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[Treebase-guts] SF.net SVN: treebase:[470] trunk/treebase-core/src/test/java/org/cipres/ treebase
|
From: <yo...@us...> - 2010-01-19 15:42:03
|
Revision: 470
http://treebase.svn.sourceforge.net/treebase/?rev=470&view=rev
Author: youjun
Date: 2010-01-19 15:41:55 +0000 (Tue, 19 Jan 2010)
Log Message:
-----------
delete out of date test
Modified Paths:
--------------
trunk/treebase-core/src/test/java/org/cipres/treebase/service/nexus/NexusParserTest.java
Removed Paths:
-------------
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/AbstractPhyloDataSet.java
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexusNCLDataSetTest.java
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetM12c11.java
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetM1389.java
trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetProvider.java
trunk/treebase-core/src/test/java/org/cipres/treebase/migration/
Deleted: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/AbstractPhyloDataSet.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/AbstractPhyloDataSet.java 2010-01-19 14:30:44 UTC (rev 469)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/AbstractPhyloDataSet.java 2010-01-19 15:41:55 UTC (rev 470)
@@ -1,128 +0,0 @@
-
-package org.cipres.treebase.domain.nexus;
-
-import java.util.Iterator;
-import java.util.List;
-
-import junit.framework.Assert;
-
-import org.cipres.CipresIDL.api1.DataMatrix;
-import org.cipres.CipresIDL.api1.Tree;
-import org.cipres.datatypes.PhyloDataset;
-
-import org.cipres.treebase.TreebaseUtil;
-import org.cipres.treebase.domain.matrix.Matrix;
-import org.cipres.treebase.domain.taxon.TaxonLabel;
-import org.cipres.treebase.domain.tree.PhyloTree;
-
-/**
- * AbstractPhyloDataSet.java
- *
- * Created on Jun 19, 2006
- *
- * @author Jin Ruan
- *
- */
-public abstract class AbstractPhyloDataSet implements PhyloDataSetProvider {
-
- /**
- * Constructor.
- */
- public AbstractPhyloDataSet() {
- super();
- }
-
- /**
- *
- * @see org.cipres.treebase.domain.nexus.PhyloDataSetProvider#getCipresData()
- */
- public abstract PhyloDataset getCipresData();
-
- /**
- *
- * @see org.cipres.treebase.domain.nexus.PhyloDataSetProvider#getTaxaLabels()
- */
- public abstract List<String> getTaxaLabels();
-
- /**
- * Return the DataMatrix.
- *
- * @return
- */
- protected abstract DataMatrix getDataMatrix();
-
- /**
- * Return the Trees field.
- *
- * @return Tree[]
- */
- protected abstract Tree[] getTrees();
-
- /**
- *
- * @see org.cipres.treebase.domain.nexus.PhyloDataSetProvider#verify(org.cipres.treebase.domain.nexus.NexusDataSet)
- */
- public void verify(NexusDataSet pNexusData) {
- verifyTaxonLabel(pNexusData.getTaxonLabels());
- verifyTrees(pNexusData.getPhyloTrees());
- verifyMatrix(pNexusData.getMatrices());
- }
-
- /**
- *
- * @param pMatrices
- */
- protected void verifyMatrix(List<Matrix> pMatrices) {
- // NCL has only one matrix in one nexus:
- Assert.assertTrue("matrix size does not match.", pMatrices.size() == 1);
-
- // TODO: verifyMatrix, need in subclass.
-
- }
-
- /**
- *
- * @param pPhyloTrees
- */
- protected void verifyTrees(List<PhyloTree> pPhyloTrees) {
- Tree[] cipresTrees = getTrees();
- Assert.assertTrue("tree size does not match.", pPhyloTrees.size() == cipresTrees.length);
-
- for (int i = 0; i < cipresTrees.length; i++) {
- Tree cipresTree = cipresTrees[i];
-
- // Iterator<PhyloTree> treeIter = pPhyloTrees.iterator();
- boolean foundMatch = false;
- for (PhyloTree aTree : pPhyloTrees) {
-
- if (TreebaseUtil.isEqual(aTree.getLabel(), cipresTree.m_name)) {
- foundMatch = true;
-
- // TODO: verifyTrees
-
- }
- }
-
- Assert.assertTrue("Cannot find match: " + cipresTree.m_name, foundMatch);
- }
-
- }
-
- /**
- *
- * @param pTaxonLabels
- */
- protected void verifyTaxonLabel(List<TaxonLabel> pTaxonLabels) {
- List<String> cipresTaxonLabels = getTaxaLabels();
- Assert.assertTrue("taxon size does not match.", pTaxonLabels.size() == cipresTaxonLabels
- .size());
-
- Iterator<TaxonLabel> labelIter = pTaxonLabels.iterator();
- for (String cipresTaxonLabel : cipresTaxonLabels) {
-
- Assert.assertTrue("taxon does not match: " + cipresTaxonLabel, cipresTaxonLabel
- .compareTo(labelIter.next().getTaxonLabel()) == 0);
- }
- }
-
-}
Deleted: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexusNCLDataSetTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexusNCLDataSetTest.java 2010-01-19 14:30:44 UTC (rev 469)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/NexusNCLDataSetTest.java 2010-01-19 15:41:55 UTC (rev 470)
@@ -1,197 +0,0 @@
-package org.cipres.treebase.domain.nexus;
-
-import java.util.List;
-import java.util.StringTokenizer;
-
-import org.cipres.treebase.dao.AbstractDAOTest;
-import org.cipres.treebase.domain.matrix.Matrix;
-import org.cipres.treebase.domain.matrix.MatrixDataTypeHome;
-import org.cipres.treebase.domain.nexus.ncl.NCLNexusConverter;
-import org.cipres.treebase.domain.taxon.TaxonLabel;
-import org.cipres.treebase.domain.taxon.TaxonLabelHome;
-import org.cipres.treebase.domain.tree.PhyloTree;
-
-/**
- * The class <code>NexusNCLDataSetTest</code> contains tests for the class {@link
- * <code>NexusDataSet</code>}
- *
- * @pattern JUnit Test Case
- *
- * @generatedBy CodePro at 6/8/06 10:21 AM
- *
- * @author Jin Ruan
- *
- * @version $Revision$
- */
-public class NexusNCLDataSetTest extends AbstractDAOTest {
-
- private NexusDataSet fixture = new NexusDataSet();
-
- private TaxonLabelHome mTaxonLabelHome;
- private MatrixDataTypeHome mMatrixDataTypeHome;
-
- /**
- * Return the object that is being tested.
- *
- * @return the test fixture
- *
- * @see org.cipres.treebase.domain.nexus.NexusDataSet
- */
- public NexusDataSet getFixture() {
- return fixture;
- }
-
- /**
- * Set the object that is being tested.
- *
- * @param fixture the test fixture
- */
- private void setFixture(NexusDataSet fixture) {
- this.fixture = fixture;
- }
-
- /**
- * Return the TaxonLabelHome field.
