1 | // =============================================================== // |
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2 | // // |
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3 | // File : DI_matr.cxx // |
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4 | // Purpose : // |
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5 | // // |
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6 | // Institute of Microbiology (Technical University Munich) // |
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7 | // http://www.arb-home.de/ // |
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8 | // // |
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9 | // =============================================================== // |
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10 | |
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11 | #include "di_protdist.hxx" |
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12 | #include "di_clusters.hxx" |
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13 | #include "dist.hxx" |
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14 | #include "di_view_matrix.hxx" |
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15 | #include "di_awars.hxx" |
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16 | |
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17 | #include <neighbourjoin.hxx> |
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18 | #include <AP_seq_dna.hxx> |
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19 | #include <AP_filter.hxx> |
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20 | #include <BI_helix.hxx> |
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21 | #include <CT_ctree.hxx> |
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22 | #include <ColumnStat.hxx> |
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23 | |
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24 | #include <awt.hxx> |
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25 | #include <awt_sel_boxes.hxx> |
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26 | #include <awt_filter.hxx> |
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27 | |
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28 | #include <aw_preset.hxx> |
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29 | #include <aw_awars.hxx> |
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30 | #include <aw_file.hxx> |
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31 | #include <aw_msg.hxx> |
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32 | #include <aw_root.hxx> |
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33 | |
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34 | #include <gui_aliview.hxx> |
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35 | |
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36 | #include <climits> |
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37 | #include <ctime> |
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38 | #include <cmath> |
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39 | #include <arb_sort.h> |
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40 | #include <arb_global_defs.h> |
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41 | #include <macros.hxx> |
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42 | #include <ad_cb.h> |
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43 | #include <awt_TreeAwars.hxx> |
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44 | #include <arb_defs.h> |
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45 | |
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46 | // -------------------------------------------------------------------------------- |
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47 | |
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48 | #define AWAR_DIST_BOOTSTRAP_COUNT AWAR_DIST_PREFIX "bootstrap/count" |
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49 | #define AWAR_DIST_CANCEL_CHARS AWAR_DIST_PREFIX "cancel/chars" |
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50 | #define AWAR_DIST_MATRIX_AUTO_RECALC AWAR_DIST_PREFIX "recalc" |
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51 | |
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52 | #define AWAR_DIST_COLUMN_STAT_NAME AWAR_DIST_COLUMN_STAT_PREFIX "name" |
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53 | |
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54 | #define AWAR_DIST_TREE_SORT_NAME "tmp/" AWAR_DIST_TREE_PREFIX "sort_tree_name" |
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55 | #define AWAR_DIST_TREE_COMP_NAME "tmp/" AWAR_DIST_TREE_PREFIX "compr_tree_name" |
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56 | #define AWAR_DIST_TREE_STD_NAME AWAR_DIST_TREE_PREFIX "tree_name" |
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57 | #define AWAR_DIST_MATRIX_AUTO_CALC_TREE AWAR_DIST_TREE_PREFIX "autocalc" |
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58 | |
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59 | #define AWAR_DIST_SAVE_MATRIX_TYPE AWAR_DIST_SAVE_MATRIX_BASE "/type" |
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60 | #define AWAR_DIST_SAVE_MATRIX_FILENAME AWAR_DIST_SAVE_MATRIX_BASE "/file_name" |
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61 | |
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62 | // -------------------------------------------------------------------------------- |
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63 | |
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64 | DI_GLOBAL_MATRIX GLOBAL_MATRIX; |
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65 | |
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66 | static MatrixDisplay *matrixDisplay = 0; |
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67 | static AP_matrix DI_dna_matrix(AP_MAX); |
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68 | |
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69 | class BoundWindowCallback : virtual Noncopyable { |
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70 | AW_window *aww; |
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71 | WindowCallback cb; |
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72 | public: |
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73 | BoundWindowCallback(AW_window *aww_, const WindowCallback& cb_) |
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74 | : aww(aww_), |
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75 | cb(cb_) |
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76 | {} |
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77 | void operator()() { cb(aww); } |
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78 | }; |
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79 | |
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80 | static SmartPtr<BoundWindowCallback> recalculate_matrix_cb; |
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81 | static SmartPtr<BoundWindowCallback> recalculate_tree_cb; |
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82 | |
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83 | static GB_ERROR last_matrix_calculation_error = NULL; |
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84 | |
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85 | static void matrix_changed_cb() { |
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86 | if (matrixDisplay) { |
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87 | matrixDisplay->mark(MatrixDisplay::NEED_SETUP); |
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88 | matrixDisplay->update_display(); |
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89 | } |
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90 | } |
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91 | |
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92 | struct RecalcNeeded { |
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93 | bool matrix; |
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94 | bool tree; |
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95 | |
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96 | RecalcNeeded() : matrix(false), tree(false) { } |
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97 | }; |
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98 | |
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99 | static RecalcNeeded need_recalc; |
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100 | |
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101 | CONSTEXPR unsigned UPDATE_DELAY = 200; |
