contains(10));
+ af.getViewport().setSearchResults(sr);
+ AlignViewControllerI avc = af.avc;
+
+ avc.markHighlightedColumns(false, false, false);
+ assertTrue("Didn't select highlighted columns", Arrays.deepEquals(af
+ .getViewport().getColumnSelection().getSelectedRanges()
+ .toArray(), new int[][] { { 1, 14 } }));
}
- // TODO testSelectMarkedColumns with combinations of invert/extend/toggle set
}