- *
- * @return TaxonLabelHome mTaxonLabelHome
- */
- private TaxonLabelHome getTaxonLabelHome() {
- return mTaxonLabelHome;
- }
-
- /**
- *
- * @param pTaxonLabelHome
- */
- public void setTaxonLabelHome(TaxonLabelHome pTaxonLabelHome) {
- mTaxonLabelHome = pTaxonLabelHome;
- }
-
- /**
- * Return the MatrixDataTypeHome field.
- *
- * @return MatrixDataTypeHome mMatrixDataTypeHome
- */
- private MatrixDataTypeHome getMatrixDataTypeHome() {
- return mMatrixDataTypeHome;
- }
-
- /**
- * Set the MatrixDataTypeHome field.
- */
- public void setMatrixDataTypeHome(MatrixDataTypeHome pNewMatrixDataTypeHome) {
- mMatrixDataTypeHome = pNewMatrixDataTypeHome;
- }
-
- /**
- *
- * Creation date: Jun 8, 2006 10:26:17 AM
- */
- public void testNewickParsing() {
- String newick = "(21,(20,(((((19,18,17,16),15,14,13,12,11),10,9,8,7,6,5),((3,2),1)),4)));";
- String delim = "(),: ";
- StringBuffer newick2 = new StringBuffer();
- PhyloDataSetProvider datasetM1389 = new PhyloDataSetM1389();
-
- int taxaSize = datasetM1389.getTaxaLabels().size();
-
- System.out.println("NexusNCLDataSetTest:newickParsingTest: ");
- System.out.println("newick: " + newick);
-
- StringTokenizer st = new StringTokenizer(newick, delim, true);
- while (st.hasMoreTokens()) {
- String element = st.nextToken();
- int i = -1;
- boolean isNumber = false;
- try {
- // Notes: NCL parsed output is 1 based.
- i = Integer.parseInt(element) - 1;
- if (i >= 0 && i < taxaSize) {
- isNumber = true;
- }
-
- } catch (NumberFormatException ex) {
- isNumber = false;
- }
-
- if (isNumber) {
- newick2.append(datasetM1389.getTaxaLabels().get(i));
- } else {
- newick2.append(element);
- }
- }
-
- System.out.println("newick2: " + newick2.toString());
-
- }
-
- /**
- *
- * Creation date: Jun 14, 2006 8:15:55 PM
- */
- public void testM1389Parsing() {
-
- String dataName = "m1389";
- PhyloDataSetProvider datasetM1389 = new PhyloDataSetM1389();
-
- parseTest(dataName, datasetM1389);
- }
-
- /**
- *
- * Creation date: Jun 14, 2006 8:15:55 PM
- */
- public void testM12c11Parsing() {
-
- String dataName = "m12c11";
- PhyloDataSetProvider dataset = new PhyloDataSetM12c11();
-
- parseTest(dataName, dataset);
-
- }
-
- /**
- *
- * @param pCipresDataSet
- */
- @SuppressWarnings("unused")
- private void parseTest(String pDataName, PhyloDataSetProvider pCipresDataSet) {
- StringBuffer newick2 = new StringBuffer();
-
- System.out.println(pDataName + " Parsing: ");
-
- NexusDataSet nexusData = new NexusDataSet();
-
- NCLNexusConverter converter = new NCLNexusConverter();
- converter.setMatrixDataTypeHome(getMatrixDataTypeHome());
- converter.setTaxonLabelHome(getTaxonLabelHome());
- converter.parsePhyloDataSet(null, nexusData, pCipresDataSet.getCipresData());
-
- List<TaxonLabel> taxonLabels = nexusData.getTaxonLabels();
- List<PhyloTree> trees = nexusData.getPhyloTrees();
- List<Matrix> matrices = nexusData.getMatrices();
-
- // verify parsing.
- pCipresDataSet.verify(nexusData);
-
- System.out.println(" " + pDataName + " parsing done: ");
- }
-
- public static void main(String[] args) {
- NexusNCLDataSetTest test = new NexusNCLDataSetTest();
- test.testNewickParsing();
-
- System.exit(0);
- }
-}
-
-/*
- * $CPS$ This comment was generated by CodePro. Do not edit it. patternId =
- * com.instantiations.assist.eclipse.pattern.testCasePattern strategyId =
- * com.instantiations.assist.eclipse.pattern.testCasePattern.junitTestCase additionalTestNames =
- * assertTrue = false callTestMethod = true createMain = false createSetUp = false createTearDown =
- * false createTestFixture = true createTestStubs = false methods = package =
- * org.cipres.treebase.domain.nexus package.sourceFolder = treebase-core/src/test/java
- * superclassType = junit.framework.TestCase testCase = NexusNCLDataSetTest testClassType =
- * org.cipres.treebase.domain.nexus.NexusDataSet
- */
\ No newline at end of file
Deleted: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetM12c11.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetM12c11.java 2010-01-19 14:30:44 UTC (rev 469)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetM12c11.java 2010-01-19 15:41:55 UTC (rev 470)
@@ -1,226 +0,0 @@
-
-package org.cipres.treebase.domain.nexus;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.cipres.CipresIDL.api1.DataMatrix;
-import org.cipres.CipresIDL.api1.DiscreteDatatypes;
-import org.cipres.CipresIDL.api1.Tree;
-import org.cipres.datatypes.PhyloDataset;
-
-/**
- * PhyloDataSetM12c11.java
- *
- * A test data set w/ char label and state label info.
- *
- * Created on Jun 14, 2006
- *
- * @author Jin Ruan
- *
- */
-public class PhyloDataSetM12c11 extends AbstractPhyloDataSet implements PhyloDataSetProvider {
-
- private PhyloDataset mCipresData;
- private List<String> mTaxaLabels;
- private Tree[] mTrees;
- private DataMatrix mDataMatrix;
-
- /**
- * Constructor.
- */
- public PhyloDataSetM12c11() {
- super();
- }
-
- /**
- *
- * @see org.cipres.treebase.domain.nexus.PhyloDataSetProvider#getCipresData()
- */
- @Override
- public PhyloDataset getCipresData() {
- if (mCipresData == null) {
- mCipresData = new PhyloDataset();
-
- mCipresData.setDataMatrix(getDataMatrix());
- mCipresData.setTrees(getTrees());
- mCipresData.setTaxaInfo(getTaxaLabels().toArray(new String[1]));
- }
- return mCipresData;
- }
-
- /**
- * Return the DataMatrix field. Uses lazy initialization.