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102 | |
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103 | static unsigned update_cb(AW_root *aw_root); |
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104 | inline void add_update_cb() { |
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105 | AW_root::SINGLETON->add_timed_callback(UPDATE_DELAY, makeTimedCallback(update_cb)); |
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106 | } |
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107 | |
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108 | inline void matrix_needs_recalc_cb() { |
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109 | need_recalc.matrix = true; |
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110 | add_update_cb(); |
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111 | } |
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112 | inline void tree_needs_recalc_cb() { |
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113 | need_recalc.tree = true; |
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114 | add_update_cb(); |
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115 | } |
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116 | |
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117 | inline void compressed_matrix_needs_recalc_cb() { |
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118 | if (GLOBAL_MATRIX.has_type(DI_MATRIX_COMPRESSED)) { |
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119 | matrix_needs_recalc_cb(); |
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120 | } |
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121 | } |
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122 | |
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123 | static unsigned update_cb(AW_root *aw_root) { |
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124 | if (need_recalc.matrix) { |
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125 | GLOBAL_MATRIX.forget(); |
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126 | need_recalc.matrix = false; // because it's forgotten |
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127 | |
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128 | int matrix_autocalc = aw_root->awar(AWAR_DIST_MATRIX_AUTO_RECALC)->read_int(); |
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129 | if (matrix_autocalc) { |
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130 | bool recalc_now = true; |
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131 | int tree_autocalc = aw_root->awar(AWAR_DIST_MATRIX_AUTO_CALC_TREE)->read_int(); |
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132 | if (!tree_autocalc) recalc_now = matrixDisplay ? matrixDisplay->willShow() : false; |
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133 | |
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134 | if (recalc_now) { |
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135 | di_assert(recalculate_matrix_cb.isSet()); |
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136 | (*recalculate_matrix_cb)(); |
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137 | di_assert(need_recalc.tree == true); |
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138 | } |
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139 | } |
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140 | di_assert(need_recalc.matrix == false); |
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141 | } |
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142 | |
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143 | if (need_recalc.tree) { |
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144 | int tree_autocalc = aw_root->awar(AWAR_DIST_MATRIX_AUTO_CALC_TREE)->read_int(); |
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145 | if (tree_autocalc) { |
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146 | di_assert(recalculate_tree_cb.isSet()); |
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147 | (*recalculate_tree_cb)(); |
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148 | need_recalc.matrix = false; // otherwise endless loop, e.g. if output-tree is used for sorting |
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149 | } |
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150 | } |
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151 | |
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152 | return 0; // do not call again |
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153 | } |
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154 | |
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155 | static void auto_calc_changed_cb(AW_root *aw_root) { |
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156 | int matrix_autocalc = aw_root->awar(AWAR_DIST_MATRIX_AUTO_RECALC)->read_int(); |
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157 | int tree_autocalc = aw_root->awar(AWAR_DIST_MATRIX_AUTO_CALC_TREE)->read_int(); |
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158 | |
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159 | if (matrix_autocalc && !GLOBAL_MATRIX.exists()) matrix_needs_recalc_cb(); |
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160 | if (tree_autocalc && (matrix_autocalc || GLOBAL_MATRIX.exists())) tree_needs_recalc_cb(); |
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161 | } |
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162 | |
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163 | static AW_window *create_dna_matrix_window(AW_root *aw_root) { |
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164 | AW_window_simple *aws = new AW_window_simple; |
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165 | aws->init(aw_root, "SET_DNA_MATRIX", "SET MATRIX"); |
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166 | aws->auto_increment(50, 50); |
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167 | aws->button_length(10); |
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168 | aws->callback(AW_POPDOWN); |
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169 | aws->create_button("CLOSE", "CLOSE"); |
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170 | |
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171 | aws->callback(makeHelpCallback("user_matrix.hlp")); |
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172 | aws->create_button("HELP", "HELP"); |
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173 | |
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174 | aws->at_newline(); |
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175 | |
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176 | DI_dna_matrix.create_input_fields(aws, AWAR_DIST_MATRIX_DNA_BASE); |
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177 | aws->window_fit(); |
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178 | return aws; |
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179 | } |
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180 | |
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181 | static void selected_tree_changed_cb() { |
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182 | if (AW_root::SINGLETON->awar(AWAR_DIST_CORR_TRANS)->read_int() == DI_TRANSFORMATION_FROM_TREE) { |
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183 | matrix_needs_recalc_cb(); |
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184 | } |
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185 | } |
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186 | |
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187 | void DI_create_matrix_variables(AW_root *aw_root, AW_default def, AW_default db) { |
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188 | GB_transaction ta(db); |
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189 | DI_dna_matrix.set_descriptions(AP_A, "A"); |
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190 | DI_dna_matrix.set_descriptions(AP_C, "C"); |
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191 | DI_dna_matrix.set_descriptions(AP_G, "G"); |
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192 | DI_dna_matrix.set_descriptions(AP_T, "TU"); |
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193 | DI_dna_matrix.set_descriptions(AP_S, "GAP"); |
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194 | |
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195 | DI_dna_matrix.create_awars(aw_root, AWAR_DIST_MATRIX_DNA_BASE); |
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196 | |
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197 | RootCallback matrix_needs_recalc_callback = makeRootCallback(matrix_needs_recalc_cb); |
