2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 import static org.junit.Assert.*;
23 import java.util.Arrays;
24 import java.util.Collection;
25 import java.util.Iterator;
26 import java.util.Vector;
28 import jalview.analysis.NJTree;
29 import jalview.analysis.SequenceIdMatcher;
30 import jalview.datamodel.SequenceI;
31 import jalview.datamodel.SequenceNode;
33 import org.jmol.util.ArrayUtil;
34 import org.junit.AfterClass;
35 import org.junit.BeforeClass;
36 import org.junit.Test;
37 import org.junit.runner.RunWith;
38 import org.junit.runners.Parameterized;
39 import org.junit.runners.Parameterized.Parameters;
45 @RunWith(Parameterized.class)
46 public class NewickFileTests
50 public static Collection data()
53 .asList(new Object[][]
58 "Simple uniref50 newick",
59 "(((FER_BRANA:128.0,FER3_RAPSA:128.0):50.75,FER_CAPAA:178.75):121.94443,(Q93Z60_ARATH:271.45456,((O80429_MAIZE:183.0,FER1_MAIZE:183.0):30.5,((Q7XA98_TRIPR:90.0,FER1_PEA:90.0):83.32143,(((FER2_ARATH:64.0,FER1_ARATH:64.0):94.375,(FER1_SPIOL:124.5,FER1_MESCR:124.5):33.875):6.4166718,((Q93XJ9_SOLTU:33.5,FER1_SOLLC:33.5):49.0,FER_CAPAN:82.5):82.29167):8.529755):40.178574):57.95456):29.239868);" },
63 "('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)|CK_Syn_MINOS11_750':1.063831);" },
66 "Tree with double escaped comma in node",
67 "('Syn_PROSU-1_IIh_3d(CA4)|CK_Syn_PROSU-1_1907':1.0638313,'Syn_MINOS11_5.3_3d(CA4)''|CK_Syn_MINOS11_750':1.063831);" } });
70 String name, testTree;
72 public NewickFileTests(String _name, String _testTree)
75 this.testTree = _testTree;
79 * @throws java.lang.Exception
82 public static void setUpBeforeClass() throws Exception
87 public void testTreeIO() throws Exception
89 String stage = "Init", treename = " '" + name + "' :";
92 stage = "Parsing testTree " + treename;
93 System.out.println(treename + "\n" + testTree);
94 NewickFile nf = new NewickFile(testTree, FormatAdapter.PASTE);
96 assertTrue(stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
98 SequenceNode tree = nf.getTree();
99 assertTrue(stage + "Null Tree", tree != null);
100 stage = "Creating newick file from testTree " + treename;
101 String gentree = new NewickFile(tree).print(nf.HasBootstrap(),
103 assertTrue(stage + "Empty string generated", gentree != null
104 && gentree.trim().length() > 0);
105 stage = "Parsing regenerated testTree " + treename;
106 NewickFile nf_regen = new NewickFile(gentree, FormatAdapter.PASTE);
109 stage + "Newick file is invalid ('"
110 + nf_regen.getWarningMessage() + "')",
112 SequenceNode tree_regen = nf.getTree();
113 assertTrue(stage + "Null Tree", tree_regen != null);
114 stage = "Compare original and generated tree" + treename;
117 oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree(),
119 assertTrue(stage + "No nodes in original tree.", oseqs.size() > 0);
120 SequenceI[] olsqs = new SequenceI[oseqs.size()];
121 for (int i = 0, iSize = oseqs.size(); i < iSize; i++)
123 olsqs[i] = (SequenceI) ((SequenceNode) oseqs.get(i)).element();
125 nseqs = (Vector) new NJTree(new SequenceI[0], nf_regen).findLeaves(
126 nf_regen.getTree(), new Vector());
127 assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0);
128 SequenceI[] nsqs = new SequenceI[nseqs.size()];
129 for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
131 nsqs[i] = (SequenceI) ((SequenceNode) nseqs.get(i)).element();
133 assertTrue(stage + " Different number of leaves (original "
134 + olsqs.length + " and regen " + nsqs.length + ")",
135 olsqs.length == nsqs.length);
136 SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs), nmatcher = new SequenceIdMatcher(
139 SequenceI[] osmatches = omatcher.findIdMatch(nsqs);
140 SequenceI[] nsmatches = nmatcher.findIdMatch(olsqs);
142 for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
144 if (nsmatches[i] == null)
146 warns += "\noriginal sequence ID '" + olsqs[i].getName()
147 + "' wasn't found in regenerated set.";
149 if (osmatches[i] == null)
151 warns += "\nregenerated sequence ID '" + nsqs[i].getName()
152 + "' wasn't found in original set.";
156 if (warns.length() > 0)
160 } catch (Exception x)
162 throw (new Exception(stage + "Exception raised", x));
167 * @throws java.lang.Exception
170 public static void tearDownAfterClass() throws Exception