- *
- * @return DataMatrix mDataMatrix
- */
- @Override
- protected DataMatrix getDataMatrix() {
- if (mDataMatrix == null) {
- mDataMatrix = new DataMatrix();
-
- // based on m1389
- mDataMatrix.m_symbols = "0123?";
- mDataMatrix.m_numStates = 4;
- mDataMatrix.m_numCharacters = 54;
- mDataMatrix.m_datatype = DiscreteDatatypes.from_int(4);
- mDataMatrix.m_charStateLookup = new short[][] { {0}, {1}, {2}, {3}, {-1, 0, 1, 2, 3},
- {0, 1, 2, 3}};
-
- mDataMatrix.m_matrix = new short[][] {
- {0, 0, 0, 0, 4, 0, 4, 4, 4, 4, 0, 0, 4, 4, 0, 0, 4, 0, 0, 4, 4, 4, 0, 0, 0, 0, 4,
- 4, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 4, 4, 4, 0, 0, 4, 4, 4, 4, 4, 4, 4, 4, 0, 0},
-
- {0, 0, 1, 0, 1, 4, 0, 1, 1, 1, 0, 1, 0, 1, 4, 4, 0, 0, 0, 0, 1, 0, 4, 4, 0, 0, 0,
- 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1},
-
- {0, 0, 0, 0, 0, 0, 0, 1, 4, 1, 0, 4, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 4, 0, 0, 0, 0,
- 0, 1, 1, 0, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 4, 0, 1, 0, 1, 0, 0, 0, 4, 0, 0, 0, 1},
-
- {0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0,
- 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 1},
-
- {0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 4, 0, 1, 1, 0, 0, 0, 0, 0, 1, 4, 1, 4, 0, 0, 0,
- 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 4, 0, 1, 0, 2},
-
- {0, 0, 1, 4, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 4, 1, 4, 0, 0, 0,
- 1, 0, 1, 0, 1, 0, 0, 0, 0, 4, 0, 0, 1, 0, 1, 0, 4, 0, 4, 0, 0, 0, 4, 0, 1, 0, 1},
-
- {0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 4, 0, 0, 1, 0, 0, 0,
- 0, 0, 0, 0, 0, 4, 0, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0, 4, 0, 1, 0, 0, 0, 0, 1, 0, 0},
-
- {0, 0, 1, 0, 0, 1, 0, 0, 0, 1, 0, 4, 0, 0, 0, 0, 0, 0, 0, 1, 4, 0, 0, 1, 4, 1, 4,
- 0, 0, 1, 0, 1, 4, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 4, 0, 1, 0, 0, 0, 4, 0, 4, 0, 1},
-
- {0, 0, 1, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 2, 0, 1, 0, 1, 4,
- 0, 0, 0, 0, 1, 4, 4, 1, 4, 0, 1, 0, 2, 0, 0, 0, 0, 4, 4, 0, 0, 0, 1, 0, 1, 0, 1},
-
- {0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 2, 4, 1, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0,
- 1, 0, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 1, 0, 0, 4, 0, 4, 0, 1, 0, 4},
-
- {0, 0, 0, 0, 0, 0, 1, 0, 0, 4, 0, 4, 2, 0, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 1, 0, 1, 0, 0, 4, 1, 0, 0, 4, 1, 1, 2, 0, 1, 0, 0, 0, 0, 0, 4, 0, 0, 0, 1},
-
- {0, 0, 1, 0, 0, 0, 0, 0, 4, 1, 0, 0, 1, 0, 2, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
- 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 4, 0, 0, 0, 0},
-
- {0, 4, 4, 0, 4, 0, 0, 0, 4, 1, 0, 4, 1, 0, 2, 4, 0, 0, 1, 1, 2, 3, 0, 4, 4, 4, 0,
- 0, 0, 1, 0, 1, 1, 1, 1, 1, 4, 1, 0, 1, 1, 1, 0, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
-
- {0, 0, 1, 1, 0, 1, 4, 0, 0, 1, 0, 0, 1, 0, 2, 0, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
- 1, 0, 1, 0, 0, 1, 0, 4, 0, 1, 0, 1, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 2, 4, 0, 2},
-
- {0, 0, 1, 0, 0, 4, 1, 0, 0, 1, 0, 1, 2, 0, 2, 0, 4, 0, 4, 4, 0, 0, 0, 0, 0, 0, 1,
- 4, 0, 1, 0, 1, 0, 0, 4, 1, 1, 0, 4, 1, 0, 2, 0, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1},
-
- {0, 0, 1, 1, 0, 0, 0, 0, 0, 1, 0, 4, 1, 0, 1, 1, 2, 0, 0, 2, 4, 2, 0, 1, 1, 0, 4,
- 0, 1, 1, 0, 1, 4, 0, 0, 4, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 4},
-
- {0, 1, 1, 0, 4, 0, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 2, 0, 0, 3, 2, 3, 0, 4, 1, 0, 1,
- 0, 0, 1, 0, 2, 1, 0, 1, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 1},
-
- {0, 4, 1, 4, 4, 0, 0, 0, 0, 1, 0, 4, 0, 1, 4, 1, 2, 0, 0, 3, 2, 3, 0, 4, 1, 0, 1,
- 0, 0, 1, 0, 2, 4, 0, 4, 4, 4, 0, 0, 2, 1, 2, 0, 1, 0, 0, 0, 0, 1, 4, 1, 0, 0, 1},
-
- {4, 4, 1, 1, 0, 4, 4, 0, 0, 1, 0, 4, 0, 0, 1, 4, 2, 0, 0, 2, 4, 1, 0, 1, 1, 0, 1,
- 0, 0, 1, 0, 1, 1, 1, 4, 0, 4, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 4, 0, 0},
-
- {1, 1, 0, 0, 4, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 2, 0, 0, 2, 1, 0, 0, 0, 0, 0, 4,
- 4, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 4, 1, 0, 1, 1},
-
- {1, 1, 4, 0, 4, 0, 0, 0, 0, 0, 1, 4, 4, 0, 4, 0, 2, 1, 0, 2, 1, 1, 0, 1, 1, 0, 1,
- 0, 0, 0, 0, 0, 0, 0, 0, 4, 1, 0, 0, 0, 0, 3, 1, 1, 0, 1, 0, 0, 0, 0, 1, 0, 4, 1},
-
- {1, 1, 2, 0, 4, 0, 0, 0, 0, 0, 1, 1, 4, 4, 4, 1, 2, 1, 0, 2, 1, 0, 0, 0, 0, 0, 1,
- 0, 0, 1, 1, 0, 1, 1, 1, 0, 1, 0, 0, 1, 0, 3, 0, 1, 0, 0, 0, 0, 0, 1, 2, 4, 1, 0},
-
- {0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 0, 2, 0, 0, 0, 0, 0, 4, 0, 1, 0, 0, 0, 0, 0, 0,
- 0, 0, 1, 1, 1, 1, 1, 0, 0, 4, 0, 0, 2, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1},
-
- {0, 0, 1, 0, 4, 0, 0, 1, 0, 1, 0, 0, 2, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 4, 0,
- 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 1},
-
- {0, 4, 1, 0, 4, 0, 4, 0, 0, 0, 0, 1, 0, 4, 0, 0, 2, 0, 1, 2, 4, 0, 0, 1, 4, 0, 4,
- 0, 0, 1, 1, 1, 1, 4, 1, 4, 1, 0, 0, 0, 0, 4, 0, 4, 0, 1, 0, 0, 0, 1, 0, 0, 4, 0},
-
- {0, 0, 0, 0, 0, 0, 4, 4, 0, 0, 0, 0, 0, 4, 0, 4, 2, 0, 1, 1, 2, 2, 0, 0, 0, 0, 1,
- 0, 0, 1, 1, 1, 1, 1, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 4, 0, 0, 0, 0, 4},
-
- {0, 0, 1, 0, 0, 0, 4, 0, 0, 0, 0, 0, 0, 4, 0, 4, 4, 0, 1, 1, 2, 2, 0, 0, 0, 0, 1,
- 0, 0, 1, 1, 1, 1, 4, 1, 4, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 4, 0, 4, 0, 0, 0, 4},
-
- {1, 1, 2, 0, 4, 4, 0, 0, 0, 0, 4, 0, 0, 1, 4, 4, 4, 4, 4, 4, 4, 1, 0, 1, 1, 0, 1,
- 0, 0, 0, 0, 1, 1, 4, 0, 0, 0, 0, 0, 0, 0, 4, 0, 4, 4, 4, 0, 0, 0, 4, 0, 0, 4, 4}};
-
- }
- return mDataMatrix;
- }
-
- /**
- * Return the Trees field. Uses lazy initialization.