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198 | aw_root->awar_int(AWAR_DIST_MATRIX_DNA_ENABLED, 0)->add_callback(matrix_needs_recalc_callback); // user matrix disabled by default |
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199 | { |
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200 | GBDATA *gbd = GB_search(AW_ROOT_DEFAULT, AWAR_DIST_MATRIX_DNA_BASE, GB_FIND); |
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201 | GB_add_callback(gbd, GB_CB_CHANGED, makeDatabaseCallback(matrix_needs_recalc_cb)); |
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202 | } |
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203 | |
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204 | aw_root->awar_string(AWAR_DIST_WHICH_SPECIES, "marked", def)->add_callback(matrix_needs_recalc_callback); |
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205 | { |
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206 | char *default_ali = GBT_get_default_alignment(db); |
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207 | aw_root->awar_string(AWAR_DIST_ALIGNMENT, "", def)->add_callback(matrix_needs_recalc_callback)->write_string(default_ali); |
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208 | free(default_ali); |
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209 | } |
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210 | aw_root->awar_string(AWAR_DIST_FILTER_ALIGNMENT, "none", def); |
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211 | aw_root->awar_string(AWAR_DIST_FILTER_NAME, "none", def); |
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212 | aw_root->awar_string(AWAR_DIST_FILTER_FILTER, "", def)->add_callback(matrix_needs_recalc_callback); |
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213 | aw_root->awar_int (AWAR_DIST_FILTER_SIMPLIFY, 0, def)->add_callback(matrix_needs_recalc_callback); |
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214 | |
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215 | aw_root->awar_string(AWAR_DIST_CANCEL_CHARS, ".", def)->add_callback(matrix_needs_recalc_callback); |
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216 | aw_root->awar_int(AWAR_DIST_CORR_TRANS, (int)DI_TRANSFORMATION_SIMILARITY, def)->add_callback(matrix_needs_recalc_callback)->set_minmax(0, DI_TRANSFORMATION_COUNT-1); |
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217 | |
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218 | aw_root->awar(AWAR_DIST_FILTER_ALIGNMENT)->map(AWAR_DIST_ALIGNMENT); |
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219 | |
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220 | AW_create_fileselection_awars(aw_root, AWAR_DIST_SAVE_MATRIX_BASE, ".", "", "infile"); |
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221 | aw_root->awar_int(AWAR_DIST_SAVE_MATRIX_TYPE, 0, def); |
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222 | |
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223 | enum treetype { CURR, SORT, COMPRESS, TREEAWARCOUNT }; |
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224 | AW_awar *tree_awar[TREEAWARCOUNT] = { NULL, NULL, NULL }; |
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225 | |
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226 | aw_root->awar_string(AWAR_DIST_TREE_STD_NAME, "tree_nj", def); |
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227 | { |
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228 | char *currentTree = aw_root->awar_string(AWAR_TREE, "", db)->read_string(); |
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229 | tree_awar[CURR] = aw_root->awar_string(AWAR_DIST_TREE_CURR_NAME, currentTree, def); |
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230 | tree_awar[SORT] = aw_root->awar_string(AWAR_DIST_TREE_SORT_NAME, currentTree, def); |
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231 | free(currentTree); |
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232 | } |
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233 | tree_awar[COMPRESS] = aw_root->awar_string(AWAR_DIST_TREE_COMP_NAME, NO_TREE_SELECTED, def); |
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234 | |
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235 | aw_root->awar_int(AWAR_DIST_BOOTSTRAP_COUNT, 1000, def); |
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236 | aw_root->awar_int(AWAR_DIST_MATRIX_AUTO_RECALC, 0, def)->add_callback(auto_calc_changed_cb); |
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237 | aw_root->awar_int(AWAR_DIST_MATRIX_AUTO_CALC_TREE, 0, def)->add_callback(auto_calc_changed_cb); |
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238 | |
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239 | aw_root->awar_float(AWAR_DIST_MIN_DIST, 0.0); |
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240 | aw_root->awar_float(AWAR_DIST_MAX_DIST, 0.0); |
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241 | |
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242 | aw_root->awar_string(AWAR_SPECIES_NAME, "", db); |
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243 | |
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244 | DI_create_cluster_awars(aw_root, def, db); |
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245 | |
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246 | #if defined(DEBUG) |
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247 | AWT_create_db_browser_awars(aw_root, def); |
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248 | #endif // DEBUG |
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249 | |
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250 | { |
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251 | GB_push_transaction(db); |
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252 | |
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253 | GBDATA *gb_species_data = GBT_get_species_data(db); |
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254 | GB_add_callback(gb_species_data, GB_CB_CHANGED, makeDatabaseCallback(matrix_needs_recalc_cb)); |
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255 | |
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256 | GB_pop_transaction(db); |
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257 | } |
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258 | |
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259 | AWT_registerTreeAwarCallback(tree_awar[CURR], makeTreeAwarCallback(selected_tree_changed_cb), true); |
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260 | AWT_registerTreeAwarCallback(tree_awar[SORT], makeTreeAwarCallback(matrix_needs_recalc_cb), true); |
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261 | AWT_registerTreeAwarCallback(tree_awar[COMPRESS], makeTreeAwarCallback(compressed_matrix_needs_recalc_cb), true); |
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262 | |
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263 | auto_calc_changed_cb(aw_root); |
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264 | } |
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265 | |
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266 | DI_ENTRY::DI_ENTRY(GBDATA *gbd, DI_MATRIX *phmatri) { |
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267 | memset((char *)this, 0, sizeof(DI_ENTRY)); |
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268 | phmatrix = phmatri; |
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269 | |
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270 | GBDATA *gb_ali = GB_entry(gbd, phmatrix->get_aliname()); |
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271 | if (gb_ali) { |
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272 | GBDATA *gb_data = GB_entry(gb_ali, "data"); |
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273 | if (gb_data) { |
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274 | if (phmatrix->is_AA) { |
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275 | sequence = sequence_protein = new AP_sequence_simple_protein(phmatrix->get_aliview()); |
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276 | } |
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277 | else { |
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278 | sequence = sequence_parsimony = new AP_sequence_parsimony(phmatrix->get_aliview()); |
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279 | } |
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280 | sequence->bind_to_species(gbd); |
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281 | sequence->lazy_load_sequence(); // load sequence |
