import org.forester.io.parsers.GeneralMsaParser;
import org.forester.msa.Msa;
import org.forester.msa.Msa.MSA_FORMAT;
-import org.forester.msa.MsaCompactor;
import org.forester.msa.MsaMethods;
+import org.forester.msa_compactor.MsaCompactor;
import org.forester.util.CommandLineArguments;
import org.forester.util.ForesterUtil;
public class msa_compactor {
- final static private String HELP_OPTION_1 = "help";
- 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 STEP_OPTION = "s";
- 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 = "0.01";
- final static private String PRG_DATE = "140221";
- final static private String E_MAIL = "phylosoft@gmail.com";
- final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
+ final static private String HELP_OPTION_1 = "help";
+ 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 STEP_OPTION = "s";
+ final static private String LENGTH_OPTION = "l";
+ final static private String REALIGN_OPTION = "r";
+ final static private String DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION = "nn";
+ final static private String PRG_NAME = "msa_compactor";
+ final static private String PRG_DESC = "multiple sequnce aligment compactor";
+ final static private String PRG_VERSION = "0.01";
+ final static private String PRG_DATE = "140221";
+ final static private String E_MAIL = "phylosoft@gmail.com";
+ final static private String WWW = "https://sites.google.com/site/cmzmasek/home/software/forester";
public static void main( final String args[] ) {
try {
int length = -1;
int step = 1;
boolean realign = false;
+ boolean norm = true;
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 );
+ allowed_options.add( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION );
allowed_options.add( STEP_OPTION );
final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
if ( dissallowed_options.length() > 0 ) {
if ( cla.isOptionSet( REALIGN_OPTION ) ) {
realign = true;
}
+ if ( cla.isOptionSet( DO_NOT_NORMALIZE_FOR_EFF_LENGTH_OPTION ) ) {
+ norm = false;
+ }
// else if ( cla.isOptionSet( STEP_OPTION ) && cla.isOptionSet( WINDOW_OPTION ) ) {
// step = cla.getOptionValueAsInt( STEP_OPTION );
// window = cla.getOptionValueAsInt( WINDOW_OPTION );
}
MsaCompactor mc = null;
if ( worst_remove > 0 ) {
- mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign );
+ mc = MsaCompactor.removeWorstOffenders( msa, worst_remove, realign, norm );
}
else if ( av > 0 ) {
mc = MsaCompactor.reduceGapAverage( msa, av, step, realign, out, 50 );