- *
- * @return Tree[] mTrees
- */
- @Override
- protected Tree[] getTrees() {
- if (mTrees == null) {
-
- // based on m1389
- mTrees = new Tree[1];
- Tree tree = new Tree();
- tree.m_name = "NYMPH-BASAL";
- tree.m_newick = "(1,((20,21),(((26,27),(25,22)),((((18,17),28),(19,16)),(((23,24),3),(((((12,13),(11,15)),10),14),(6,(8,(5,(4,(2,(9,7))))))))))));";
- tree.m_score = null; // not needed.
- tree.m_leafSet = new int[] {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
- 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28};
-
- mTrees[0] = tree;
- }
- return mTrees;
- }
-
- /**
- *
- * @see org.cipres.treebase.domain.nexus.PhyloDataSetProvider#getTaxaLabels()
- */
- @Override
- public List<String> getTaxaLabels() {
- if (mTaxaLabels == null) {
- // based on m1389:
- mTaxaLabels = new ArrayList<String>();
-
- mTaxaLabels.add("Hyp. Ancestor");
- mTaxaLabels.add("GMagnoliaceae");
- mTaxaLabels.add("Winteraceae");
- mTaxaLabels.add("Degeneria");
- mTaxaLabels.add("Eupomatia");
- mTaxaLabels.add("Himantandraceae");
- mTaxaLabels.add("Annonaceae");
- mTaxaLabels.add("Canellaceae");
- mTaxaLabels.add("Myristicaceae");
- mTaxaLabels.add("Austrobaileya");
-
- mTaxaLabels.add("Amborella");
- mTaxaLabels.add("Trimeniaceae");
- mTaxaLabels.add("Chloranthaceae");
- mTaxaLabels.add("Calycanthaceae");
- mTaxaLabels.add("Monimiaceae");
- mTaxaLabels.add("Lactoris");
- mTaxaLabels.add("Saururaceae");
- mTaxaLabels.add("Piperaceae");
- mTaxaLabels.add("Aritolochiaceae");
- mTaxaLabels.add("Nymphaeaceae");
-
- mTaxaLabels.add("Cobombaceae");
- mTaxaLabels.add("Nelumbo");
- mTaxaLabels.add("Illicium");
- mTaxaLabels.add("Schisandraceae");
- mTaxaLabels.add("Ranunculaceae");
- mTaxaLabels.add("Trochodendrales");
- mTaxaLabels.add("Hamamelidales");
- mTaxaLabels.add("Liliopsida");
- }
- return mTaxaLabels;
- }
-
-}
Deleted: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetM1389.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetM1389.java 2010-01-19 14:30:44 UTC (rev 469)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetM1389.java 2010-01-19 15:41:55 UTC (rev 470)
@@ -1,427 +0,0 @@
-
-package org.cipres.treebase.domain.nexus;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.cipres.CipresIDL.api1.DataMatrix;
-import org.cipres.CipresIDL.api1.DiscreteDatatypes;
-import org.cipres.CipresIDL.api1.Tree;
-import org.cipres.datatypes.PhyloDataset;
-
-/**
- * PhyloDataSetM1389.java
- *
- * Created on Jun 14, 2006
- *
- * @author Jin Ruan
- *
- */
-public class PhyloDataSetM1389 extends AbstractPhyloDataSet implements PhyloDataSetProvider {
-
- private PhyloDataset mCipresData;
- private List<String> mTaxaLabels;
- private Tree[] mTrees;
- private DataMatrix mDataMatrix;
-
- /**
- * Constructor.
- */
- public PhyloDataSetM1389() {
- super();
- }
-
- /**
- *
- * @see org.cipres.treebase.domain.nexus.PhyloDataSetProvider#getCipresData()
- */
- @Override
- public PhyloDataset getCipresData() {
- if (mCipresData == null) {
- mCipresData = new PhyloDataset();
-
- mCipresData.setDataMatrix(getDataMatrix());
- mCipresData.setTrees(getTrees());
- mCipresData.setTaxaInfo(getTaxaLabels().toArray(new String[1]));
- }
- return mCipresData;
- }
-
- /**
- * Return the DataMatrix field. Uses lazy initialization.
- *
- * @return DataMatrix mDataMatrix
- */
- @Override
- protected DataMatrix getDataMatrix() {
- if (mDataMatrix == null) {
- mDataMatrix = new DataMatrix();
-
- // based on m1389
- mDataMatrix.m_symbols = "ACGT?NYRW";
- mDataMatrix.m_numStates = 4;
- mDataMatrix.m_numCharacters = 350;
- mDataMatrix.m_datatype = DiscreteDatatypes.from_int(0);
- mDataMatrix.m_charStateLookup = new short[][] { {0}, {1}, {2}, {3}, {-1, 0, 1, 2, 3},
- {0, 1, 2, 3}, {1, 3}, {0, 2}, {0, 3},};
-
- mDataMatrix.m_matrix = new short[][] {
- {0, 3, 3, 1, 1, 1, 2, 2, 1, 1, 2, 1, 3, 3, 0, 0, 0, 1, 1, 0, 0, 0, 1, 3, 3, 1, 2,