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282 | |
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283 | name = GBT_read_string(gbd, "name"); |
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284 | full_name = GBT_read_string(gbd, "full_name"); |
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285 | } |
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286 | } |
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287 | } |
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288 | |
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289 | DI_ENTRY::DI_ENTRY(char *namei, DI_MATRIX *phmatri) |
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290 | { |
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291 | memset((char *)this, 0, sizeof(DI_ENTRY)); |
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292 | phmatrix = phmatri; |
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293 | this->name = strdup(namei); |
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294 | } |
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295 | |
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296 | DI_ENTRY::~DI_ENTRY() |
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297 | { |
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298 | delete sequence_protein; |
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299 | delete sequence_parsimony; |
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300 | free(name); |
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301 | free(full_name); |
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302 | |
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303 | } |
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304 | |
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305 | DI_MATRIX::DI_MATRIX(const AliView& aliview_, AW_root *awr) { |
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306 | memset((char *)this, 0, sizeof(*this)); |
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307 | aw_root = awr; |
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308 | aliview = new AliView(aliview_); |
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309 | } |
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310 | |
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311 | char *DI_MATRIX::unload() { |
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312 | for (size_t i=0; i<nentries; i++) { |
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313 | delete entries[i]; |
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314 | } |
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315 | freenull(entries); |
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316 | nentries = 0; |
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317 | return 0; |
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318 | } |
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319 | |
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320 | DI_MATRIX::~DI_MATRIX() |
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321 | { |
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322 | unload(); |
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323 | delete matrix; |
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324 | delete aliview; |
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325 | } |
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326 | |
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327 | struct TreeOrderedSpecies { |
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328 | GBDATA *gbd; |
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329 | int order_index; |
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330 | |
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331 | TreeOrderedSpecies(const MatrixOrder& order, GBDATA *gb_spec) |
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332 | : gbd(gb_spec), |
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333 | order_index(order.get_index(GBT_read_name(gbd))) |
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334 | {} |
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335 | }; |
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336 | |
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337 | MatrixOrder::MatrixOrder(GBDATA *gb_main, GB_CSTR sort_tree_name) |
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338 | : name2pos(NULL), |
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339 | leafs(0) |
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340 | { |
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341 | if (sort_tree_name) { |
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342 | int size; |
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343 | GBT_TREE *sort_tree = GBT_read_tree_and_size(gb_main, sort_tree_name, GBT_TREE_NodeFactory(), &size); |
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344 | |
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345 | if (sort_tree) { |
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346 | leafs = size+1; |
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347 | name2pos = GBS_create_hash(leafs, GB_IGNORE_CASE); |
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348 | |
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349 | IF_ASSERTION_USED(int leafsLoaded = leafs); |
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350 | leafs = 0; |
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351 | insert_in_hash(sort_tree); |
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352 | |
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353 | arb_assert(leafsLoaded == leafs); |
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354 | } |
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355 | else { |
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356 | GB_clear_error(); |
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357 | } |
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358 | } |
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359 | } |
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360 | static int TreeOrderedSpecies_cmp(const void *p1, const void *p2, void *) { |
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361 | TreeOrderedSpecies *s1 = (TreeOrderedSpecies*)p1; |
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362 | TreeOrderedSpecies *s2 = (TreeOrderedSpecies*)p2; |
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363 | |
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364 | return s2->order_index - s1->order_index; |
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365 | } |
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366 | |
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367 | void MatrixOrder::applyTo(TreeOrderedSpecies **species_array, size_t array_size) const { |
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368 | GB_sort((void**)species_array, 0, array_size, TreeOrderedSpecies_cmp, NULL); |
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369 | } |
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370 | |
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371 | GB_ERROR DI_MATRIX::load(LoadWhat what, const MatrixOrder& order, bool show_warnings, GBDATA **species_list) { |
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372 | GBDATA *gb_main = get_gb_main(); |
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373 | const char *use = get_aliname(); |
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374 | |
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375 | GB_transaction ta(gb_main); |
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376 | |
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377 | seq_len = GBT_get_alignment_len(gb_main, use); |
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378 | is_AA = GBT_is_alignment_protein(gb_main, use); |
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379 | gb_species_data = GBT_get_species_data(gb_main); |
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380 | entries_mem_size = 1000; |
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381 | |
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382 | entries = (DI_ENTRY **)calloc(sizeof(DI_ENTRY*), entries_mem_size); |
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383 | |
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384 | nentries = 0; |
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385 | |
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386 | size_t no_of_species = -1U; |
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387 | switch (what) { |
