import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
import org.forester.io.parsers.HmmPfamOutputParser;
-import org.forester.io.parsers.nexus.PaupLogParser;
import org.forester.io.parsers.nhx.NHXParser;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
return false;
}
System.out.println( "OK." );
- System.out.print( " Paup log parser: " );
- if ( !TestSurfacing.testPaupLogParser( test_dir ) ) {
- System.out.println( "failed." );
- return false;
- }
- System.out.println( "OK." );
+
System.out.print( " Binary state matrix to gain loss matrix: " );
if ( !TestSurfacing.testBinaryStateMatrixToGainLossMatrix( test_dir ) ) {
System.out.println( "failed." );
return true;
}
- private static boolean testPaupLogParser( final File test_dir ) {
- try {
- final PaupLogParser parser = new PaupLogParser();
- parser.setSource( new File( test_dir + ForesterUtil.getFileSeparator() + "paup_log_test_1" ) );
- final CharacterStateMatrix<BinaryStates> matrix = parser.parse();
- if ( matrix.getNumberOfIdentifiers() != 8 ) {
- return false;
- }
- if ( !matrix.getIdentifier( 0 ).equals( "MOUSE" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 1 ).equals( "NEMVE" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 2 ).equals( "MONBE" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 3 ).equals( "DICDI" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 4 ).equals( "ARATH" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 5 ).equals( "6" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 6 ).equals( "7" ) ) {
- return false;
- }
- if ( !matrix.getIdentifier( 7 ).equals( "8" ) ) {
- return false;
- }
- if ( matrix.getNumberOfCharacters() != ( 66 + 66 + 28 ) ) {
- return false;
- }
- if ( matrix.getState( 0, 4 ) != BinaryStates.ABSENT ) {
- return false;
- }
- if ( matrix.getState( 0, 5 ) != BinaryStates.PRESENT ) {
- return false;
- }
- if ( matrix.getState( 1, 5 ) != BinaryStates.PRESENT ) {
- return false;
- }
- if ( matrix.getState( 7, 154 ) != BinaryStates.ABSENT ) {
- return false;
- }
- if ( matrix.getState( 7, 155 ) != BinaryStates.PRESENT ) {
- return false;
- }
- if ( matrix.getState( 7, 156 ) != BinaryStates.PRESENT ) {
- return false;
- }
- if ( matrix.getState( 7, 157 ) != BinaryStates.ABSENT ) {
- return false;
- }
- if ( matrix.getState( 7, 158 ) != BinaryStates.PRESENT ) {
- return false;
- }
- if ( matrix.getState( 7, 159 ) != BinaryStates.ABSENT ) {
- return false;
- }
- }
- catch ( final Exception e ) {
- e.printStackTrace( System.out );
- return false;
- }
- return true;
- }
+
}