- 3, 3, 0, 3, 3, 3, 0, 3, 0, 0, 0, 0, 0, 2, 0, 2, 0, 0, 2, 2, 3, 3, 3, 0, 3, 0,
- 1, 3, 0, 3, 2, 2, 0, 1, 0, 0, 3, 2, 3, 0, 2, 3, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
- 2, 2, 0, 3, 3, 0, 0, 3, 1, 0, 3, 2, 2, 3, 3, 3, 3, 0, 3, 2, 1, 1, 1, 0, 3, 3,
- 2, 3, 3, 2, 3, 3, 2, 0, 0, 2, 1, 0, 2, 3, 3, 3, 1, 2, 3, 3, 0, 1, 1, 0, 0, 0,
- 3, 3, 0, 3, 0, 3, 3, 0, 1, 3, 3, 2, 0, 0, 3, 3, 3, 1, 3, 0, 0, 3, 0, 0, 0, 3,
- 3, 0, 0, 2, 1, 2, 0, 2, 3, 0, 0, 0, 3, 3, 3, 0, 3, 2, 6, 2, 0, 3, 3, 3, 3, 1,
- 3, 0, 3, 0, 0, 3, 2, 1, 0, 0, 3, 3, 0, 0, 3, 3, 3, 3, 0, 3, 3, 2, 2, 3, 3, 0,
- 3, 3, 3, 3, 0, 3, 3, 3, 3, 3, 0, 3, 3, 0, 1, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0,
- 0, 0, 3, 3, 1, 0, 1, 0, 0, 0, 3, 3, 2, 3, 3, 0, 0, 0, 0, 0, 3, 1, 3, 3, 1, 2,
- 3, 2, 0, 0, 3, 3, 3, 0, 3, 3, 0, 0, 0, 1, 2, 2, 3, 3, 1, 3, 3, 3, 0, 0, 3, 1,
- 0, 0, 0, 3, 0, 3, 1, 0, 0, 0, 0, 1, 0, 0, 3, 0, 0, 3, 3, 2, -1, -1, 3, 0, 0, 0,
- 0, 3, 2, 0, 1, 3, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0, 0, 0, 3, 3, 3, 1, 0, 0, 0,
- 0, 3, 1, 3, 2, 3, 2, 1, 0, 0, 0},
- {0, 3, 0, 1, 1, 3, 2, 2, 3, 1, 2, 1, 3, 3, 0, 0, 0, 1, 1, 0, 0, 0, 1, 3, 3, 1, 2,
- 3, 3, 0, 3, 3, 3, 0, 3, 0, 0, 0, 0, 0, 2, 2, 2, 0, 0, 2, 2, 3, 3, 3, 0, 3, 0,
- 1, 3, 0, 1, 2, 2, 2, 1, 0, 0, 3, 2, 3, 0, 2, 1, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
- 2, 2, 0, 3, 3, 0, 0, 3, 1, 0, 3, 2, 2, 3, 3, 3, 3, 0, 3, 2, 1, 1, 3, 0, 3, 3,
- 2, 3, 3, 2, 3, 3, 2, 0, 0, 2, 1, 0, 2, 3, 3, 3, 1, 0, 3, 3, 0, 1, 1, 0, 0, 0,
- 3, 3, 0, 1, 0, 3, 3, 0, 1, 1, 3, 2, 0, 0, 3, 3, 3, 1, 1, 0, 0, 3, 0, 0, 0, 3,
- 3, 0, 0, 2, 1, 2, 0, 2, 3, 0, 0, 0, 3, 3, 3, 0, 3, 2, 0, 2, 0, 2, 3, 3, 3, 1,
- 1, 2, 3, 0, 2, 3, 0, 1, 0, 0, 1, 3, 0, 0, 1, 3, 3, 3, 0, 3, 3, 2, 2, 3, 3, 0,
- 3, 3, 3, 3, 0, 3, 3, 3, 3, 3, 0, 3, 3, 0, 1, 3, 3, 3, 3, 3, 0, 0, 3, 3, 1, 0,
- 0, 0, 3, 3, 1, 2, 1, 0, 0, 2, 3, 3, 2, 3, 3, 0, 0, 0, 0, 0, 3, 1, 3, 3, 1, 2,
- 1, 2, 0, 2, 3, 3, 0, 2, 3, 3, 0, 0, 0, 1, 0, 2, 3, 3, 1, 3, 3, 1, 0, 0, 0, 1,
- 0, 0, 0, 3, 0, 3, 1, 0, 0, 0, 0, 3, 0, 2, 3, 0, 0, 3, 3, 2, -1, -1, 0, 0, 0, 0,
- 0, 3, 2, 0, 1, 1, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0, 0, 0, 3, 3, 3, 1, 0, 0, 0,
- 0, 3, 1, 3, 2, 3, 2, 1, 0, 0, 0},
- {0, 3, 0, 1, 1, 3, 2, 2, 1, 1, 2, 1, 3, 3, 0, 0, 0, 1, 1, 0, 0, 0, 1, 3, 3, 1, 2,
- 3, 3, 0, 3, 3, 3, 0, 3, 0, 0, 0, 0, 0, 2, 2, 2, 0, 0, 2, 2, 3, 3, 3, 0, 3, 0,
- 1, 3, 0, 1, 2, 2, 2, 1, 0, 0, 3, 2, 3, 0, 2, 1, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
- 2, 2, 0, 3, 3, 0, 0, 3, 1, 0, 3, 2, 2, 3, 3, 3, 3, 0, 3, 2, 1, 1, 3, 0, 3, 3,
- 2, 3, 3, 2, 3, 3, 2, 0, 0, 2, 1, 0, 2, 3, 3, 3, 1, 0, 3, 3, 0, 1, 1, 0, 0, 0,
- 3, 3, 0, 1, 0, 3, 3, 0, 1, 1, 3, 2, 0, 0, 3, 3, 3, 1, 1, 0, 0, 3, 0, 0, 0, 3,
- 3, 0, 0, 2, 1, 2, 0, 2, 3, 0, 0, 0, 3, 3, 3, 0, 3, 2, 0, 2, 0, 2, 3, 3, 3, 1,
- 1, 2, 3, 0, 2, 3, 0, 1, 0, 0, 1, 3, 0, 0, 1, 3, 3, 3, 0, 3, 3, 2, 2, 3, 3, 0,
- 3, 3, 3, 3, 0, 3, 3, 3, 3, 3, 0, 3, 3, 0, 1, 3, 3, 3, 3, 3, 0, 0, 3, 3, 1, 0,
- 0, 0, 3, 3, 1, 2, 1, 0, 0, 2, 3, 3, 2, 3, 3, 0, 0, 0, 0, 0, 3, 1, 3, 3, 1, 2,
- 1, 2, 0, 2, 3, 3, 0, 2, 3, 3, 0, 0, 0, 1, 0, 2, 3, 3, 1, 3, 3, 1, 0, 0, 0, 1,
- 0, 0, 0, 3, 2, 3, 1, 0, 0, 0, 0, 3, 0, 2, 3, 0, 0, 3, 3, 2, -1, -1, 0, 0, 0, 0,
- 0, 3, 2, 0, 1, 1, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0, 0, 0, 3, 3, 3, 1, 0, 0, 0,
- 0, 3, 1, 3, 2, 3, 2, 1, 0, 0, 0},
- {0, 3, 3, 1, 1, 3, 2, 2, 3, 1, 2, 3, 3, 3, 0, 0, 0, 3, 1, 0, 0, 0, 1, 1, 3, 1, 0,
- 3, 3, 0, 3, 3, 3, 0, 3, 0, 0, 0, 0, 0, 2, 0, 2, 0, 0, 2, 2, 3, 3, 3, 0, 3, 0,
- 3, 3, 0, 1, 2, 2, 0, 1, 0, 0, 3, 2, 3, 0, 2, 1, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
- 2, 0, 0, 3, 3, 0, 0, 3, 1, 0, 1, 2, 2, 1, 3, 3, 3, 0, 3, 2, 1, 1, 3, 0, 3, 3,
- 2, 3, 3, 2, 3, 3, 2, 0, 0, 2, 1, 0, 2, 3, 3, 3, 1, 2, 1, 3, 0, 1, 1, 0, 0, 0,
- 3, 3, 0, 1, 0, 3, 3, 0, 1, 3, 3, 2, 0, 0, 3, 3, 3, 1, 3, 0, 0, 3, 0, 0, 0, 3,
