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1 # $Id: Result.pm,v 1.2 2002/10/22 07:45:24 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Tools::Phylo::Molphy::Result
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Tools::Phylo::Molphy::Result - DESCRIPTION of Object
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16
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17 =head1 SYNOPSIS
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18
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19 Give standard usage here
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20
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21 =head1 DESCRIPTION
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22
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23 Describe the object here
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24
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25 =head1 FEEDBACK
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26
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27 =head2 Mailing Lists
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28
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29 User feedback is an integral part of the evolution of this and other
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30 Bioperl modules. Send your comments and suggestions preferably to
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31 the Bioperl mailing list. Your participation is much appreciated.
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32
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33 bioperl-l@bioperl.org - General discussion
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34 http://bioperl.org/MailList.shtml - About the mailing lists
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35
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36 =head2 Reporting Bugs
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37
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38 Report bugs to the Bioperl bug tracking system to help us keep track
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39 of the bugs and their resolution. Bug reports can be submitted via
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40 email or the web:
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41
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42 bioperl-bugs@bioperl.org
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43 http://bugzilla.bioperl.org/
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44
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45 =head1 AUTHOR - Jason Stajich
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46
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47 Email jason@bioperl.org
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48
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49 Describe contact details here
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50
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51 =head1 CONTRIBUTORS
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52
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53 Additional contributors names and emails here
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54
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55 =head1 APPENDIX
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56
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57 The rest of the documentation details each of the object methods.
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58 Internal methods are usually preceded with a _
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59
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60 =cut
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61
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62
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63 # Let the code begin...
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64
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65
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66 package Bio::Tools::Phylo::Molphy::Result;
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67 use vars qw(@ISA);
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68 use strict;
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69
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70 # Object preamble - inherits from Bio::Root::Root
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71
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72 use Bio::Root::Root;
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73
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74
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75 @ISA = qw(Bio::Root::Root );
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76
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77 =head2 new
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78
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79 Title : new
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80 Usage : my $obj = new Bio::Tools::Phylo::Molphy::Result();
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81 Function: Builds a new Bio::Tools::Phylo::Molphy::Result object
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82 Returns : Bio::Tools::Phylo::Molphy::Result
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83 Args :
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84
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85
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86 =cut
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87
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88 sub new {
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89 my($class,@args) = @_;
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90
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91 my $self = $class->SUPER::new(@args);
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92 my ($trees,
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93 $smat,$tmat,$freq,
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94 $model, $sspace,
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95 ) = $self->_rearrange([qw(TREES SUBSTITUTION_MATRIX
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96 TRANSITION_MATRIX FREQUENCIES
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97 MODEL SEARCH_SPACE)], @args);
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98
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99 if( $trees ) {
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100 if(ref($trees) !~ /ARRAY/i ) {
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101 $self->warn("Must have provided a valid array reference to initialize trees");
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102 } else {
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103 foreach my $t ( @$trees ) {
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104 $self->add_tree($t);
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105 }
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106 }
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107 }
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108 # initialize things through object methods to be a good
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109 # little OO programmer
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110 if( ref($smat) =~ /HASH/i ) {
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111 $self->substitution_matrix($smat);
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112 }
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113 if( ref($tmat) =~ /HASH/i ) {
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114 $self->transition_probability_matrix($tmat);
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115 }
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116 if( ref($freq) =~ /HASH/i ) {
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117 $self->residue_frequencies($freq);
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118 }
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119
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120 $model && $self->model($model);
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121 $sspace && $self->search_space($sspace);
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122 $self->{'_treeiterator'} = 0;
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123
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124 return $self;
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125 }
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126
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127 =head2 model
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128
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129 Title : model
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130 Usage : $obj->model($newval)
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131 Function:
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132 Returns : value of model
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133 Args : newvalue (optional)
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134
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135
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136 =cut
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137
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138 sub model{
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139 my ($self,$value) = @_;
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140 if( defined $value) {
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141 $self->{'model'} = $value;
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142 }
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143 return $self->{'model'};
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144
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145 }
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146
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147 =head2 substitution_matrix
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148
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149 Title : substitution_matrix
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150 Usage : my $smat = $result->subsitution_matrix;
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151 Function: Get the relative substitution matrix calculated in the ML procedure
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152 Returns : reference to hash of hashes where key is the aa/nt name and value
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153 is another hash ref which contains keys for all the aa/nt
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154 possibilities
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155 Args : none
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156
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157
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158 =cut
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159
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160 sub substitution_matrix{
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161 my ($self,$val) = @_;
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162 if(defined $val ) {
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163 if( ref($val) =~ /HASH/ ) {
