forester/java/src/org/forester/archaeopteryx/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: www.phylosoft.org/forester
  26
  27 package org.forester.archaeopteryx;
  28
  29 import java.io.File;
  30
  31 import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD;
  32 import org.forester.msa.Mafft;
  33
  34 public final class PhylogeneticInferenceOptions {
  35
  36     private static final int                 BOOTSTRAP_RESAMPLES_DEFAULT                  = 100;
  37     private static final PWD_DISTANCE_METHOD PWD_DISTANCE_METHOD_DEFAULT                  = PWD_DISTANCE_METHOD.KIMURA_DISTANCE;
  38     public static final long                 RANDOM_NUMBER_SEED_DEFAULT                   = 42L;
  39     private static final boolean             PERFORM_BOOTSTRAP_RESAMPLING_DEFAULT         = false;
  40     private static final double              msa_processing_max_allowed_gap_ratio_default = 0.5;
  41     private static final int                 msa_processing_min_allowed_length_default    = 50;
  42     private int                              _bootstrap_samples;
  43     private PWD_DISTANCE_METHOD              _pwd_distance_method;
  44     private long                             _random_number_generator_seed;
  45     private boolean                          _perform_bootstrap_resampling;
  46     private String                           _intermediate_files_base;
  47     private String                           _msa_prg_parameters;
  48     private boolean                          _execute_msa_processing;
  49     private boolean                          _msa_processing_remove_all_gap_columns;
  50     private double                           _msa_processing_max_allowed_gap_ratio;
  51     private int                              _msa_processing_min_allowed_length;
  52     private boolean                          _save_pwd_file;
  53     private boolean                          _save_processed_msa;
  54     private boolean                          _save_original_msa;
  55     private File                             _pwd_outfile;
  56     private File                             _processed_msa_outfile;
  57     private File                             _original_msa_outfile;
  58
  59     public synchronized String getMsaPrgParameters() {
  60         return _msa_prg_parameters;
  61     }
  62
  63     public synchronized void setMsaPrgParameters( final String msa_prg_parameters ) {
  64         _msa_prg_parameters = new String( msa_prg_parameters );
  65     }
  66
  67     public synchronized String getIntermediateFilesBase() {
  68         return _intermediate_files_base;
  69     }
  70
  71     public synchronized String getMsaPrg() {
  72         return "MAFFT";
  73     }
  74
  75     public synchronized void setIntermediateFilesBase( final String intermediate_files_base ) {
  76         _intermediate_files_base = new String( intermediate_files_base );
  77     }
  78
  79     public PhylogeneticInferenceOptions() {
  80         init();
  81     }
  82
  83     // Deep copy.
  84     public synchronized PhylogeneticInferenceOptions copy() {
  85         final PhylogeneticInferenceOptions o = new PhylogeneticInferenceOptions();
  86         o._bootstrap_samples = _bootstrap_samples;
  87         o._pwd_distance_method = _pwd_distance_method;
  88         o._random_number_generator_seed = _random_number_generator_seed;
  89         o._perform_bootstrap_resampling = _perform_bootstrap_resampling;
  90         o._intermediate_files_base = new String( _intermediate_files_base );
  91         o._msa_prg_parameters = new String( _msa_prg_parameters );
  92         o._msa_processing_max_allowed_gap_ratio = _msa_processing_max_allowed_gap_ratio;
  93         o._msa_processing_min_allowed_length = _msa_processing_min_allowed_length;
  94         o._execute_msa_processing = _execute_msa_processing;
  95         o._msa_processing_remove_all_gap_columns = _msa_processing_remove_all_gap_columns;
  96         o._save_pwd_file = _save_pwd_file;
  97         o._save_processed_msa = _save_processed_msa;
  98         o._save_original_msa = _save_original_msa;
  99         if ( _pwd_outfile != null ) {
 100             o._pwd_outfile = new File( _pwd_outfile.toString() );
 101         }
 102         if ( _processed_msa_outfile != null ) {
 103             o._processed_msa_outfile = new File( _processed_msa_outfile.toString() );
 104         }
 105         if ( _original_msa_outfile != null ) {
 106             o._original_msa_outfile = new File( _original_msa_outfile.toString() );
 107         }
 108         return o;
 109     }
 110
 111     private synchronized void init() {
 112         _bootstrap_samples = BOOTSTRAP_RESAMPLES_DEFAULT;
 113         _pwd_distance_method = PWD_DISTANCE_METHOD_DEFAULT;
 114         _random_number_generator_seed = RANDOM_NUMBER_SEED_DEFAULT;
 115         _perform_bootstrap_resampling = PERFORM_BOOTSTRAP_RESAMPLING_DEFAULT;
 116         _intermediate_files_base = "";
 117         _msa_prg_parameters = Mafft.getDefaultParameters();