- 3, 0, 0, 2, 1, 2, 0, 2, 3, 0, 0, 2, 3, 3, 3, 0, 3, 2, 0, 0, 0, 0, 3, 1, 3, 1,
- 3, 2, 3, 0, 2, 3, 2, 1, 0, 0, 1, 3, 0, 0, 3, 3, 3, 3, 0, 3, 3, 0, 2, 3, 3, 0,
- 3, 3, 3, 3, 0, 3, 3, 3, 3, 3, 2, 3, 3, 0, 1, 3, 3, 3, 3, 3, 0, 0, 3, 3, 1, 2,
- 0, 0, 3, 3, 1, 0, 1, 0, 0, 0, 3, 0, 2, 3, 3, 0, 0, 0, 0, 0, 3, 3, 3, 3, 1, 2,
- 3, 2, 0, 2, 3, 3, 2, 0, 3, 3, 0, 0, 0, 1, 0, 2, 3, 3, 3, 3, 3, 1, 0, 0, 0, 1,
- 0, 0, 0, 3, 0, 3, 1, 0, 0, 0, 0, 1, 0, 2, 3, 0, 0, 3, 3, 0, 1, -1, 0, 0, 0, 0,
- 0, 3, 2, 0, 1, 3, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0, 0, 0, 3, 3, 3, 1, 0, 0, 0,
- 0, 3, 1, 1, 2, 3, 0, 1, 0, 0, 0},
- {0, 3, 0, 1, 1, 3, 2, 2, 3, 1, 2, 3, 3, 3, 0, 0, 0, 1, 1, 0, 0, 0, 1, 3, 3, 1, 0,
- 3, 3, 0, 3, 3, 3, 0, 3, 0, 0, 0, 0, 0, 2, 0, 2, 0, 0, 2, 2, 1, 3, 3, 2, 3, 0,
- 3, 3, 0, 3, 2, 2, 2, 1, 0, 0, 3, 2, 3, 0, 2, 3, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
- 2, 0, 0, 3, 3, 0, 0, 3, 1, 0, 3, 2, 2, 3, 3, 3, 3, 0, 3, 2, 1, 1, 3, 0, 3, 3,
- 2, 3, 3, 2, 3, 3, 2, 0, 0, 2, 1, 2, 2, 3, 3, 3, 1, 2, 1, 3, 0, 1, 1, 0, 0, 0,
- 3, 3, 0, 1, 0, 3, 3, 0, 1, 3, 3, 2, 2, 0, 3, 3, 3, 1, 3, 0, 0, 1, 0, 0, 0, 3,
- 3, 0, 0, 2, 1, 2, 0, 2, 3, 0, 0, 0, 3, 3, 3, 0, 3, 2, 0, 7, 0, 0, 3, 3, 3, 1,
- 3, 2, 3, 0, 3, 3, 2, 1, 0, 0, 1, 3, 2, 0, 1, 3, 3, 3, 0, 1, 3, 2, 2, 3, 3, 2,
- 3, 3, 3, 3, 0, 3, 3, 3, 3, 3, 0, 3, 3, 0, 1, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0,
- 0, 0, 3, 3, 1, 0, 1, 0, 0, 0, 3, 1, 2, 3, 3, 0, 0, 0, 0, 0, 1, 0, 3, 3, 1, 2,
- 3, 2, 0, 2, 3, 3, 2, 0, 3, 3, 0, 0, 0, 1, 0, 2, 3, 3, 1, 3, 3, 1, 0, 0, 0, 1,
- 0, 0, 0, 3, 0, 3, 1, 0, 0, 0, 0, 1, 0, 2, 3, 0, 0, 3, 3, 2, 0, -1, 0, 0, 0, 8,
- 0, 3, 2, 0, 1, 3, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0, 0, 0, 3, 3, 3, 1, 0, 0, 0,
- 0, 3, 1, 1, 2, 3, 2, 1, 0, 0, 0},
- {0, 3, 0, 1, 1, 3, 2, 2, 3, 1, 2, 3, 3, 3, 0, 0, 0, 1, 1, 0, 0, 0, 1, 3, 3, 1, 0,
- 3, 3, 0, 3, 3, 3, 0, 3, 0, 0, 0, 0, 0, 2, 0, 2, 0, 0, 2, 2, 1, 3, 3, 2, 3, 0,
- 3, 3, 0, 3, 2, 2, 2, 1, 0, 0, 3, 2, 3, 0, 2, 3, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
- 2, 0, 0, 3, 3, 0, 0, 3, 1, 0, 3, 2, 2, 3, 3, 3, 3, 0, 3, 2, 1, 1, 3, 0, 3, 3,
- 2, 3, 3, 2, 3, 3, 2, 0, 0, 2, 1, 2, 2, 3, 3, 3, 1, 2, 1, 3, 0, 1, 1, 0, 0, 0,
- 3, 3, 0, 1, 0, 3, 3, 0, 1, 3, 3, 2, 2, 0, 3, 3, 3, 1, 3, 0, 0, 1, 0, 0, 0, 3,
- 3, 0, 0, 2, 1, 2, 0, 2, 3, 0, 0, 0, 3, 3, 3, 0, 3, 2, 0, 2, 0, 0, 3, 3, 3, 1,
- 3, 2, 3, 0, 3, 3, 7, 1, 0, 0, 1, 3, 2, 0, 1, 3, 3, 3, 0, 1, 3, 2, 2, 3, 3, 2,
- 3, 3, 3, 3, 0, 3, 3, 3, 3, 3, 0, 3, 3, 0, 1, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0,
- 0, 0, 3, 3, 1, 0, 1, 0, 0, 0, 3, 1, 2, 3, 3, 0, 0, 0, 0, 0, 1, 0, 3, 3, 1, 2,
- 3, 2, 0, 2, 3, 3, 2, 0, 3, 3, 0, 0, 0, 1, 0, 2, 3, 3, 1, 3, 3, 1, 0, 0, 0, 1,
- 0, 0, 0, 3, 0, 3, 1, 0, 0, 0, 0, 1, 0, 2, 3, 0, 0, 3, 3, 2, 0, -1, 0, 0, 0, 0,
- 0, 3, 2, 0, 1, 3, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0, 0, 0, 3, 3, 3, 1, 0, 0, 0,
- 0, 3, 1, 1, 2, 3, 2, 1, 0, 0, 0},
- {0, 3, 0, 1, 1, 3, 2, 2, 3, 1, 2, 3, 3, 3, 0, 0, 0, 1, 1, 0, 0, 0, 1, 3, 3, 1, 0,
- 3, 3, 0, 3, 3, 3, 0, 3, 0, 0, 0, 0, 0, 2, 0, 2, 0, 0, 2, 2, 1, 3, 3, 2, 3, 0,
- 3, 3, 0, 3, 2, 2, 2, 1, 0, 0, 3, 2, 3, 0, 2, 3, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
- 2, 0, 0, 3, 3, 0, 0, 3, 1, 0, 3, 2, 2, 3, 3, 3, 3, 0, 3, 2, 1, 1, 3, 0, 3, 3,
- 2, 3, 3, 2, 3, 3, 2, 0, 0, 2, 1, 2, 2, 3, 3, 3, 1, 2, 1, 3, 0, 1, 1, 0, 0, 0,
- 3, 3, 0, 1, 0, 3, 3, 0, 1, 3, 3, 2, 2, 0, 3, 3, 3, 1, 3, 0, 0, 1, 0, 0, 0, 3,
- 3, 0, 0, 2, 1, 2, 0, 2, 3, 0, 0, 0, 3, 3, 3, 0, 3, 2, 0, 2, 0, 0, 3, 3, 3, 1,
- 3, 2, 3, 0, 3, 3, 2, 1, 0, 0, 1, 3, 2, 0, 1, 3, 3, 3, 0, 1, 3, 2, 2, 3, 3, 2,
- 3, 3, 3, 3, 0, 3, 3, 3, 3, 3, 0, 3, 3, 0, 1, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0,
- 0, 0, 3, 3, 1, 0, 1, 0, 0, 0, 3, 1, 2, 3, 3, 0, 0, 0, 0, 0, 1, 0, 3, 3, 1, 2,
- 3, 2, 0, 2, 3, 3, 2, 0, 3, 3, 0, 0, 0, 1, 0, 2, 3, 3, 1, 3, 3, 1, 0, 0, 0, 1,