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388 | case DI_LOAD_ALL: |
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389 | no_of_species = GBT_get_species_count(gb_main); |
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390 | break; |
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391 | case DI_LOAD_MARKED: |
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392 | no_of_species = GBT_count_marked_species(gb_main); |
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393 | break; |
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394 | case DI_LOAD_LIST: |
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395 | di_assert(species_list); |
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396 | for (no_of_species = 0; species_list[no_of_species]; ++no_of_species) ; |
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397 | break; |
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398 | } |
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399 | |
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400 | di_assert(no_of_species != -1U); |
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401 | if (no_of_species<2) { |
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402 | return GBS_global_string("Not enough input species (%zu)", no_of_species); |
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403 | } |
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404 | |
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405 | TreeOrderedSpecies *species_to_load[no_of_species]; |
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406 | |
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407 | { |
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408 | size_t i = 0; |
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409 | switch (what) { |
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410 | case DI_LOAD_ALL: { |
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411 | for (GBDATA *gb_species = GBT_first_species_rel_species_data(gb_species_data); gb_species; gb_species = GBT_next_species(gb_species), ++i) { |
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412 | species_to_load[i] = new TreeOrderedSpecies(order, gb_species); |
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413 | } |
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414 | break; |
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415 | } |
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416 | case DI_LOAD_MARKED: { |
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417 | for (GBDATA *gb_species = GBT_first_marked_species_rel_species_data(gb_species_data); gb_species; gb_species = GBT_next_marked_species(gb_species), ++i) { |
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418 | species_to_load[i] = new TreeOrderedSpecies(order, gb_species); |
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419 | } |
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420 | break; |
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421 | } |
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422 | case DI_LOAD_LIST: { |
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423 | for (i = 0; species_list[i]; ++i) { |
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424 | species_to_load[i] = new TreeOrderedSpecies(order, species_list[i]); |
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425 | } |
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426 | break; |
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427 | } |
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428 | } |
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429 | arb_assert(i == no_of_species); |
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430 | } |
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431 | |
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432 | if (order.defined()) { |
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433 | order.applyTo(species_to_load, no_of_species); |
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434 | if (show_warnings) { |
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435 | int species_not_in_sort_tree = 0; |
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436 | for (size_t i = 0; i<no_of_species; ++i) { |
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437 | if (!species_to_load[i]->order_index) { |
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438 | species_not_in_sort_tree++; |
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439 | } |
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440 | } |
---|
441 | if (species_not_in_sort_tree) { |
---|
442 | aw_message(GBS_global_string("Warning: %i of the affected species are not in sort-tree", species_not_in_sort_tree)); |
---|
443 | } |
---|
444 | } |
---|
445 | } |
---|
446 | else { |
---|
447 | if (show_warnings) { |
---|
448 | static bool shown = false; |
---|
449 | if (!shown) { // showing once is enough |
---|
450 | aw_message("Warning: No valid tree given to sort matrix (using default database order)"); |
---|
451 | shown = true; |
---|
452 | } |
---|
453 | } |
---|
454 | } |
---|
455 | |
---|
456 | if (no_of_species>entries_mem_size) { |
---|
457 | entries_mem_size = no_of_species; |
---|
458 | realloc_unleaked(entries, sizeof(DI_ENTRY*)*entries_mem_size); |
---|
459 | if (!entries) return "out of memory"; |
---|
460 | } |
---|
461 | |
---|
462 | GB_ERROR error = NULL; |
---|
463 | arb_progress progress("Preparing sequence data", no_of_species); |
---|
464 | for (size_t i = 0; i<no_of_species && !error; ++i) { |
---|
465 | DI_ENTRY *phentry = new DI_ENTRY(species_to_load[i]->gbd, this); |
---|
466 | if (phentry->sequence) { // a species found |
---|
467 | arb_assert(nentries<entries_mem_size); |
---|
468 | entries[nentries++] = phentry; |
---|
469 | } |
---|
470 | else { |
---|
471 | delete phentry; |
---|
472 | } |
---|
473 | delete species_to_load[i]; |
---|
474 | species_to_load[i] = NULL; |
---|
475 | |
---|
476 | progress.inc_and_check_user_abort(error); |
---|
477 | } |
---|
478 | |
---|
479 | return error; |
---|
480 | } |
---|
481 | |
---|
482 | void DI_MATRIX::clear(DI_MUT_MATR &hits) |
---|
483 | { |
---|
484 | int i, j; |
---|
485 | for (i=0; i<AP_MAX; i++) { |
---|
486 | for (j=0; j<AP_MAX; j++) { |
---|
487 | hits[i][j] = 0; |
---|
488 | } |
---|
489 | } |
---|
490 | } |
---|
491 | |
---|
492 | void DI_MATRIX::make_sym(DI_MUT_MATR &hits) |
---|
493 | { |
---|
494 | int i, j; |
---|
495 | for (i=AP_A; i<AP_MAX; i*=2) { |
---|
496 | for (j=AP_A; j<=i; j*=2) { |
---|
497 | hits[i][j] = hits[j][i] = hits[i][j] + hits[j][i]; |
---|
498 | } |
---|
499 | } |
---|
500 | } |
---|
501 | |
---|
502 | void DI_MATRIX::rate_write(DI_MUT_MATR &hits, FILE *out) { |
---|
503 | int i, j; |
---|
504 | for (i=AP_A; i<AP_MAX; i*=2) { |
---|
505 | for (j=AP_A; j<AP_MAX; j*=2) { |
---|
506 | fprintf(out, "%5li ", hits[i][j]); |
---|
507 | } |
---|
508 | fprintf(out, "\n"); |
---|
509 | } |
---|
510 | } |
---|
511 | |
---|
512 | long *DI_MATRIX::create_helix_filter(BI_helix *helix, const AP_filter *filter) { |
---|
513 | long *result = (long *)calloc(sizeof(long), filter->get_filtered_length()); |
---|
514 | long *temp = (long *)calloc(sizeof(long), filter->get_filtered_length()); |
---|
515 | int count = 0; |
---|
516 | size_t i; |
---|
517 | |
---|
518 | for (i=0; i<filter->get_length(); i++) { |
---|
519 | if (filter->use_position(i)) { |
---|
520 | temp[i] = count; |
---|
521 | if (helix->pairtype(i) == HELIX_PAIR) { |
---|
522 | result[count] = helix->opposite_position(i); |
---|
523 | } |
---|
524 | else { |
---|
525 | result[count] = -1; |
---|
526 | } |
---|
527 | count++; |
---|
528 | } |
---|
529 | } |
---|
530 | while (--count >= 0) { |
---|
531 | if (result[count] >= 0) { |
---|
532 | result[count] = temp[result[count]]; |
---|
533 | } |
---|
534 | } |
---|
535 | free(temp); |
---|
536 | return result; |
---|
537 | } |
---|
538 | |
---|
539 | GB_ERROR DI_MATRIX::calculate_rates(DI_MUT_MATR &hrates, DI_MUT_MATR &nrates, DI_MUT_MATR &pairs, long *filter) { |
---|
540 | if (nentries<=1) { |
---|
541 | return "Not enough species selected to calculate rates"; |
---|
542 | } |
---|
543 | |
---|
544 | arb_progress progress("rates", matrix_halfsize(nentries, false)); |
---|
545 | GB_ERROR error = NULL; |
---|
546 | |
---|
547 | long s_len = aliview->get_length(); |
---|
548 | |
---|
549 | this->clear(hrates); |
---|
550 | this->clear(nrates); |
---|
551 | this->clear(pairs); |
---|
552 | |
---|
553 | for (size_t row = 0; row<nentries && !error; row++) { |
---|
554 | for (size_t col=0; col<row; col++) { |
---|
555 | const unsigned char *seq1 = entries[row]->sequence_parsimony->get_usequence(); |
