From 6dbb3925303243ac10f4f0db558634b5a23acdc1 Mon Sep 17 00:00:00 2001 From: cmzmasek Date: Thu, 10 Aug 2017 17:58:28 -0700 Subject: [PATCH] tests... --- .../forester/clade_analysis/CladeAnalysisTest.java | 585 ++++++++++++++++++++ 1 file changed, 585 insertions(+) create mode 100644 forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java diff --git a/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java new file mode 100644 index 0000000..a78e8fe --- /dev/null +++ b/forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java @@ -0,0 +1,585 @@ + +package org.forester.clade_analysis; + +import java.io.File; + +import org.forester.io.parsers.PhylogenyParser; +import org.forester.io.parsers.util.ParserUtils; +import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; +import org.forester.phylogeny.factories.PhylogenyFactory; +import org.forester.util.ForesterUtil; + +public class CladeAnalysisTest { + + private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator() + + "test_data" + ForesterUtil.getFileSeparator(); + + public static void main( final String[] args ) { + boolean failed = false; + if ( !testCladeAnalysis1() ) { + System.out.println( "Clade analysis 1 failed" ); + failed = true; + } + if ( !testCladeAnalysis2() ) { + System.out.println( "Clade analysis 2 failed" ); + failed = true; + } + if ( !failed ) { + System.out.println( "OK" ); + } + } + + public static boolean test() { + if ( !testCladeAnalysis1() ) { + return false; + } + if ( !testCladeAnalysis2() ) { + return false; + } + return true; + } + + private static boolean testCladeAnalysis1() { + try { + final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_1.xml" ); + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true ); + final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ]; + Result res = Analysis.execute( p1, "A.1.1.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 4 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.1.1.2", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 4 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.1.1.3", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 4 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.1.1.4", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.1.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 3 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.1.2.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 17 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.2.1.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.2.1.2" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 17 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.2.1.2", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.2.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 17 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.3.1.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1.2" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.3.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 2 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.3.1.2", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.3.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 2 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.3.2.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.3.3.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 3 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.3.3.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.3" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 10 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.4.1.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.4.1.1.a" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.4.1.2" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 3 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.4.1.1.a", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.4.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A.4.1.2" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 3 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.4.1.2", "." ); + res = Analysis.execute( p1, "A.4.1.2.a", "." ); + res = Analysis.execute( p1, "A.5.1.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.5.1.2" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 10 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.5.1.2", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A.5.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 10 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "A.6.3.12", "." ); + if ( !res.getGreatestCommonPrefix().equals( "A" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "A" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 17 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "B.1.1.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "B.1.234.3" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 25 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 2 ) { + return false; + } + res = Analysis.execute( p1, "B.1.234.3", "." ); + if ( !res.getGreatestCommonPrefix().equals( "" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "B.1.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 25 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 2 ) { + return false; + } + res = Analysis.execute( p1, "C.1.1.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1.2" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "C.1.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 2 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "C.1.1.2", "." ); + if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "C.1.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 2 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "C.1.2.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "C" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "C.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 3 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "C.2.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "C" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "C.1" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "C.3" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 4 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "C.3", "." ); + if ( !res.getGreatestCommonPrefix().equals( "" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "C" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "QE.1.1.1.2.1" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 5 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 1 ) { + return false; + } + res = Analysis.execute( p1, "QE.1.1.1.2.1", "." ); + if ( !res.getGreatestCommonPrefix().equals( "" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "C" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 25 ) { + return false; + } + if ( res.getTreeSize() != 25 ) { + return false; + } + if ( res.getWarnings().size() != 2 ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testCladeAnalysis2() { + try { + final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_2.xml" ); + final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); + final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true ); + final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ]; + Result res = Analysis.execute( p1, "6_DQ278891", null ); + if ( !res.getGreatestCommonPrefix().equals( "6_" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "6_DQ278893" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "6_JX183550" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 2 ) { + return false; + } + if ( res.getTreeSize() != 219 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "6xa_EU408330", null ); + if ( !res.getGreatestCommonPrefix().equals( "6xa_EU40833" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "6xa_EU408331" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "6xa_EU408332" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 2 ) { + return false; + } + if ( res.getTreeSize() != 219 ) { + return false; + } + if ( res.getWarnings().size() != 0 ) { + return false; + } + res = Analysis.execute( p1, "7a_EF108306", null ); + if ( !res.getGreatestCommonPrefix().equals( "" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixDown().equals( "2" ) ) { + return false; + } + if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) { + return false; + } + if ( res.getLeastEncompassingCladeSize() != 219 ) { + return false; + } + if ( res.getTreeSize() != 219 ) { + return false; + } + if ( res.getWarnings().size() != 2 ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } +} -- 1.7.10.2