import org.forester.io.parsers.FastaParser;
import org.forester.io.parsers.GeneralMsaParser;
import org.forester.msa.Msa;
import org.forester.io.parsers.FastaParser;
import org.forester.io.parsers.GeneralMsaParser;
import org.forester.msa.Msa;
import org.forester.msa.MsaCompactor;
import org.forester.msa.MsaMethods;
import org.forester.util.CommandLineArguments;
import org.forester.msa.MsaCompactor;
import org.forester.msa.MsaMethods;
import org.forester.util.CommandLineArguments;
final static private String HELP_OPTION_2 = "h";
final static private String REMOVE_WORST_OFFENDERS_OPTION = "w";
final static private String AV_GAPINESS_OPTION = "a";
final static private String HELP_OPTION_2 = "h";
final static private String REMOVE_WORST_OFFENDERS_OPTION = "w";
final static private String AV_GAPINESS_OPTION = "a";
final static private String LENGTH_OPTION = "l";
final static private String REALIGN_OPTION = "r";
final static private String PRG_NAME = "msa_compactor";
final static private String PRG_DESC = "multiple sequnce aligment compactor";
final static private String LENGTH_OPTION = "l";
final static private String REALIGN_OPTION = "r";
final static private String PRG_NAME = "msa_compactor";
final static private String PRG_DESC = "multiple sequnce aligment compactor";
- final static private String PRG_VERSION = "0.90";
- final static private String PRG_DATE = "2012.07.11";
+ final static private String PRG_VERSION = "0.01";
+ final static private String PRG_DATE = "140221";
public static void main( final String args[] ) {
try {
final CommandLineArguments cla = new CommandLineArguments( args );
public static void main( final String args[] ) {
try {
final CommandLineArguments cla = new CommandLineArguments( args );
final List<String> allowed_options = new ArrayList<String>();
allowed_options.add( REMOVE_WORST_OFFENDERS_OPTION );
allowed_options.add( AV_GAPINESS_OPTION );
allowed_options.add( LENGTH_OPTION );
allowed_options.add( REALIGN_OPTION );
final List<String> allowed_options = new ArrayList<String>();
allowed_options.add( REMOVE_WORST_OFFENDERS_OPTION );
allowed_options.add( AV_GAPINESS_OPTION );
allowed_options.add( LENGTH_OPTION );
allowed_options.add( REALIGN_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
MsaCompactor mc = null;
if ( worst_remove > 0 ) {
mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign );
}
else if ( av > 0 ) {
MsaCompactor mc = null;
if ( worst_remove > 0 ) {
mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign );
}
else if ( av > 0 ) {
- mc = MsaCompactor.reduceGapAverage( msa, av, step, realign );
+ mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, out, 50 );
}
else if ( length > 0 ) {
mc = MsaCompactor.reduceLength( msa, length, step, realign );
}
}
else if ( length > 0 ) {
mc = MsaCompactor.reduceLength( msa, length, step, realign );
}
- // System.out.println( " -" + FROM_OPTION + "=<integer>: from (msa column)" );
- // System.out.println( " -" + TO_OPTION + "=<integer>: to (msa column)" );
- // System.out.println( " or" );
- // System.out.println( " -" + WINDOW_OPTION + "=<integer>: window size (msa columns)" );