---|
556 | const unsigned char *seq2 = entries[col]->sequence_parsimony->get_usequence(); |
---|
557 | for (long pos = 0; pos < s_len; pos++) { |
---|
558 | if (filter[pos]>=0) { |
---|
559 | hrates[*seq1][*seq2]++; |
---|
560 | } |
---|
561 | else { |
---|
562 | nrates[*seq1][*seq2]++; |
---|
563 | } |
---|
564 | seq1++; seq2++; |
---|
565 | } |
---|
566 | progress.inc_and_check_user_abort(error); |
---|
567 | } |
---|
568 | } |
---|
569 | for (size_t row = 0; row<nentries; row++) { |
---|
570 | const unsigned char *seq1 = entries[row]->sequence_parsimony->get_usequence(); |
---|
571 | for (long pos = 0; pos < s_len; pos++) { |
---|
572 | if (filter[pos]>=0) { |
---|
573 | pairs[seq1[pos]][seq1[filter[pos]]]++; |
---|
574 | } |
---|
575 | } |
---|
576 | } |
---|
577 | progress.done(); |
---|
578 | return error; |
---|
579 | } |
---|
580 | |
---|
581 | // ---------------------------------------------------------------- |
---|
582 | // Some test functions to check correlated base correction |
---|
583 | |
---|
584 | GB_ERROR DI_MATRIX::haeschoe(const char *path) { |
---|
585 | static BI_helix *helix = 0; |
---|
586 | if (!helix) helix = new BI_helix; |
---|
587 | |
---|
588 | GB_ERROR error = helix->init(get_gb_main()); |
---|
589 | if (!error) { |
---|
590 | FILE *out = fopen(path, "w"); |
---|
591 | if (!out) { |
---|
592 | GB_export_IO_error("writing", path); |
---|
593 | error = GB_await_error(); |
---|
594 | } |
---|
595 | else { |
---|
596 | arb_progress progress("Calculating distance matrix"); |
---|
597 | |
---|
598 | fprintf(out, "Pairs in helical regions:\n"); |
---|
599 | long *filter = create_helix_filter(helix, aliview->get_filter()); |
---|
600 | |
---|
601 | DI_MUT_MATR temp, temp2, pairs; |
---|
602 | error = calculate_rates(temp, temp2, pairs, filter); |
---|
603 | if (!error) { |
---|
604 | rate_write(pairs, out); |
---|
605 | make_sym(temp); make_sym(temp2); |
---|
606 | fprintf(out, "\nRatematrix helical parts:\n"); |
---|
607 | rate_write(temp, out); |
---|
608 | fprintf(out, "\nRatematrix non helical parts:\n"); |
---|
609 | rate_write(temp2, out); |
---|
610 | |
---|
611 | long pos; |
---|
612 | long s_len; |
---|
613 | |
---|
614 | s_len = aliview->get_length(); |
---|
615 | fprintf(out, "\nDistance matrix (Helixdist Helixlen Nonhelixdist Nonhelixlen):"); |
---|
616 | fprintf(out, "\n%zu", nentries); |
---|
617 | |
---|
618 | const int MAXDISTDEBUG = 1000; |
---|
619 | double distdebug[MAXDISTDEBUG]; |
---|
620 | |
---|
621 | for (pos = 0; pos<MAXDISTDEBUG; pos++) distdebug[pos] = 0.0; |
---|
622 | |
---|
623 | arb_progress dist_progress("distance", matrix_halfsize(nentries, false)); |
---|
624 | for (size_t row = 0; row<nentries && !error; row++) { |
---|
625 | fprintf (out, "\n%s ", entries[row]->name); |
---|
626 | |
---|
627 | for (size_t col=0; col<row && !error; col++) { |
---|
628 | const unsigned char *seq1, *seq2; |
---|
629 | |
---|
630 | seq1 = entries[row]->sequence_parsimony->get_usequence(); |
---|
631 | seq2 = entries[col]->sequence_parsimony->get_usequence(); |
---|
632 | this->clear(temp); |
---|
633 | this->clear(temp2); |
---|
634 | |
---|
635 | for (pos = 0; pos < s_len; pos++) { |
---|
636 | if (filter[pos]>=0) temp [*seq1][*seq2]++; |
---|
637 | else temp2[*seq1][*seq2]++; |
---|
638 | seq1++; seq2++; |
---|
639 | } |
---|
640 | long hdist = 0, hall2 = 0; |
---|
641 | int i, j; |
---|
642 | for (i=AP_A; i<AP_MAX; i*=2) { |
---|
643 | for (j=AP_A; j<AP_MAX; j*=2) { |
---|
644 | hall2 += temp[i][j]; |
---|
645 | if (i!=j) hdist += temp[i][j]; |
---|
646 | } |
---|
647 | } |
---|
648 | |
---|
649 | long dist = 0, all = 0; |
---|
650 | for (i=AP_A; i<=AP_T; i*=2) { |
---|
651 | for (j=AP_A; j<=AP_T; j*=2) { |
---|
652 | all += temp2[i][j]; |
---|
653 | if (i!=j) dist += temp2[i][j]; |
---|
654 | } |
---|
655 | } |
---|
656 | fprintf(out, "(%4li:%4li %4li:%4li) ", hdist, hall2, dist, all); |
---|
657 | if (all>100) { |
---|
658 | distdebug[dist*MAXDISTDEBUG/all] = (double)hdist/(double)hall2; |
---|
659 | } |
---|
660 | dist_progress.inc_and_check_user_abort(error); |
---|
661 | } |
---|
662 | } |
---|
663 | |
---|
664 | if (!error) { |
---|
665 | fprintf (out, "\n"); |
---|
666 | fprintf (out, "\nhdist/dist:\n"); |
---|
667 | |
---|
668 | for (pos = 1; pos<MAXDISTDEBUG; pos++) { |
---|
669 | if (distdebug[pos]) { |
---|
670 | fprintf(out, "%4f %5f\n", (double)pos/(double)MAXDISTDEBUG, distdebug[pos]/(double)pos*(double)MAXDISTDEBUG); |
---|
671 | } |
---|
672 | } |
---|
673 | } |
---|
674 | } |
---|
675 | |
---|
676 | fclose(out); |
---|
677 | } |
---|
678 | } |
---|
679 | return error; |
---|
680 | } |
---|
681 | |
---|
682 | char *DI_MATRIX::calculate_overall_freqs(double rel_frequencies[AP_MAX], char *cancel) |
---|
683 | { |
---|
684 | long hits2[AP_MAX]; |
---|
685 | long sum = 0; |
---|
686 | int i; |
---|
687 | int pos; |
---|
688 | int b; |
---|
689 | long s_len = aliview->get_length(); |
---|
690 | |
---|
691 | memset((char *) &hits2[0], 0, sizeof(hits2)); |
---|
692 | for (size_t row = 0; row < nentries; row++) { |
---|
693 | const char *seq1 = entries[row]->sequence_parsimony->get_sequence(); |
---|
694 | for (pos = 0; pos < s_len; pos++) { |
---|
695 | b = *(seq1++); |
---|
696 | if (cancel[b]) continue; |
---|
697 | hits2[b]++; |
---|
698 | } |
---|
699 | } |
---|
700 | for (i = 0; i < AP_MAX; i++) sum += hits2[i]; |
---|
701 | for (i = 0; i < AP_MAX; i++) rel_frequencies[i] = hits2[i] / (double) sum; |
---|
702 | return 0; |
---|
703 | } |
---|
704 | |
---|
705 | double DI_MATRIX::corr(double dist, double b, double & sigma) { |
---|
706 | const double eps = 0.01; |
---|
707 | double ar = 1.0 - dist/b; |
---|
708 | sigma = 1000.0; |
---|
709 | if (ar< eps) return 3.0; |
---|
710 | sigma = b/ar; |
---|
711 | return - b * log(1-dist/b); |
---|
712 | } |
---|
713 | |
---|
714 | GB_ERROR DI_MATRIX::calculate(AW_root *awr, char *cancel, double /* alpha */, DI_TRANSFORMATION transformation, bool *aborted_flag) |
---|
715 | { |
---|
716 | if (transformation == DI_TRANSFORMATION_HAESCH) { |
---|
717 | GB_ERROR error = haeschoe("outfile"); |
---|
718 | if (error) return error; |
---|
719 | return "Your matrices have been written to 'outfile'\nSorry I can not make a tree"; |
---|
720 | } |
---|
721 | int user_matrix_enabled = awr->awar(AWAR_DIST_MATRIX_DNA_ENABLED)->read_int(); |
---|
722 | if (user_matrix_enabled) { // set transformation Matrix |
---|
723 | switch (transformation) { |
---|
724 | case DI_TRANSFORMATION_NONE: |
---|
725 | case DI_TRANSFORMATION_SIMILARITY: |
---|
726 | case DI_TRANSFORMATION_JUKES_CANTOR: |
---|
727 | break; |
---|
728 | default: |
---|
729 | aw_message("Sorry not implemented:\n" |
---|
730 | " This kind of distance correction does not support\n" |
---|
731 | " a user defined matrix - it will be ignored"); |
---|
732 | user_matrix_enabled = false; |
---|
733 | break; |
---|
734 | } |
---|
735 | DI_dna_matrix.read_awars(awr, AWAR_DIST_MATRIX_DNA_BASE); |
---|
736 | DI_dna_matrix.normize(); |
---|
737 | } |
---|
738 | |
---|
739 | |
---|
740 | |
---|
741 | matrix = new AP_smatrix(nentries); |
---|
742 | |
---|
743 | long s_len = aliview->get_length(); |
---|
744 | long hits[AP_MAX][AP_MAX]; |
---|
745 | size_t i; |
---|
746 | |
---|
747 | if (nentries<=1) { |
---|
748 | return "Not enough species selected to calculate matrix"; |
---|
749 | } |
---|
750 | memset(&cancel_columns[0], 0, 256); |
---|
751 | |
---|
752 | for (i=0; i<strlen(cancel); i++) { |
---|
753 | int j = cancel[i]; |
---|
754 | j = AP_sequence_parsimony::table[j]; |
---|
755 | cancel_columns[j] = 1; |
---|
756 | } |
---|
757 | long columns; |
---|
758 | double b; |
---|
759 | long frequencies[AP_MAX]; |
---|
760 | double rel_frequencies[AP_MAX]; |
---|
761 | double S_square=0; |
---|
762 | |
---|
763 | switch (transformation) { |
---|
764 | case DI_TRANSFORMATION_FELSENSTEIN: |
---|
765 | this->calculate_overall_freqs(rel_frequencies, cancel_columns); |
---|
766 | S_square = 0.0; |
---|
767 | for (i=0; i<AP_MAX; i++) S_square += rel_frequencies[i]*rel_frequencies[i]; |
---|
768 | break; |
---|
769 | default: break; |
---|
770 | }; |
---|
771 | |
---|
772 | arb_progress progress("Calculating distance matrix", matrix_halfsize(nentries, true)); |
---|
773 | GB_ERROR error = NULL; |
---|
774 | for (size_t row = 0; row<nentries && !error; row++) { |
---|
775 | for (size_t col=0; col<=row && !error; col++) { |
---|
776 | columns = 0; |
---|
777 | |
---|
778 | const unsigned char *seq1 = entries[row]->sequence_parsimony->get_usequence(); |
---|
779 | const unsigned char *seq2 = entries[col]->sequence_parsimony->get_usequence(); |
---|
780 | |
---|
781 | b = 0.0; |
