forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferenceOptions.java

   1 // $Id:
   2 // $
   3 // FORESTER -- software libraries and applications
   4 // for evolutionary biology research and applications.
   5 //
   6 // Copyright (C) 2008-2009 Christian M. Zmasek
   7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.archaeopteryx.tools;
  28
  29 import java.io.File;
  30
  31 import org.forester.archaeopteryx.Configuration;
  32 import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
  33 import org.forester.msa.Mafft;
  34
  35 public final class PhylogeneticInferenceOptions {
  36
  37     private static final int                 BOOTSTRAP_RESAMPLES_DEFAULT                  = 100;
  38     private static final PWD_DISTANCE_METHOD PWD_DISTANCE_METHOD_DEFAULT                  = PWD_DISTANCE_METHOD.KIMURA_DISTANCE;
  39     public static final long                 RANDOM_NUMBER_SEED_DEFAULT                   = 42L;
  40     private static final boolean             PERFORM_BOOTSTRAP_RESAMPLING_DEFAULT         = false;
  41     private static final double              msa_processing_max_allowed_gap_ratio_default = 0.5;
  42     private static final int                 msa_processing_min_allowed_length_default    = 50;
  43     private int                              _bootstrap_samples;
  44     private PWD_DISTANCE_METHOD              _pwd_distance_method;
  45     private long                             _random_number_generator_seed;
  46     private boolean                          _perform_bootstrap_resampling;
  47     private String                           _intermediate_files_base;
  48     private String                           _msa_prg_parameters;
  49     private boolean                          _execute_msa_processing;
  50     private boolean                          _msa_processing_remove_all_gap_columns;
  51     private double                           _msa_processing_max_allowed_gap_ratio;
  52     private int                              _msa_processing_min_allowed_length;
  53     private boolean                          _save_pwd_file;
  54     private boolean                          _save_processed_msa;
  55     private boolean                          _save_original_msa;
  56     private File                             _pwd_outfile;
  57     private File                             _processed_msa_outfile;
  58     private File                             _original_msa_outfile;
  59
  60     public synchronized String getMsaPrgParameters() {
  61         return _msa_prg_parameters;
  62     }
  63
  64     public synchronized void setMsaPrgParameters( final String msa_prg_parameters ) {
  65         _msa_prg_parameters = new String( msa_prg_parameters );
  66     }
  67
  68     public synchronized String getIntermediateFilesBase() {
  69         return _intermediate_files_base;
  70     }
  71
  72     public synchronized String getMsaPrg() {
  73         return "MAFFT";
  74     }
  75
  76     public synchronized void setIntermediateFilesBase( final String intermediate_files_base ) {
  77         _intermediate_files_base = new String( intermediate_files_base );
  78     }
  79
  80     public PhylogeneticInferenceOptions() {
  81         init();
  82     }
  83
  84     // Deep copy.
  85     public synchronized PhylogeneticInferenceOptions copy() {
  86         final PhylogeneticInferenceOptions o = new PhylogeneticInferenceOptions();
  87         o._bootstrap_samples = _bootstrap_samples;
  88         o._pwd_distance_method = _pwd_distance_method;
  89         o._random_number_generator_seed = _random_number_generator_seed;
  90         o._perform_bootstrap_resampling = _perform_bootstrap_resampling;
  91         o._intermediate_files_base = new String( _intermediate_files_base );
  92         o._msa_prg_parameters = new String( _msa_prg_parameters );
  93         o._msa_processing_max_allowed_gap_ratio = _msa_processing_max_allowed_gap_ratio;
  94         o._msa_processing_min_allowed_length = _msa_processing_min_allowed_length;
  95         o._execute_msa_processing = _execute_msa_processing;
  96         o._msa_processing_remove_all_gap_columns = _msa_processing_remove_all_gap_columns;
  97         o._save_pwd_file = _save_pwd_file;
  98         o._save_processed_msa = _save_processed_msa;
  99         o._save_original_msa = _save_original_msa;
 100         if ( _pwd_outfile != null ) {
 101             o._pwd_outfile = new File( _pwd_outfile.toString() );
 102         }
 103         if ( _processed_msa_outfile != null ) {
 104             o._processed_msa_outfile = new File( _processed_msa_outfile.toString() );
 105         }
 106         if ( _original_msa_outfile != null ) {
 107             o._original_msa_outfile = new File( _original_msa_outfile.toString() );
 108         }
 109         return o;
 110     }
 111
 112     private synchronized void init() {
 113         _bootstrap_samples = BOOTSTRAP_RESAMPLES_DEFAULT;
 114         _pwd_distance_method = PWD_DISTANCE_METHOD_DEFAULT;
 115         _random_number_generator_seed = RANDOM_NUMBER_SEED_DEFAULT;
 116         _perform_bootstrap_resampling = PERFORM_BOOTSTRAP_RESAMPLING_DEFAULT;
