import static org.testng.ConversionUtils.wrapDataProvider;
-import jalview.analysis.NJTree;
import jalview.analysis.SequenceIdMatcher;
+import jalview.analysis.TreeModel;
+import jalview.datamodel.BinaryNode;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
+import jalview.gui.JvOptionPane;
import java.util.Arrays;
import java.util.Collection;
public class NewickFileTests
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Factory
public static Object[] factoryData()
{
@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;
{
stage = "Parsing testTree " + treename;
System.out.println(treename + "\n" + testTree);
- NewickFile nf = new NewickFile(testTree, FormatAdapter.PASTE);
+ NewickFile nf = new NewickFile(testTree, DataSourceType.PASTE);
nf.parse();
AssertJUnit.assertTrue(
stage + "Invalid Tree '" + nf.getWarningMessage() + "'",
nf.isValid());
- SequenceNode tree = nf.getTree();
+ BinaryNode 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(),
AssertJUnit.assertTrue(stage + "Empty string generated",
gentree != null && gentree.trim().length() > 0);
stage = "Parsing regenerated testTree " + treename;
- NewickFile nf_regen = new NewickFile(gentree, FormatAdapter.PASTE);
+ NewickFile nf_regen = new NewickFile(gentree, DataSourceType.PASTE);
nf_regen.parse();
AssertJUnit.assertTrue(
stage + "Newick file is invalid ('"
+ nf_regen.getWarningMessage() + "')",
nf_regen.isValid());
- SequenceNode tree_regen = nf.getTree();
+ BinaryNode tree_regen = nf.getTree();
AssertJUnit.assertTrue(stage + "Null Tree", tree_regen != null);
stage = "Compare original and generated tree" + treename;
- Vector<SequenceNode> oseqs, nseqs;
- oseqs = new NJTree(new SequenceI[0], nf).findLeaves(nf.getTree());
+ Vector<BinaryNode> oseqs, nseqs;
+ 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()];
{
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()];
{
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);