X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FNewickFileTests.java;h=f1680e7349d33299ee80b1b712efe0e04fcdffed;hb=556647d95b0a68273fce9ade5ff97f1de9292b2c;hp=d198f0f90db99a27a15c3c655baa76f880dba7e7;hpb=483e7163b1fb8d4bcb9393014816c944befce328;p=jalview.git

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
index d198f0f..f1680e7 100644
--- a/test/jalview/io/NewickFileTests.java
+++ b/test/jalview/io/NewickFileTests.java
@@ -22,8 +22,8 @@ package jalview.io;
 
 import static org.testng.ConversionUtils.wrapDataProvider;
 
-import jalview.analysis.NJTree;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.analysis.TreeModel;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.gui.JvOptionPane;
@@ -63,18 +63,17 @@ 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);" } });
+    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;
@@ -109,8 +108,8 @@ public class NewickFileTests
       SequenceNode tree = nf.getTree();
       AssertJUnit.assertTrue(stage + "Null Tree", tree != null);
       stage = "Creating newick file from testTree " + treename;
-      String gentree = new NewickFile(tree).print(nf.HasBootstrap(),
-              nf.HasDistances());
+      String gentree = new NewickFile(tree).print(nf.hasBootstrap(),
+              nf.hasDistances());
       AssertJUnit.assertTrue(stage + "Empty string generated",
               gentree != null && gentree.trim().length() > 0);
       stage = "Parsing regenerated testTree " + treename;
@@ -125,7 +124,8 @@ public class NewickFileTests
       stage = "Compare original and generated tree" + treename;
 
       Vector<SequenceNode> oseqs, nseqs;
-      oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree());
+      oseqs = new TreeModel(new SequenceI[0], null, nf)
+              .findLeaves(nf.getTree());
       AssertJUnit.assertTrue(stage + "No nodes in original tree.",
               oseqs.size() > 0);
       SequenceI[] olsqs = new SequenceI[oseqs.size()];
@@ -133,8 +133,8 @@ public class NewickFileTests
       {
         olsqs[i] = (SequenceI) oseqs.get(i).element();
       }
-      nseqs = new NJTree(new SequenceI[0], nf_regen).findLeaves(nf_regen
-              .getTree());
+      nseqs = new TreeModel(new SequenceI[0], null, nf_regen)
+              .findLeaves(nf_regen.getTree());
       AssertJUnit.assertTrue(stage + "No nodes in regerated tree.",
               nseqs.size() > 0);
       SequenceI[] nsqs = new SequenceI[nseqs.size()];
@@ -142,12 +142,12 @@ public class NewickFileTests
       {
         nsqs[i] = (SequenceI) nseqs.get(i).element();
       }
-      AssertJUnit.assertTrue(stage
-              + " Different number of leaves (original " + olsqs.length
-              + " and regen " + nsqs.length + ")",
+      AssertJUnit.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);
+      SequenceIdMatcher omatcher = new SequenceIdMatcher(olsqs),
+              nmatcher = new SequenceIdMatcher(nsqs);
 
       SequenceI[] osmatches = omatcher.findIdMatch(nsqs);
       SequenceI[] nsmatches = nmatcher.findIdMatch(olsqs);