- 0, 0, 0, 3, 0, 3, 1, 0, 0, 0, 0, 1, 0, 2, 3, 0, 0, 3, 3, 2, 0, -1, 0, 0, 0, 0,
- 0, 3, 2, 0, 1, 3, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0, 0, 0, 3, 3, 3, 1, 0, 0, 0,
- 0, 3, 1, 1, 2, 3, 2, 1, 0, 0, 0},
- {0, 3, 0, 1, 1, 3, 2, 2, 3, 1, 2, 3, 3, 3, 0, 0, 0, 1, 1, 0, 0, 0, 1, 3, 3, 1, 0,
- 3, 3, 0, 3, 3, 3, 0, 3, 0, 0, 0, 0, 0, 2, 0, 2, 0, 0, 2, 2, 1, 3, 3, 2, 3, 0,
- 3, 3, 0, 3, 2, 2, 2, 1, 0, 0, 3, 2, 3, 0, 2, 3, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
- 2, 0, 0, 3, 3, 0, 0, 3, 1, 0, 3, 2, 2, 3, 3, 3, 3, 0, 3, 2, 1, 1, 3, 0, 3, 3,
- 2, 3, 3, 2, 3, 3, 2, 0, 0, 2, 1, 2, 2, 3, 3, 3, 1, 2, 1, 3, 0, 1, 1, 0, 0, 0,
- 3, 3, 0, 1, 0, 3, 3, 0, 1, 3, 3, 2, 2, 0, 3, 3, 3, 1, 3, 0, 0, 1, 0, 0, 0, 3,
- 3, 0, 0, 2, 1, 2, 0, 2, 3, 0, 0, 0, 3, 3, 3, 0, 3, 2, 0, 2, 0, 0, 3, 3, 3, 1,
- 3, 2, 3, 0, 3, 3, 2, 1, 0, 0, 1, 3, 2, 0, 1, 3, 3, 3, 0, 1, 3, 2, 2, 3, 3, 2,
- 3, 3, 3, 3, 0, 3, 3, 3, 3, 3, 0, 3, 3, 0, 1, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0,
- 0, 0, 3, 3, 1, 0, 1, 0, 0, 0, 3, 1, 2, 3, 3, 0, 0, 0, 0, 0, 1, 0, 3, 3, 1, 2,
- 3, 2, 0, 2, 3, 3, 2, 0, 3, 3, 0, 0, 0, 1, 0, 2, 3, 3, 1, 3, 3, 1, 0, 0, 0, 1,
- 0, 0, 0, 3, 0, 3, 1, 0, 0, 0, 0, 1, 0, 2, 3, 0, 0, 3, 3, 2, 0, -1, 0, 0, 0, 0,
- 0, 3, 2, 0, 1, 3, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0, 0, 0, 3, 3, 3, 1, 0, 0, 0,
- 0, 3, 1, 1, 2, 3, 2, 1, 0, 0, 0},
- {0, 3, 0, 1, 1, 3, 2, 2, 3, 1, 2, 3, 3, 3, 0, 0, 0, 1, 1, 0, 0, 0, 1, 3, 3, 1, 0,
- 3, 3, 0, 3, 3, 3, 0, 3, 0, 0, 0, 0, 0, 2, 0, 2, 0, 0, 2, 2, 1, 3, 3, 2, 3, 0,
- 3, 3, 0, 3, 2, 2, 2, 1, 0, 0, 3, 2, 3, 0, 2, 3, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
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- 0, 3, 1, 1, 2, 3, 2, 1, 0, 8, 0},
- {0, 3, 3, 1, 1, 3, 2, 2, 1, 1, 2, 3, 3, 3, 0, 0, 0, 3, 1, 0, 0, 0, 1, 3, 3, 1, 0,
- 3, 3, 2, 3, 3, 3, 0, 3, 0, 0, 0, 0, 1, 2, 0, 2, 0, 0, 2, 2, 0, 3, 3, 2, 3, 0,
- 3, 3, 0, 3, 2, 2, 2, 1, 0, 0, 3, 2, 1, 0, 2, 1, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
- 2, 0, 0, 3, 3, 0, 0, 3, 1, 0, 3, 2, 2, 2, 3, 3, 3, 0, 3, 2, 1, 1, 3, 0, 3, 3,
- 2, 3, 3, 2, 3, 3, 2, 0, 0, 2, 1, 2, 2, 3, 1, 3, 1, 0, 3, 3, 0, 1, 1, 0, 0, 0,
- 3, 3, 0, 3, 0, 3, 3, 0, 1, 3, 3, 2, 0, 0, 3, 1, 3, 1, 3, 0, 0, 3, 0, 0, 0, 3,
- 3, 0, 0, 2, 1, 2, 0, 0, 3, 0, 2, 0, 3, 3, 3, 0, 3, 2, 0, 2, 0, 0, 3, 3, 3, 1,
- 3, 2, 3, 0, 0, 3, 0, 1, 0, 0, 3, 3, 0, 0, 3, 3, 3, 3, 0, 3, 3, 0, 0, 3, 3, 0,
- 3, 3, 3, 3, 0, 3, 3, 3, 3, 3, 0, 3, 3, 0, 3, 3, 3, 3, 3, 3, 0, 0, 3, 3, 1, 0,
- 0, 0, 3, 3, 1, 0, 1, 0, 0, 0, 3, 3, 2, 3, 3, 0, 0, 0, 0, 0, 1, 3, 3, 3, 1, 2,
- 3, 2, 0, 0, 3, 3, 2, 0, 3, 1, 0, 0, 0, 1, 0, 0, 3, 3, 3, 3, 3, 1, 0, 0, 0, 1,
- 0, 0, 0, 3, 0, 3, 1, 0, 0, 0, 0, 3, 0, 2, 3, 0, 0, 3, 3, 2, 3, -1, 0, 0, 0, 0,
- 0, 3, 2, 2, 1, 3, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0, 2, 0, 3, 3, 3, 1, 0, 0, 0,
- 0, 3, 1, 3, 0, 3, 0, 1, 0, 0, 0},
- {0, 3, 3, 1, 1, 3, 2, 2, 1, 1, 2, 3, 3, 3, 0, 0, 0, 3, 1, 0, 0, 0, 1, 3, 3, 1, 0,
- 3, 3, 2, 3, 3, 3, 0, 3, 0, 0, 0, 0, 1, 2, 0, 2, 0, 0, 2, 2, 0, 3, 3, 2, 3, 0,
- 3, 3, 0, 3, 2, 2, 2, 1, 0, 0, 3, 2, 1, 0, 2, 1, 2, 0, 2, 0, 3, 3, 3, 2, 3, 2,
- 2, 0, 0, 3, 3, 0, 0, 3, 1, 0, 3, 2, 2, 2, 3, 3, 3, 0, 3, 2, 1, 1, 3, 0, 3, 3,
- 2, 3, 3, 2, 3, 3, 2, 0, 0, 2, 1, 2, 2, 3, 1, 3, 1, 0, 3, 3, 0, 1, 1, 0, 0, 0,
- 3, 3, 0, 3, 0, 3, 3, 0, 1, 3, 3, 2, 0, 0, 3, 1, 3, 1, 3, 0, 0, 3, 0, 0, 0, 3,
- 3, 0, 0, 2, 1, 2, 0, 0, 3, 0, 2, 0, 3, 3, 3, 0, 3, 2, 0, 2, 0, 0, 3, 3, 3, 1,
- 3, 2, 3, 0, 0, 3, 0, 1, 0, 0, 3, 3, 0, 0, 3, 3, 3, 3, 0, 3, 3, 0, 0, 3, 3, 0,
- 3, 3, 3, 3, 0, 3, 3, 3, 3, 3, 0, 3, 3, 0, 3, 3, 3, 3, 3, 3, 0, 0, 3, 3, 1, 0,
- 0, 0, 3, 3, 1, 0, 1, 0, 0, 0, 3, 3, 2, 3, 3, 0, 0, 0, 0, 0, 1, 3, 3, 3, 1, 2,
- 3, 2, 0, 0, 3, 3, 2, 0, 3, 1, 0, 0, 0, 1, 0, 0, 3, 3, 3, 3, 3, 1, 0, 0, 0, 1,
- 0, 0, 0, 3, 0, 3, 1, 0, 0, 0, 0, 3, 0, 2, 3, 0, 0, 3, 3, 2, 3, -1, 0, 0, 0, 0,