---|
782 | switch (transformation) { |
---|
783 | case DI_TRANSFORMATION_FROM_TREE: |
---|
784 | di_assert(0); |
---|
785 | break; |
---|
786 | case DI_TRANSFORMATION_JUKES_CANTOR: |
---|
787 | b = 0.75; |
---|
788 | // fall-through |
---|
789 | case DI_TRANSFORMATION_NONE: |
---|
790 | case DI_TRANSFORMATION_SIMILARITY: { |
---|
791 | double dist = 0.0; |
---|
792 | if (user_matrix_enabled) { |
---|
793 | memset((char *)hits, 0, sizeof(long) * AP_MAX * AP_MAX); |
---|
794 | int pos; |
---|
795 | for (pos = s_len; pos >= 0; pos--) { |
---|
796 | hits[*(seq1++)][*(seq2++)]++; |
---|
797 | } |
---|
798 | int x, y; |
---|
799 | double diffsum = 0.0; |
---|
800 | double all_sum = 0.001; |
---|
801 | for (x = AP_A; x < AP_MAX; x*=2) { |
---|
802 | for (y = AP_A; y < AP_MAX; y*=2) { |
---|
803 | if (x==y) { |
---|
804 | all_sum += hits[x][y]; |
---|
805 | } |
---|
806 | else { |
---|
807 | diffsum += hits[x][y] * DI_dna_matrix.get(x, y); |
---|
808 | all_sum += hits[x][y] * DI_dna_matrix.get(x, y); |
---|
809 | } |
---|
810 | } |
---|
811 | } |
---|
812 | dist = diffsum / all_sum; |
---|
813 | } |
---|
814 | else { |
---|
815 | for (int pos = s_len; pos >= 0; pos--) { |
---|
816 | int b1 = *(seq1++); |
---|
817 | int b2 = *(seq2++); |
---|
818 | if (cancel_columns[b1]) continue; |
---|
819 | if (cancel_columns[b2]) continue; |
---|
820 | columns++; |
---|
821 | if (b1&b2) continue; |
---|
822 | dist+=1.0; |
---|
823 | } |
---|
824 | if (columns == 0) columns = 1; |
---|
825 | dist /= columns; |
---|
826 | } |
---|
827 | if (transformation==DI_TRANSFORMATION_SIMILARITY) { |
---|
828 | dist = (1.0-dist); |
---|
829 | } |
---|
830 | else if (b) { |
---|
831 | double sigma; |
---|
832 | dist = this->corr(dist, b, sigma); |
---|
833 | } |
---|
834 | matrix->set(row, col, dist); |
---|
835 | break; |
---|
836 | } |
---|
837 | case DI_TRANSFORMATION_KIMURA: |
---|
838 | case DI_TRANSFORMATION_OLSEN: |
---|
839 | case DI_TRANSFORMATION_FELSENSTEIN: { |
---|
840 | int pos; |
---|
841 | double dist = 0.0; |
---|
842 | long N, P, Q, M; |
---|
843 | double p, q; |
---|
844 | |
---|
845 | memset((char *)hits, 0, sizeof(long) * AP_MAX * AP_MAX); |
---|
846 | for (pos = s_len; pos >= 0; pos--) { |
---|
847 | hits[*(seq1++)][*(seq2++)]++; |
---|
848 | } |
---|
849 | switch (transformation) { |
---|
850 | case DI_TRANSFORMATION_KIMURA: |
---|
851 | P = hits[AP_A][AP_G] + |
---|
852 | hits[AP_G][AP_A] + |
---|
853 | hits[AP_C][AP_T] + |
---|
854 | hits[AP_T][AP_C]; |
---|
855 | Q = hits[AP_A][AP_C] + |
---|
856 | hits[AP_A][AP_T] + |
---|
857 | hits[AP_C][AP_A] + |
---|
858 | hits[AP_T][AP_A] + |
---|
859 | hits[AP_G][AP_C] + |
---|
860 | hits[AP_G][AP_T] + |
---|
861 | hits[AP_C][AP_G] + |
---|
862 | hits[AP_T][AP_G]; |
---|
863 | M = hits[AP_A][AP_A] + |
---|
864 | hits[AP_C][AP_C] + |
---|
865 | hits[AP_G][AP_G] + |
---|
866 | hits[AP_T][AP_T]; |
---|
867 | N = P+Q+M; |
---|
868 | if (N==0) N=1; |
---|
869 | p = (double)P/(double)N; |
---|
870 | q = (double)Q/(double)N; |
---|
871 | dist = - .5 * log( |
---|
872 | (1.0-2.0*p-q)*sqrt(1.0-2.0*q) |
---|
873 | ); |
---|
874 | break; |
---|
875 | |
---|
876 | case DI_TRANSFORMATION_OLSEN: |
---|
877 | case DI_TRANSFORMATION_FELSENSTEIN: |
---|
878 | |
---|
879 | memset((char *)frequencies, 0, |
---|
880 | sizeof(long) * AP_MAX); |
---|
881 | |
---|
882 | N = 0; |
---|
883 | M = 0; |
---|
884 | |
---|
885 | for (i=0; i<AP_MAX; i++) { |
---|
886 | if (cancel_columns[i]) continue; |
---|
887 | unsigned int j; |
---|
888 | for (j=0; j<i; j++) { |
---|
889 | if (cancel_columns[j]) continue; |
---|
890 | frequencies[i] += |
---|
891 | hits[i][j]+ |
---|
892 | hits[j][i]; |
---|
893 | } |
---|
894 | frequencies[i] += hits[i][i]; |
---|
895 | N += frequencies[i]; |
---|
896 | M += hits[i][i]; |
---|
897 | } |
---|
898 | if (N==0) N=1; |
---|
899 | if (transformation == DI_TRANSFORMATION_OLSEN) { // Calc sum square freq individually for each line |
---|
900 | S_square = 0.0; |
---|
901 | for (i=0; i<AP_MAX; i++) S_square += frequencies[i]*frequencies[i]; |
---|
902 | b = 1.0 - S_square/((double)N*(double)N); |
---|
903 | } |
---|
904 | else { |
---|
905 | b = 1.0 - S_square; |
---|
906 | } |
---|
907 | |
---|
908 | dist = ((double)(N-M)) / (double) N; |
---|
909 | double sigma; |
---|
910 | dist = this->corr(dist, b, sigma); |
---|
911 | break; |
---|
912 | |
---|
913 | default: return "Sorry: Transformation not implemented"; |
---|
914 | } |
---|
915 | matrix->set(row, col, dist); |
---|
916 | break; |
---|
917 | } |
---|
918 | default:; |
---|
919 | } // switch |
---|
920 | progress.inc_and_check_user_abort(error); |
---|
921 | } |
---|
922 | } |
---|
923 | if (aborted_flag && progress.aborted()) *aborted_flag = true; |
---|
924 | return error; |
---|
925 | } |
---|
926 | |
---|
927 | GB_ERROR DI_MATRIX::calculate_pro(DI_TRANSFORMATION transformation, bool *aborted_flag) { |
---|
928 | di_cattype whichcat; |
---|
929 | di_codetype whichcode = UNIVERSAL; |
---|
930 | |
---|
931 | switch (transformation) { |
---|
932 | case DI_TRANSFORMATION_NONE: whichcat = NONE; break; |
---|
933 | case DI_TRANSFORMATION_SIMILARITY: whichcat = SIMILARITY; break; |
---|
934 | case DI_TRANSFORMATION_KIMURA: whichcat = KIMURA; break; |
---|
935 | case DI_TRANSFORMATION_PAM: whichcat = PAM; break; |
---|
936 | case DI_TRANSFORMATION_CATEGORIES_HALL: whichcat = HALL; break; |
---|
937 | case DI_TRANSFORMATION_CATEGORIES_BARKER: whichcat = GEORGE; break; |
---|
938 | case DI_TRANSFORMATION_CATEGORIES_CHEMICAL: whichcat = CHEMICAL; break; |
---|
939 | default: |
---|
940 | return "This correction is not available for protein data"; |
---|
941 | } |
---|
942 | matrix = new AP_smatrix(nentries); |
---|
943 | |
---|
944 | di_protdist prodist(whichcode, whichcat, nentries, entries, aliview->get_length(), matrix); |
---|
945 | return prodist.makedists(aborted_flag); |
---|
946 | } |
---|
947 | |
---|
948 | struct lessCCP { bool operator()(const char *s1, const char *s2) const { return strcmp(s1, s2)<0; } }; |
---|
949 | typedef std::map<const char*, GBT_TREE*, lessCCP> NamedNodes; |
---|
950 | |
---|
951 | GB_ERROR link_to_tree(NamedNodes& named, GBT_TREE *node) { |
---|
952 | GB_ERROR error = NULL; |
---|
953 | if (node->is_leaf) { |
---|
954 | NamedNodes::iterator found = named.find(node->name); |
---|
955 | if (found != named.end()) { |
---|
956 | if (found->second) { |
---|
957 | error = GBS_global_string("Invalid tree (two nodes named '%s')", node->name); |
---|
958 | } |
---|
959 | else { |
---|
960 | found->second = node; |
---|
961 | } |
---|
962 | } |
---|
963 | // otherwise, we do not care about the node (e.g. because it is not marked) |
---|
964 | } |
---|
965 | else { |
---|
966 | error = link_to_tree(named, node->get_leftson()); |
---|
967 | if (!error) error = link_to_tree(named, node->get_rightson()); |
---|
968 | } |
---|
969 | return error; |
---|
970 | } |
---|
971 | |
---|
972 | static GBT_TREE *findNode(GBT_TREE *node, const char *name) { |
---|
973 | if (node->is_leaf) { |
---|
974 | return strcmp(node->name, name) == 0 ? node : NULL; |
---|
975 | } |
---|
976 | |
---|
977 | GBT_TREE *found = findNode(node->get_leftson(), name); |
---|
978 | if (!found) found = findNode(node->get_rightson(), name); |
---|
979 | return found; |
---|
980 | } |
---|
981 | |
---|
982 | static GB_ERROR init(NamedNodes& node, GBT_TREE *tree, const DI_ENTRY*const*const entries, size_t nentries) { |
---|
983 | GB_ERROR error = NULL; |
---|
984 | for (size_t n = 0; n<nentries; ++n) { |
---|
985 | node[entries[n]->name] = NULL; |
---|
986 | } |
---|
987 | error = link_to_tree(node, tree); |
---|
988 | if (!error) { // check for missing species (needed but not in tree) |
---|
989 | size_t missing = 0; |
---|
990 | const char *exampleName = NULL; |
---|
991 | |
---|
992 | for (size_t n = 0; n<nentries; ++n) { |
---|
993 | NamedNodes::iterator found = node.find(entries[n]->name); |
---|
994 | if (found == node.end()) { |
---|
995 | ++missing; |
---|
996 | exampleName = entries[n]->name; |
---|
997 | } |
---|
998 | else { |
---|
999 | di_assert(node[entries[n]->name] == findNode(tree, entries[n]->name)); |
---|
1000 | if (!node[entries[n]->name]) { |
---|
1001 | ++missing; |
---|
1002 | exampleName = entries[n]->name; |
---|
1003 | } |
---|
1004 | } |
---|
1005 | } |
---|
1006 | |
---|
1007 | if (missing) { |
---|
1008 | error = GBS_global_string("Tree is missing %zu required species (e.g. '%s')", missing, exampleName); |
---|
1009 | } |
---|
1010 | } |
---|
1011 | return error; |
---|
1012 | } |
---|
1013 | |
---|
1014 | GB_ERROR DI_MATRIX::extract_from_tree(const char *treename, bool *aborted_flag) { |
---|
1015 | GB_ERROR error = NULL; |
---|