 117         _intermediate_files_base = "";
 118         _msa_prg_parameters = Mafft.getDefaultParameters();
 119         _msa_processing_max_allowed_gap_ratio = msa_processing_max_allowed_gap_ratio_default;
 120         _msa_processing_min_allowed_length = msa_processing_min_allowed_length_default;
 121         _execute_msa_processing = false;
 122         _msa_processing_remove_all_gap_columns = false;
 123         _save_pwd_file = false;
 124         _save_processed_msa = false;
 125         _save_original_msa = false;
 126         _pwd_outfile = null;
 127         _processed_msa_outfile = null;
 128         _original_msa_outfile = null;
 129     }
 130
 131     public synchronized void setBootstrapSamples( final int bootstrap_samples ) {
 132         _bootstrap_samples = bootstrap_samples;
 133     }
 134
 135     public synchronized int getBootstrapSamples() {
 136         return _bootstrap_samples;
 137     }
 138
 139     public synchronized void setPwdDistanceMethod( final PWD_DISTANCE_METHOD pwd_distance_method ) {
 140         _pwd_distance_method = pwd_distance_method;
 141     }
 142
 143     public synchronized PWD_DISTANCE_METHOD getPwdDistanceMethod() {
 144         return _pwd_distance_method;
 145     }
 146
 147     public synchronized void setRandomNumberGeneratorSeed( final long random_number_generator_seed ) {
 148         _random_number_generator_seed = random_number_generator_seed;
 149     }
 150
 151     public synchronized long getRandomNumberGeneratorSeed() {
 152         return _random_number_generator_seed;
 153     }
 154
 155     public synchronized void setPerformBootstrapResampling( final boolean perform_bootstrap_resampling ) {
 156         _perform_bootstrap_resampling = perform_bootstrap_resampling;
 157     }
 158
 159     public synchronized boolean isPerformBootstrapResampling() {
 160         return _perform_bootstrap_resampling;
 161     }
 162
 163     public static PhylogeneticInferenceOptions createInstance( final Configuration configuration ) {
 164         final PhylogeneticInferenceOptions o = new PhylogeneticInferenceOptions();
 165         if ( configuration.getDefaultBootstrapSamples() >= 0 ) {
 166             o.setBootstrapSamples( configuration.getDefaultBootstrapSamples() );
 167         }
 168         return o;
 169     }
 170
 171     public File getTempDir() {
 172         //TODO
 173         return new File( "/Users/zma/Desktop/tmp/" );
 174     }
 175
 176     public void setMsaProcessingMaxAllowedGapRatio( final double msa_processing_max_allowed_gap_ratio ) {
 177         _msa_processing_max_allowed_gap_ratio = msa_processing_max_allowed_gap_ratio;
 178     }
 179
 180     public double getMsaProcessingMaxAllowedGapRatio() {
 181         return _msa_processing_max_allowed_gap_ratio;
 182     }
 183
 184     public void setMsaProcessingMinAllowedLength( final int msa_processing_min_allowed_length ) {
 185         _msa_processing_min_allowed_length = msa_processing_min_allowed_length;
 186     }
 187
 188     public int getMsaProcessingMinAllowedLength() {
 189         return _msa_processing_min_allowed_length;
 190     }
 191
 192     boolean isExecuteMsaProcessing() {
 193         return _execute_msa_processing;
 194     }
 195
 196     void setExecuteMsaProcessing( final boolean execute_msa_processing ) {
 197         _execute_msa_processing = execute_msa_processing;
 198     }
 199
 200     boolean isMsaProcessingRemoveAllGapColumns() {
 201         return _msa_processing_remove_all_gap_columns;
 202     }
 203
 204     void setMsaProcessingRemoveAllGapColumns( final boolean msa_processing_remove_all_gap_columns ) {
 205         _msa_processing_remove_all_gap_columns = msa_processing_remove_all_gap_columns;
 206     }
 207
 208     boolean isSavePwdFile() {
 209         return _save_pwd_file;
 210     }
 211
 212     void setSavePwdFile( final boolean save_pwd_file ) {
 213         _save_pwd_file = save_pwd_file;
 214     }
 215
 216     boolean isSaveProcessedMsa() {
 217         return _save_processed_msa;
 218     }
 219
 220     void setSaveProcessedMsa( final boolean save_processed_msa ) {
 221         _save_processed_msa = save_processed_msa;
 222     }
 223
 224     boolean isSaveOriginalMsa() {
 225         return _save_original_msa;
 226     }
 227
 228     void setSaveOriginalMsa( final boolean save_original_msa ) {
 229         _save_original_msa = save_original_msa;
 230     }
 231
 232     File getPwdOutfile() {
 233         return _pwd_outfile;
 234     }
 235
 236     void setPwdOutfile( final File pwd_outfile ) {
 237         _pwd_outfile = pwd_outfile;
 238     }
 239
 240     File getProcesseMsaOutfile() {
 241         return _processed_msa_outfile;
 242     }
 243
 244     void setProcesseMsaOutfile( final File processed_msa_outfile ) {
 245         _processed_msa_outfile = processed_msa_outfile;
 246     }
 247
 248     File getOriginalMsaOutfile() {
 249         return _original_msa_outfile;
 250     }
 251
 252     void setOriginalMsaOutfile( final File original_msa_outfile ) {
 253         _original_msa_outfile = original_msa_outfile;
 254     }
 255 }