+++ /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.assertTrue;
-
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.gui.JvOptionPane;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
-public class ConservationTest
-{
-
- @BeforeClass(alwaysRun = true)
- public void setUpJvOptionPane()
- {
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
- }
-
- @Test(groups = "Functional")
- public void testRecordConservation()
- {
- Map<String, Integer> resultMap = new HashMap<String, Integer>();
-
- // V is hydrophobic, aliphatic, small
- Conservation.recordConservation(resultMap, "V");
- assertEquals(resultMap.get("hydrophobic").intValue(), 1);
- assertEquals(resultMap.get("aliphatic").intValue(), 1);
- assertEquals(resultMap.get("small").intValue(), 1);
- assertEquals(resultMap.get("tiny").intValue(), 0);
- assertEquals(resultMap.get("polar").intValue(), 0);
- assertEquals(resultMap.get("charged").intValue(), 0);
-
- // now add S: not hydrophobic, small, tiny, polar, not aliphatic
- Conservation.recordConservation(resultMap, "s");
- assertEquals(resultMap.get("hydrophobic").intValue(), -1);
- assertEquals(resultMap.get("aliphatic").intValue(), -1);
- assertEquals(resultMap.get("small").intValue(), 1);
- assertEquals(resultMap.get("tiny").intValue(), -1);
- assertEquals(resultMap.get("polar").intValue(), -1);
- assertEquals(resultMap.get("charged").intValue(), 0);
- }
-
- @Test(groups = "Functional")
- public void testCountConservationAndGaps()
- {
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- seqs.add(new Sequence("seq1", "VGnY")); // not case sensitive
- seqs.add(new Sequence("seq2", "-G-y"));
- seqs.add(new Sequence("seq3", "VG-Y"));
- seqs.add(new Sequence("seq4", "VGNW"));
-
- Conservation cons = new Conservation("", seqs, 0, 50);
- int[] counts = cons.countConservationAndGaps(0);
- assertEquals(counts[0], 1); // conserved
- assertEquals(counts[1], 1); // gap count
- counts = cons.countConservationAndGaps(1);
- assertEquals(counts[0], 1);
- assertEquals(counts[1], 0);
- counts = cons.countConservationAndGaps(2);
- assertEquals(counts[0], 1);
- assertEquals(counts[1], 2);
- counts = cons.countConservationAndGaps(3);
- assertEquals(counts[0], 0); // not conserved
- assertEquals(counts[1], 0);
- }
-
- @Test(groups = "Functional")
- public void testCalculate_noThreshold()
- {
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- seqs.add(new Sequence("seq1", "VGIV-N"));
- seqs.add(new Sequence("seq2", "V-iL-N")); // not case sensitive
- seqs.add(new Sequence("seq3", "V-IW-N"));
- seqs.add(new Sequence("seq4", "VGLH-L"));
-
- Conservation cons = new Conservation("", 0, seqs, 0, 5);
- cons.calculate();
-
- /*
- * column 0: all V (hydrophobic/aliphatic/small)
- */
- Map<String, Integer> colCons = cons.total[0];
- assertEquals(colCons.get("hydrophobic").intValue(), 1);
- assertEquals(colCons.get("aliphatic").intValue(), 1);
- assertEquals(colCons.get("small").intValue(), 1);
- assertEquals(colCons.get("tiny").intValue(), 0);
- assertEquals(colCons.get("proline").intValue(), 0);
- assertEquals(colCons.get("charged").intValue(), 0);
- assertEquals(colCons.get("negative").intValue(), 0);
- assertEquals(colCons.get("polar").intValue(), 0);
- assertEquals(colCons.get("positive").intValue(), 0);
- assertEquals(colCons.get("aromatic").intValue(), 0);
-
- /*
- * column 1: all G (hydrophobic/small/tiny)
- * gaps take default value of property present
- */
- colCons = cons.total[1];
- assertEquals(colCons.get("hydrophobic").intValue(), 1);
- assertEquals(colCons.get("aliphatic").intValue(), -1);
- assertEquals(colCons.get("small").intValue(), 1);
- assertEquals(colCons.get("tiny").intValue(), 1);
- assertEquals(colCons.get("proline").intValue(), -1);