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164 foreach my $v (values %{$val} ) {
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165 if( ref($v) !~ /HASH/i ) {
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166 $self->warn("Must be a valid hashref of hashrefs for substition_matrix");
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167 return undef;
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168 }
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169 }
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170 $self->{'_substitution_matrix'} = $val;
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171 } else {
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172 $self->warn("Must be a valid hashref of hashrefs for substition_matrix");
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173 return undef;
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174 }
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175 }
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176 return $self->{'_substitution_matrix'};
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177 }
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178
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179 =head2 transition_probability_matrix
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180
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181 Title : transition_probability_matrix
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182 Usage : my $matrixref = $molphy->transition_probablity_matrix();
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183 Function: Gets the observed transition probability matrix
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184 Returns : hash of hashes of aa/nt transition to each other aa/nt
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185 Args : none
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186
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187
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188 =cut
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189
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190 sub transition_probability_matrix{
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191 my ($self,$val) = @_;
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192 if(defined $val ) {
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193 if( ref($val) =~ /HASH/ ) {
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194 foreach my $v (values %{$val} ) {
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195 if( ref($v) !~ /HASH/i ) {
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196 $self->warn("Must be a valid hashref of hashrefs for transition_probability_matrix");
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197 return undef;
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198 }
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199 }
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200 $self->{'_TPM'} = $val;
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201 } else {
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202 $self->warn("Must be a valid hashref of hashrefs for transition_probablity_matrix");
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203 return undef;
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204 }
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205 }
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206
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207 # fix this for nucml where there are 2 values (one is just a transformation
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208 # of the either, but how to represent?)
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209 return $self->{'_TPM'};
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210 }
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211
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212 =head2 residue_frequencies
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213
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214 Title : residue_frequencies
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215 Usage : my %data = $molphy->residue_frequencies()
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216 Function: Get the modeled and expected frequencies for
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217 each of the residues in the sequence
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218 Returns : hash of either aa (protml) or nt (nucml) frequencies
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219 each key will point to an array reference where
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220 1st slot is model's expected frequency
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221 2nd slot is observed frequency in the data
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222 $hash{'A'}->[0] =
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223 Args : none
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224
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225
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226 =cut
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227
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228 #'
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229
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230 sub residue_frequencies{
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231 my ($self,$val) = @_;
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232 if(defined $val ) {
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233 if( ref($val) =~ /HASH/ ) {
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234 $self->{'_residue_frequencies'} = $val;
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235 } else {
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236 $self->warn("Must be a valid hashref of hashrefs for residue_frequencies");
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237 }
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238 }
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239 return %{$self->{'_residue_frequencies'}};
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240 }
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241
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242 =head2 next_tree
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243
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244 Title : next_tree
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245 Usage : my $tree = $factory->next_tree;
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246 Function: Get the next tree from the factory
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247 Returns : L<Bio::Tree::TreeI>
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248 Args : none
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249
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250 =cut
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251
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252 sub next_tree{
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253 my ($self,@args) = @_;
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254 return $self->{'_trees'}->[$self->{'_treeiterator'}++] || undef;
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255 }
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256
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257 =head2 rewind_tree
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258
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259 Title : rewind_tree_iterator
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260 Usage : $result->rewind_tree()
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261 Function: Rewinds the tree iterator so that next_tree can be
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262 called again from the beginning
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263 Returns : none
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264 Args : none
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265
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266 =cut
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267
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268 sub rewind_tree_iterator {
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269 shift->{'_treeiterator'} = 0;
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270 }
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271
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272 =head2 add_tree
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273
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274 Title : add_tree
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275 Usage : $result->add_tree($tree);
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276 Function: Adds a tree
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277 Returns : integer which is the number of trees stored
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278 Args : L<Bio::Tree::TreeI>
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279
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280 =cut
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281
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282 sub add_tree{
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283 my ($self,$tree) = @_;
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284 if( $tree && ref($tree) && $tree->isa('Bio::Tree::TreeI') ) {
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285 push @{$self->{'_trees'}},$tree;
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286 }
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287 return scalar @{$self->{'_trees'}};
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288 }
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289
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290 =head2 search_space
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291
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292 Title : search_space
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293 Usage : $obj->search_space($newval)
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294 Function:
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295 Returns : value of search_space
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296 Args : newvalue (optional)
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297
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298
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299 =cut
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300
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301 sub search_space{
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302 my ($self,$value) = @_;
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303 if( defined $value) {
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304 $self->{'search_space'} = $value;
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305 }
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306 return $self->{'search_space'};
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307 }
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308
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309 1;
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