 118         _msa_processing_max_allowed_gap_ratio = msa_processing_max_allowed_gap_ratio_default;
 119         _msa_processing_min_allowed_length = msa_processing_min_allowed_length_default;
 120         _execute_msa_processing = false;
 121         _msa_processing_remove_all_gap_columns = false;
 122         _save_pwd_file = false;
 123         _save_processed_msa = false;
 124         _save_original_msa = false;
 125         _pwd_outfile = null;
 126         _processed_msa_outfile = null;
 127         _original_msa_outfile = null;
 128     }
 129
 130     public synchronized void setBootstrapSamples( final int bootstrap_samples ) {
 131         _bootstrap_samples = bootstrap_samples;
 132     }
 133
 134     public synchronized int getBootstrapSamples() {
 135         return _bootstrap_samples;
 136     }
 137
 138     public synchronized void setPwdDistanceMethod( final PWD_DISTANCE_METHOD pwd_distance_method ) {
 139         _pwd_distance_method = pwd_distance_method;
 140     }
 141
 142     public synchronized PWD_DISTANCE_METHOD getPwdDistanceMethod() {
 143         return _pwd_distance_method;
 144     }
 145
 146     public synchronized void setRandomNumberGeneratorSeed( final long random_number_generator_seed ) {
 147         _random_number_generator_seed = random_number_generator_seed;
 148     }
 149
 150     public synchronized long getRandomNumberGeneratorSeed() {
 151         return _random_number_generator_seed;
 152     }
 153
 154     public synchronized void setPerformBootstrapResampling( final boolean perform_bootstrap_resampling ) {
 155         _perform_bootstrap_resampling = perform_bootstrap_resampling;
 156     }
 157
 158     public synchronized boolean isPerformBootstrapResampling() {
 159         return _perform_bootstrap_resampling;
 160     }
 161
 162     public static PhylogeneticInferenceOptions createInstance( final Configuration configuration ) {
 163         final PhylogeneticInferenceOptions o = new PhylogeneticInferenceOptions();
 164         if ( configuration.getDefaultBootstrapSamples() >= 0 ) {
 165             o.setBootstrapSamples( configuration.getDefaultBootstrapSamples() );
 166         }
 167         return o;
 168     }
 169
 170     public File getTempDir() {
 171         //TODO
 172         return new File( "/Users/zma/Desktop/tmp/" );
 173     }
 174
 175     public void setMsaProcessingMaxAllowedGapRatio( final double msa_processing_max_allowed_gap_ratio ) {
 176         _msa_processing_max_allowed_gap_ratio = msa_processing_max_allowed_gap_ratio;
 177     }
 178
 179     public double getMsaProcessingMaxAllowedGapRatio() {
 180         return _msa_processing_max_allowed_gap_ratio;
 181     }
 182
 183     public void setMsaProcessingMinAllowedLength( final int msa_processing_min_allowed_length ) {
 184         _msa_processing_min_allowed_length = msa_processing_min_allowed_length;
 185     }
 186
 187     public int getMsaProcessingMinAllowedLength() {
 188         return _msa_processing_min_allowed_length;
 189     }
 190
 191     boolean isExecuteMsaProcessing() {
 192         return _execute_msa_processing;
 193     }
 194
 195     void setExecuteMsaProcessing( final boolean execute_msa_processing ) {
 196         _execute_msa_processing = execute_msa_processing;
 197     }
 198
 199     boolean isMsaProcessingRemoveAllGapColumns() {
 200         return _msa_processing_remove_all_gap_columns;
 201     }
 202
 203     void setMsaProcessingRemoveAllGapColumns( final boolean msa_processing_remove_all_gap_columns ) {
 204         _msa_processing_remove_all_gap_columns = msa_processing_remove_all_gap_columns;
 205     }
 206
 207     boolean isSavePwdFile() {
 208         return _save_pwd_file;
 209     }
 210
 211     void setSavePwdFile( final boolean save_pwd_file ) {
 212         _save_pwd_file = save_pwd_file;
 213     }
 214
 215     boolean isSaveProcessedMsa() {
 216         return _save_processed_msa;
 217     }
 218
 219     void setSaveProcessedMsa( final boolean save_processed_msa ) {
 220         _save_processed_msa = save_processed_msa;
 221     }
 222
 223     boolean isSaveOriginalMsa() {
 224         return _save_original_msa;
 225     }
 226
 227     void setSaveOriginalMsa( final boolean save_original_msa ) {
 228         _save_original_msa = save_original_msa;
 229     }
 230
 231     File getPwdOutfile() {
 232         return _pwd_outfile;
 233     }
 234
 235     void setPwdOutfile( final File pwd_outfile ) {
 236         _pwd_outfile = pwd_outfile;
 237     }
 238
 239     File getProcesseMsaOutfile() {
 240         return _processed_msa_outfile;
 241     }
 242
 243     void setProcesseMsaOutfile( final File processed_msa_outfile ) {
 244         _processed_msa_outfile = processed_msa_outfile;
 245     }
 246
 247     File getOriginalMsaOutfile() {
 248         return _original_msa_outfile;
 249     }
 250
 251     void setOriginalMsaOutfile( final File original_msa_outfile ) {
 252         _original_msa_outfile = original_msa_outfile;
 253     }
 254 }