- assertEquals(colCons.get("charged").intValue(), -1);
- assertEquals(colCons.get("negative").intValue(), -1);
- assertEquals(colCons.get("polar").intValue(), -1);
- assertEquals(colCons.get("positive").intValue(), -1);
- assertEquals(colCons.get("aromatic").intValue(), -1);
-
- /*
- * column 2: I/L (aliphatic/hydrophobic), all others negatively conserved
- */
- colCons = cons.total[2];
- assertEquals(colCons.get("hydrophobic").intValue(), 1);
- assertEquals(colCons.get("aliphatic").intValue(), 1);
- assertEquals(colCons.get("small").intValue(), 0);
- assertEquals(colCons.get("tiny").intValue(), 0);
- assertEquals(colCons.get("proline").intValue(), 0);
- assertEquals(colCons.get("charged").intValue(), 0);
- assertEquals(colCons.get("negative").intValue(), 0);
- assertEquals(colCons.get("polar").intValue(), 0);
- assertEquals(colCons.get("positive").intValue(), 0);
- assertEquals(colCons.get("aromatic").intValue(), 0);
-
- /*
- * column 3: VLWH all hydrophobic, none is tiny, negative or proline
- */
- colCons = cons.total[3];
- assertEquals(colCons.get("hydrophobic").intValue(), 1);
- assertEquals(colCons.get("aliphatic").intValue(), -1);
- assertEquals(colCons.get("small").intValue(), -1);
- assertEquals(colCons.get("tiny").intValue(), 0);
- assertEquals(colCons.get("proline").intValue(), 0);
- assertEquals(colCons.get("charged").intValue(), -1);
- assertEquals(colCons.get("negative").intValue(), 0);
- assertEquals(colCons.get("polar").intValue(), -1);
- assertEquals(colCons.get("positive").intValue(), -1);
- assertEquals(colCons.get("aromatic").intValue(), -1);
-
- /*
- * column 4: all gaps - counted as having all properties
- */
- colCons = cons.total[4];
- assertEquals(colCons.get("hydrophobic").intValue(), 1);
- assertEquals(colCons.get("aliphatic").intValue(), 1);
- assertEquals(colCons.get("small").intValue(), 1);
- assertEquals(colCons.get("tiny").intValue(), 1);
- assertEquals(colCons.get("proline").intValue(), 1);
- assertEquals(colCons.get("charged").intValue(), 1);
- assertEquals(colCons.get("negative").intValue(), 1);
- assertEquals(colCons.get("polar").intValue(), 1);
- assertEquals(colCons.get("positive").intValue(), 1);
- assertEquals(colCons.get("aromatic").intValue(), 1);
-
- /*
- * column 5: N (small polar) and L (aliphatic hydrophobic)
- * have nothing in common!
- */
- colCons = cons.total[5];
- assertEquals(colCons.get("hydrophobic").intValue(), -1);
- assertEquals(colCons.get("aliphatic").intValue(), -1);
- assertEquals(colCons.get("small").intValue(), -1);
- assertEquals(colCons.get("tiny").intValue(), 0);
- assertEquals(colCons.get("proline").intValue(), 0);
- assertEquals(colCons.get("charged").intValue(), 0);
- assertEquals(colCons.get("negative").intValue(), 0);
- assertEquals(colCons.get("polar").intValue(), -1);
- assertEquals(colCons.get("positive").intValue(), 0);
- assertEquals(colCons.get("aromatic").intValue(), 0);
- }
-
- /**
- * Test for the case whether the number of non-gapped sequences in a column
- * has to be above a threshold
- */
- @Test(groups = "Functional")
- public void testCalculate_threshold()
- {
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- seqs.add(new Sequence("seq1", "VGIV-"));
- seqs.add(new Sequence("seq2", "V-iL-")); // not case sensitive
- seqs.add(new Sequence("seq3", "V-IW-"));
- seqs.add(new Sequence("seq4", "VGLH-"));
- seqs.add(new Sequence("seq5", "VGLH-"));
-
- /*
- * threshold 50% means a residue has to occur 3 or more times
- * in a column to be counted for conservation
- */
- // TODO: ConservationThread uses a value of 3
- // calculateConservation states it is the minimum number of sequences
- // but it is treated as percentage threshold in calculate() ?