- 0, 3, 2, 2, 1, 3, 3, 3, 3, 3, 3, 0, 0, 1, 3, 1, 0, 2, 0, 3, 3, 3, 1, 0, 0, 0,
- 0, 3, 1, 3, 0, 3, 0, 1, 0, 0, 0}};
- }
- return mDataMatrix;
- }
-
- /**
- * Return the Trees field. Uses lazy initialization.
- *
- * @return Tree[] mTrees
- */
- @Override
- protected Tree[] getTrees() {
- if (mTrees == null) {
-
- // based on m1389
- mTrees = new Tree[1];
- Tree tree = new Tree();
- tree.m_name = "Fig. 5";
- tree.m_newick = "(21,(20,(((((19,18,17,16),15,14,13,12,11),10,9,8,7,6,5),((3,2),1)),4)));";
- tree.m_score = null; // not needed.
- tree.m_leafSet = new int[] {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
- 18, 19, 20, 21};
-
- mTrees[0] = tree;
- }
- return mTrees;
- }
-
- /**
- *
- * @see org.cipres.treebase.domain.nexus.PhyloDataSetProvider#getTaxaLabels()
- */
- @Override
- public List<String> getTaxaLabels() {
- if (mTaxaLabels == null) {
- // based on m1389:
- mTaxaLabels = new ArrayList<String>();
-
- mTaxaLabels.add("Grateloupia sp Spain 3");
- mTaxaLabels.add("Grateloupia sp Oregon");
- mTaxaLabels.add("Grateloupia sp California");
- mTaxaLabels.add("Grateloupia sp northcarolina 1");
- mTaxaLabels.add("Grateloupia doryphora Roscoff 1");
- mTaxaLabels.add("Grateloupia doryphora Roscoff 2");
- mTaxaLabels.add("Grateloupia doryphora Herault 10");
- mTaxaLabels.add("Grateloupia doryphora Herault 4");
- mTaxaLabels.add("Grateloupia doryphora Roscoff 5");
- mTaxaLabels.add("Grateloupia doryphora Roscoff 4");
-
- mTaxaLabels.add("Grateloupia doryphora England 1");
- mTaxaLabels.add("Grateloupia doryphora Netherlands 2");
- mTaxaLabels.add("Grateloupia doryphora Netherlands 1");
- mTaxaLabels.add("Grateloupia doryphora FortBloque 3");
- mTaxaLabels.add("Grateloupia doryphora England 2");
- mTaxaLabels.add("Grateloupia doryphora RhodeIsland 4");
- mTaxaLabels.add("Grateloupia doryphora RhodeIsland 11");
- mTaxaLabels.add("Grateloupia doryphora RhodeIsland 10");
- mTaxaLabels.add("Grateloupia doryphora RhodeIsland 6");
- mTaxaLabels.add("Grateloupia sp Herault 3");
-
- mTaxaLabels.add("Grateloupia sp Herault 1");
- }
- return mTaxaLabels;
- }
-
-}
Deleted: trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetProvider.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetProvider.java 2010-01-19 14:30:44 UTC (rev 469)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/domain/nexus/PhyloDataSetProvider.java 2010-01-19 15:41:55 UTC (rev 470)
@@ -1,41 +0,0 @@
-
-package org.cipres.treebase.domain.nexus;
-
-import java.util.List;
-
-import org.cipres.datatypes.PhyloDataset;
-
-/**
- * PhyloDataSetProvider.java
- *
- * Created on Jun 16, 2006
- *
- * @author Jin Ruan
- *
- */
-public interface PhyloDataSetProvider {
-
- /**
- * Return the cipres phylo data set field.
- *
- * @return PhyloDataset
- */
- PhyloDataset getCipresData();
-
- /**
- * Return the TaxaLabels field.
- *
- * @return List<String>
- */
- List<String> getTaxaLabels();
-
- /**
- * Verify the nexus data set is mapped from the cipres phylodataset.
- *
- * Use Assert.assert to check the mapping.
- *
- * @param pNexusData
- */
- void verify(NexusDataSet pNexusData);
-
-}
\ No newline at end of file
Modified: trunk/treebase-core/src/test/java/org/cipres/treebase/service/nexus/NexusParserTest.java
===================================================================
--- trunk/treebase-core/src/test/java/org/cipres/treebase/service/nexus/NexusParserTest.java 2010-01-19 14:30:44 UTC (rev 469)
+++ trunk/treebase-core/src/test/java/org/cipres/treebase/service/nexus/NexusParserTest.java 2010-01-19 15:41:55 UTC (rev 470)
@@ -2,10 +2,8 @@
import java.io.File;
-import org.cipres.CipresIDL.api1.DataMatrix;
-import org.cipres.CipresIDL.api1.Tree;
-import org.cipres.datatypes.PhyloDataset;
+
import org.cipres.treebase.service.AbstractServiceTest;
/**
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