From e2e9c56d6e257a5d9f1285b07ffe56a002454125 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 14 Jun 2013 15:06:42 +0100
Subject: [PATCH] JAL-1316 JAL-1313 newick IO test harness

---
 test/jalview/io/NewickFileTests.java |  159 ++++++++++++++++++++++++++++++++++
 1 file changed, 159 insertions(+)
 create mode 100644 test/jalview/io/NewickFileTests.java

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
new file mode 100644
index 0000000..2ee3623
--- /dev/null
+++ b/test/jalview/io/NewickFileTests.java
@@ -0,0 +1,159 @@
+/**
+ * 
+ */
+package jalview.io;
+
+import static org.junit.Assert.*;
+
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Iterator;
+import java.util.Vector;
+
+import jalview.analysis.NJTree;
+import jalview.analysis.SequenceIdMatcher;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+
+import org.jmol.util.ArrayUtil;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+/**
+ * @author jimp
+ * 
+ */
+@RunWith(Parameterized.class)
+public class NewickFileTests
+{
+
+  @Parameters
+  public static Collection data()
+  {
+    return Arrays
+            .asList(new Object[][]
+            {
+                    
+                new String[]
+                {
+                    "Simple uniref50 newick",
+                    "(((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);" },
+                new String[]
+                {
+                    "Tree with quotes",
+                    "('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);" },
+                new String[]
+                {
+                    "Tree with double escaped comma in node",
+                    "('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);" } });
+  };
+
+  String name, testTree;
+
+  public NewickFileTests(String _name, String _testTree)
+  {
+    this.name = _name;
+    this.testTree = _testTree;
+  }
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @BeforeClass
+  public static void setUpBeforeClass() throws Exception
+  {
+  }
+
+  @Test
+  public void testTreeIO() throws Exception
+  {
+    String stage = "Init", treename = " '" + name + "' :";
+    try
+    {
+      stage = "Parsing testTree " + treename;
+      System.out.println(treename + "\n" + testTree);
+      NewickFile nf = new NewickFile(testTree, FormatAdapter.PASTE);
+      nf.parse();
+      assertTrue(stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
+              nf.isValid());
+      SequenceNode tree = nf.getTree();
+      assertTrue(stage + "Null Tree", tree != null);
+      stage = "Creating newick file from testTree " + treename;
+      String gentree = new NewickFile(tree).print(nf.HasBootstrap(),
+              nf.HasDistances());
+      assertTrue(stage + "Empty string generated", gentree != null
+              && gentree.trim().length() > 0);
+      stage = "Parsing regenerated testTree " + treename;
+      NewickFile nf_regen = new NewickFile(gentree, FormatAdapter.PASTE);
+      nf_regen.parse();
+      assertTrue(
+              stage + "Newick file is invalid ('"
+                      + nf_regen.getWarningMessage() + "')",
+              nf_regen.isValid());
+      SequenceNode tree_regen = nf.getTree();
+      assertTrue(stage + "Null Tree", tree_regen != null);
+      stage = "Compare original and generated tree" + treename;
+
+      Vector oseqs, nseqs;
+      oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree(),
+              new Vector());
+      assertTrue(stage + "No nodes in original tree.", oseqs.size() > 0);
+      SequenceI[] olsqs = new SequenceI[oseqs.size()];
+      for (int i = 0, iSize = oseqs.size(); i < iSize; i++)
+      {
+        olsqs[i] = (SequenceI) ((SequenceNode) oseqs.get(i)).element();
+      }
+      nseqs = (Vector) new NJTree(new SequenceI[0], nf_regen).findLeaves(
+              nf_regen.getTree(), new Vector());
+      assertTrue(stage + "No nodes in regerated tree.", nseqs.size() > 0);
+      SequenceI[] nsqs = new SequenceI[nseqs.size()];
+      for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
+      {
+        nsqs[i] = (SequenceI) ((SequenceNode) nseqs.get(i)).element();
+      }
+      assertTrue(stage + " Different number of leaves (original "
+              + olsqs.length + " and regen " + nsqs.length + ")",
+              olsqs.length == nsqs.length);
+      SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs), nmatcher = new SequenceIdMatcher(
+              nsqs);
+
+      SequenceI[] osmatches = omatcher.findIdMatch(nsqs);
+      SequenceI[] nsmatches = nmatcher.findIdMatch(olsqs);
+      String warns = "";
+      for (int i = 0, iSize = nseqs.size(); i < iSize; i++)
+      {
+        if (nsmatches[i] == null)
+        {
+          warns += "\noriginal sequence ID '" + olsqs[i].getName()
+                  + "' wasn't found in regenerated set.";
+        }
+        if (osmatches[i] == null)
+        {
+          warns += "\nregenerated sequence ID '" + nsqs[i].getName()
+                  + "' wasn't found in original set.";
+        }
+      }
+
+      if (warns.length() > 0)
+      {
+        fail(stage + warns);
+      }
+    } catch (Exception x)
+    {
+      throw (new Exception(stage + "Exception raised", x));
+    }
+  }
+
+  /**
+   * @throws java.lang.Exception
+   */
+  @AfterClass
+  public static void tearDownAfterClass() throws Exception
+  {
+  }
+
+}
-- 
1.7.10.2