/*
* 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.analysis;
import static org.testng.Assert.assertSame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import java.util.Arrays;
import java.util.List;
import junit.extensions.PA;
import org.testng.annotations.Test;
public class AlignmentSorterTest
{
@Test(groups = "Functional")
public void testSortByFeature_score()
{
SequenceI seq1 = new Sequence("Seq1", "ABC--D-EFGHIJ");
SequenceI seq2 = new Sequence("Seq2", "ABCDEFGHIJ");
SequenceI seq3 = new Sequence("Seq3", "ABCDE-FGHIJ");
SequenceI seq4 = new Sequence("Seq4", "ABCDEFGHIJ");
SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4 };
AlignmentI al = new Alignment(seqs);
al.setDataset(null);
/*
* sort with no score features does nothing
*/
PA.setValue(AlignmentSorter.getInstance(), "sortByFeatureCriteria", null);
AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
AlignmentSorter.FEATURE_SCORE);
assertSame(al.getSequenceAt(0), seq1);
assertSame(al.getSequenceAt(1), seq2);
assertSame(al.getSequenceAt(2), seq3);
assertSame(al.getSequenceAt(3), seq4);
/*
* add score and non-score features
* seq1 Cath(2.0) Pfam(4.0) average 3.0
* seq2 Cath(2.5) Metal(NaN) average 2.5
* seq3 KD(-4), KD(3.0) average -0.5
* seq4 Helix(NaN) - should sort as if largest score
*/
seq1.addSequenceFeature(
new SequenceFeature("Cath", "", 2, 3, 2.0f, "g1"));
seq1.addSequenceFeature(
new SequenceFeature("Pfam", "", 4, 5, 4.0f, "g2"));
seq2.addSequenceFeature(
new SequenceFeature("Cath", "", 2, 3, 2.5f, "g3"));
seq2.addSequenceFeature(
new SequenceFeature("Metal", "", 2, 3, Float.NaN, "g4"));
seq3.addSequenceFeature(new SequenceFeature("kD", "", 2, 3, -4f, "g5"));
seq3.addSequenceFeature(
new SequenceFeature("kD", "", 5, 6, 3.0f, "g6"));
seq4.addSequenceFeature(
new SequenceFeature("Helix", "", 2, 3, Float.NaN, "g7"));
/*
* sort by ascending score, no filter on feature type or group
* NB sort order for the same feature set (none) gets toggled, so descending
*/
PA.setValue(AlignmentSorter.getInstance(), "sortByFeatureAscending", true);
AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
AlignmentSorter.FEATURE_SCORE);
assertSame(al.getSequenceAt(3), seq3); // -0.5
assertSame(al.getSequenceAt(2), seq2); // 2.5
assertSame(al.getSequenceAt(1), seq1); // 3.0
assertSame(al.getSequenceAt(0), seq4); // maximum 'score'
/*
* repeat sort toggles order - now ascending
*/
AlignmentSorter.sortByFeature(null, null, 0, al.getWidth(), al,
AlignmentSorter.FEATURE_SCORE);
assertSame(al.getSequenceAt(0), seq3); // -0.5
assertSame(al.getSequenceAt(1), seq2); // 2.5
assertSame(al.getSequenceAt(2), seq1); // 3.0
assertSame(al.getSequenceAt(3), seq4);
/*
* specify features, excluding Pfam
* seq1 average is now 2.0
* next sort is ascending (not toggled) as for a different feature set
*/
List types = Arrays.asList(new String[] { "Cath", "kD" });
AlignmentSorter.sortByFeature(types, null, 0, al.getWidth(), al,
AlignmentSorter.FEATURE_SCORE);
assertSame(al.getSequenceAt(0), seq3); // -0.5
assertSame(al.getSequenceAt(1), seq1); // 2.0
assertSame(al.getSequenceAt(2), seq2); // 2.5
assertSame(al.getSequenceAt(3), seq4);
/*
* specify groups, excluding g5 (kD -4 score)
* seq3 average is now 3.0
* next sort is ascending (not toggled) as for a different group spec
*/
List groups = Arrays
.asList(new String[]
{ "g1", "g2", "g3", "g6" });
AlignmentSorter.sortByFeature(types, groups, 0, al.getWidth(), al,
AlignmentSorter.FEATURE_SCORE);
assertSame(al.getSequenceAt(0), seq1); // 2.0
assertSame(al.getSequenceAt(1), seq2); // 2.5
assertSame(al.getSequenceAt(2), seq3); // 3.0
assertSame(al.getSequenceAt(3), seq4);
/*
* limit to columns 0-4, excluding 2nd feature of seq1 and seq3
* seq1 is now 2.0, seq3 is now -4
*/
// fails because seq1.findPosition(4) returns 4
// although residue 4 is in column 5! - JAL-2544
AlignmentSorter.sortByFeature(null, null, 0, 4, al,
AlignmentSorter.FEATURE_SCORE);
assertSame(al.getSequenceAt(0), seq3); // -4
assertSame(al.getSequenceAt(1), seq1); // 2.0
assertSame(al.getSequenceAt(2), seq2); // 2.5
assertSame(al.getSequenceAt(3), seq4);
}
@Test(groups = "Functional")
public void testSortByFeature_density()
{
// TODO
}
}