- Conservation cons = new Conservation("", 50, seqs, 0, 4);
- cons.calculate();
-
- /*
- * column 0: all V (hydrophobic/aliphatic/small)
- */
- Map<String, Integer> colCons = cons.total[0];
- assertEquals(colCons.get("hydrophobic").intValue(), 1);
- assertEquals(colCons.get("aliphatic").intValue(), 1);
- assertEquals(colCons.get("small").intValue(), 1);
- assertEquals(colCons.get("tiny").intValue(), 0);
- assertEquals(colCons.get("proline").intValue(), 0);
- assertEquals(colCons.get("charged").intValue(), 0);
- assertEquals(colCons.get("negative").intValue(), 0);
- assertEquals(colCons.get("polar").intValue(), 0);
- assertEquals(colCons.get("positive").intValue(), 0);
- assertEquals(colCons.get("aromatic").intValue(), 0);
-
- /*
- * column 1: all G (hydrophobic/small/tiny)
- * gaps are ignored as not above threshold
- */
- colCons = cons.total[1];
- assertEquals(colCons.get("hydrophobic").intValue(), 1);
- assertEquals(colCons.get("aliphatic").intValue(), 0);
- assertEquals(colCons.get("small").intValue(), 1);
- assertEquals(colCons.get("tiny").intValue(), 1);
- assertEquals(colCons.get("proline").intValue(), 0);
- assertEquals(colCons.get("charged").intValue(), 0);
- assertEquals(colCons.get("negative").intValue(), 0);
- assertEquals(colCons.get("polar").intValue(), 0);
- assertEquals(colCons.get("positive").intValue(), 0);
- assertEquals(colCons.get("aromatic").intValue(), 0);
-
- /*
- * column 2: I/L (aliphatic/hydrophobic), all others negatively conserved
- */
- colCons = cons.total[2];
- assertEquals(colCons.get("hydrophobic").intValue(), 1);
- assertEquals(colCons.get("aliphatic").intValue(), 1);
- assertEquals(colCons.get("small").intValue(), 0);
- assertEquals(colCons.get("tiny").intValue(), 0);
- assertEquals(colCons.get("proline").intValue(), 0);
- assertEquals(colCons.get("charged").intValue(), 0);
- assertEquals(colCons.get("negative").intValue(), 0);
- assertEquals(colCons.get("polar").intValue(), 0);
- assertEquals(colCons.get("positive").intValue(), 0);
- assertEquals(colCons.get("aromatic").intValue(), 0);
-
- /*
- * column 3: nothing above threshold
- */
- colCons = cons.total[3];
- assertTrue(colCons.isEmpty());
-
- /*
- * column 4: all gaps - counted as having all properties
- */
- colCons = cons.total[4];
- assertEquals(colCons.get("hydrophobic").intValue(), 1);
- assertEquals(colCons.get("aliphatic").intValue(), 1);
- assertEquals(colCons.get("small").intValue(), 1);
- assertEquals(colCons.get("tiny").intValue(), 1);
- assertEquals(colCons.get("proline").intValue(), 1);
- assertEquals(colCons.get("charged").intValue(), 1);
- assertEquals(colCons.get("negative").intValue(), 1);
- assertEquals(colCons.get("polar").intValue(), 1);
- assertEquals(colCons.get("positive").intValue(), 1);
- assertEquals(colCons.get("aromatic").intValue(), 1);
- }
-
- /**
- * Test the method that derives the conservation 'sequence' and the mouseover
- * tooltips from the computed conservation
- */
- @Test(groups = "Functional")
- public void testVerdict()
- {
- List<SequenceI> seqs = new ArrayList<SequenceI>();
- seqs.add(new Sequence("seq1", "VGIVV-H"));
- seqs.add(new Sequence("seq2", "VGILL-H"));
- seqs.add(new Sequence("seq3", "VGIW--R"));
- seqs.add(new Sequence("seq4", "VGLHH--"));
- seqs.add(new Sequence("seq5", "VGLHH-R"));
- seqs.add(new Sequence("seq6", "VGLHH--"));
- seqs.add(new Sequence("seq7", "VGLHH-R"));
- seqs.add(new Sequence("seq8", "VGLHH-R"));
-
- // calculate with no threshold
- Conservation cons = new Conservation("", 0, seqs, 0, 6);
- cons.calculate();
- // positive and negative conservation where <25% gaps in columns
- cons.verdict(false, 25);
-
- /*
- * verify conservation 'sequence'
- * cols 0 fully conserved and above threshold (*)
- * col 2 properties fully conserved (+)
- * col 3 VLWH 1 positively and 3 negatively conserved properties
- * col 4 has 1 positively conserved property, but because gap contributes a
- * 'positive' for all properties, no negative conservation is counted
- * col 5 is all gaps
- * col 6 has 25% gaps so fails threshold test
- */
- assertEquals(cons.getConsSequence().getSequenceAsString(), "**+41--");
-
- /*
- * verify tooltips; conserved properties are sorted alphabetically within
- * positive followed by negative
- */
- assertEquals(
- cons.getTooltip(0),
- "aliphatic hydrophobic small !aromatic !charged !negative !polar !positive !proline !tiny");
- assertEquals(
- cons.getTooltip(1),
- "hydrophobic small tiny !aliphatic !aromatic !charged !negative !polar !positive !proline");
- assertEquals(
- cons.getTooltip(2),
- "aliphatic hydrophobic !aromatic !charged !negative !polar !positive !proline !small !tiny");
- assertEquals(cons.getTooltip(3), "hydrophobic !negative !proline !tiny");
- assertEquals(cons.getTooltip(4), "hydrophobic");
- assertEquals(cons.getTooltip(5), "");
- assertEquals(cons.getTooltip(6), "");
- }
-}
git://source.jalview.org / jalview.git / blobdiff