1016 | if (nentries<=1) error = "Not enough species selected to calculate matrix"; |
---|
1017 | else { |
---|
1018 | GBT_TREE *tree; |
---|
1019 | { |
---|
1020 | GB_transaction ta(get_gb_main()); |
---|
1021 | tree = GBT_read_tree(get_gb_main(), treename, GBT_TREE_NodeFactory()); |
---|
1022 | } |
---|
1023 | if (!tree) error = GB_await_error(); |
---|
1024 | else { |
---|
1025 | arb_progress progress("Extracting distances from tree", matrix_halfsize(nentries, true)); |
---|
1026 | NamedNodes node; |
---|
1027 | |
---|
1028 | error = init(node, tree, entries, nentries); |
---|
1029 | matrix = new AP_smatrix(nentries); |
---|
1030 | |
---|
1031 | for (size_t row = 0; row<nentries && !error; row++) { |
---|
1032 | GBT_TREE *rnode = node[entries[row]->name]; |
---|
1033 | for (size_t col=0; col<=row && !error; col++) { |
---|
1034 | double dist; |
---|
1035 | if (col != row) { |
---|
1036 | GBT_TREE *cnode = node[entries[col]->name]; |
---|
1037 | dist = rnode->intree_distance_to(cnode); |
---|
1038 | } |
---|
1039 | else { |
---|
1040 | dist = 0.0; |
---|
1041 | } |
---|
1042 | matrix->set(row, col, dist); |
---|
1043 | progress.inc_and_check_user_abort(error); |
---|
1044 | } |
---|
1045 | } |
---|
1046 | delete tree; |
---|
1047 | if (aborted_flag && progress.aborted()) *aborted_flag = true; |
---|
1048 | if (error) progress.done(); |
---|
1049 | } |
---|
1050 | } |
---|
1051 | return error; |
---|
1052 | } |
---|
1053 | |
---|
1054 | __ATTR__USERESULT static GB_ERROR di_calculate_matrix(AW_root *aw_root, const WeightedFilter *weighted_filter, bool bootstrap_flag, bool show_warnings, bool *aborted_flag) { |
---|
1055 | // sets 'aborted_flag' to true, if it is non-NULL and the calculation has been aborted |
---|
1056 | GB_ERROR error = NULL; |
---|
1057 | |
---|
1058 | if (GLOBAL_MATRIX.exists()) { |
---|
1059 | di_assert(!need_recalc.matrix); |
---|
1060 | } |
---|
1061 | else { |
---|
1062 | GB_transaction ta(GLOBAL_gb_main); |
---|
1063 | |
---|
1064 | char *use = aw_root->awar(AWAR_DIST_ALIGNMENT)->read_string(); |
---|
1065 | long ali_len = GBT_get_alignment_len(GLOBAL_gb_main, use); |
---|
1066 | |
---|
1067 | if (ali_len<=0) { |
---|
1068 | error = "Please select a valid alignment"; |
---|
1069 | GB_clear_error(); |
---|
1070 | } |
---|
1071 | else { |
---|
1072 | arb_progress progress("Calculating matrix"); |
---|
1073 | char *cancel = aw_root->awar(AWAR_DIST_CANCEL_CHARS)->read_string(); |
---|
1074 | AliView *aliview = weighted_filter->create_aliview(use, error); |
---|
1075 | |
---|
1076 | if (!error) { |
---|
1077 | if (bootstrap_flag) aliview->get_filter()->enable_bootstrap(); |
---|
1078 | |
---|
1079 | char *load_what = aw_root->awar(AWAR_DIST_WHICH_SPECIES)->read_string(); |
---|
1080 | char *sort_tree_name = aw_root->awar(AWAR_DIST_TREE_SORT_NAME)->read_string(); |
---|
1081 | |
---|
1082 | LoadWhat all_flag = (strcmp(load_what, "all") == 0) ? DI_LOAD_ALL : DI_LOAD_MARKED; |
---|
1083 | { |
---|
1084 | DI_MATRIX *phm = new DI_MATRIX(*aliview, aw_root); |
---|
1085 | phm->matrix_type = DI_MATRIX_FULL; |
---|
1086 | |
---|
1087 | static SmartCharPtr last_sort_tree_name; |
---|
1088 | static SmartPtr<MatrixOrder> last_order; |
---|
1089 | |
---|
1090 | if (last_sort_tree_name.isNull() || !sort_tree_name || strcmp(&*last_sort_tree_name, sort_tree_name) != 0) { |
---|
1091 | last_sort_tree_name = nulldup(sort_tree_name); |
---|
1092 | last_order = new MatrixOrder(GLOBAL_gb_main, sort_tree_name); |
---|
1093 | } |
---|
1094 | di_assert(last_order.isSet()); |
---|
1095 | error = phm->load(all_flag, *last_order, show_warnings, NULL); |
---|
1096 | |
---|
1097 | free(sort_tree_name); |
---|
1098 | error = ta.close(error); |
---|
1099 | |
---|
1100 | bool aborted = false; |
---|
1101 | if (!error) { |
---|
1102 | if (progress.aborted()) { |
---|
1103 | phm->unload(); |
---|
1104 | error = "Aborted by user"; |
---|
1105 | aborted = true; |
---|
1106 | } |
---|
1107 | else { |
---|
1108 | DI_TRANSFORMATION trans = (DI_TRANSFORMATION)aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int(); |
---|
1109 | |
---|
1110 | if (trans == DI_TRANSFORMATION_FROM_TREE) { |
---|
1111 | const char *treename = aw_root->awar(AWAR_DIST_TREE_CURR_NAME)->read_char_pntr(); |
---|
1112 | error = phm->extract_from_tree(treename, &aborted); |
---|
1113 | } |
---|
1114 | else { |
---|
1115 | if (phm->is_AA) error = phm->calculate_pro(trans, &aborted); |
---|
1116 | else error = phm->calculate(aw_root, cancel, 0.0, trans, &aborted); |
---|
1117 | } |
---|
1118 | } |
---|
1119 | } |
---|
1120 | |
---|
1121 | if (aborted) { |
---|
1122 | di_assert(error); |
---|
1123 | if (aborted_flag) *aborted_flag = true; |
---|
1124 | } |
---|
1125 | if (error) { |
---|
1126 | delete phm; |
---|
1127 | GLOBAL_MATRIX.forget(); |
---|
1128 | } |
---|
1129 | else { |
---|
1130 | GLOBAL_MATRIX.replaceBy(phm); |
---|
1131 | tree_needs_recalc_cb(); |
---|
1132 | need_recalc.matrix = false; |
---|
1133 | } |
---|
1134 | } |
---|
1135 | free(load_what); |
---|
1136 | } |
---|
1137 | |
---|
1138 | free(cancel); |
---|
1139 | delete aliview; |
---|
1140 | } |
---|
1141 | free(use); |
---|
1142 | |
---|
1143 | di_assert(contradicted(error, GLOBAL_MATRIX.exists())); |
---|
1144 | } |
---|
1145 | return error; |
---|
1146 | } |
---|
1147 | |
---|
1148 | static void di_mark_by_distance(AW_window *aww, WeightedFilter *weighted_filter) { |
---|
1149 | AW_root *aw_root = aww->get_root(); |
---|
1150 | double lowerBound = aw_root->awar(AWAR_DIST_MIN_DIST)->read_float(); |
---|
1151 | double upperBound = aw_root->awar(AWAR_DIST_MAX_DIST)->read_float(); |
---|
1152 | |
---|
1153 | GB_ERROR error = 0; |
---|
1154 | if (lowerBound >= upperBound) { |
---|
1155 | error = GBS_global_string("Lower bound (%f) has to be smaller than upper bound (%f)", lowerBound, upperBound); |
---|
1156 | } |
---|
1157 | else if (lowerBound<0.0 || lowerBound > 1.0) { |
---|
1158 | error = GBS_global_string("Lower bound (%f) is not in allowed range [0.0 .. 1.0]", lowerBound); |
---|
1159 | } |
---|
1160 | else if (upperBound<0.0 || upperBound > 1.0) { |
---|
1161 | error = GBS_global_string("Upper bound (%f) is not in allowed range [0.0 .. 1.0]", upperBound); |
---|
1162 | } |
---|
1163 | else { |
---|
1164 | GB_transaction ta(GLOBAL_gb_main); |
---|
1165 | |
---|
1166 | char *selected = aw_root->awar(AWAR_SPECIES_NAME)->read_string(); |
---|
1167 | if (!selected[0]) { |
---|
1168 | error = "Please select a species"; |
---|
1169 | } |
---|
1170 | else { |
---|
1171 | GBDATA *gb_selected = GBT_find_species(GLOBAL_gb_main, selected); |
---|
1172 | if (!gb_selected) { |
---|
1173 | error = GBS_global_string("Couldn't find species '%s'", selected); |
---|
1174 | } |
---|
1175 | else { |
---|
1176 | char *use = aw_root->awar(AWAR_DIST_ALIGNMENT)->read_string(); |
---|
1177 | char *cancel = aw_root->awar(AWAR_DIST_CANCEL_CHARS)->read_string(); |
---|
1178 | DI_TRANSFORMATION trans = (DI_TRANSFORMATION)aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int(); |
---|
1179 | AliView *aliview = weighted_filter->create_aliview(use, error); |
---|
1180 | |
---|
1181 | if (!error) { |
---|
1182 | DI_MATRIX *prev_global = GLOBAL_MATRIX.swap(NULL); |
---|
1183 | |
---|
1184 | size_t speciesCount = GBT_get_species_count(GLOBAL_gb_main); |
---|
1185 | bool markedSelected = false; |
---|
1186 | |
---|
1187 | arb_progress progress("Mark species by distance", speciesCount); |
---|
1188 | MatrixOrder order(GLOBAL_gb_main, NULL); |
---|
1189 | |
---|
1190 | for (GBDATA *gb_species = GBT_first_species(GLOBAL_gb_main); |
---|
1191 | gb_species && !error; |
---|
1192 | gb_species = GBT_next_species(gb_species)) |
---|
1193 | { |
---|
1194 | DI_MATRIX *phm = new DI_MATRIX(*aliview, aw_root); |
---|
1195 | phm->matrix_type = DI_MATRIX_FULL; |
---|
1196 | GBDATA *species_pair[] = { gb_selected, gb_species, NULL }; |
---|
1197 | |
---|
1198 | error = phm->load(DI_LOAD_LIST, order, false, species_pair); |
---|
1199 | |
---|
1200 | if (phm->nentries == 2) { // if species has no alignment -> nentries<2 |
---|
1201 | if (!error) { |
---|
1202 | if (phm->is_AA) { |
---|
1203 | error = phm->calculate_pro(trans, NULL); |
---|
1204 | } |
---|
1205 | else { |
---|
1206 | error = phm->calculate(aw_root, cancel, 0.0, trans, NULL); |
---|
1207 | } |
---|
1208 | } |
---|
1209 | |
---|
1210 | if (!error) { |
---|
1211 | double dist_value = phm->matrix->get(0, 1); // distance or conformance |
---|
1212 | bool mark = (lowerBound <= dist_value && dist_value <= upperBound); |
---|
1213 | GB_write_flag(gb_species, mark); |
---|
1214 | |
---|
1215 | if (!markedSelected) { |
---|
1216 | dist_value = phm->matrix->get(0, 0); // distance or conformance to self |
---|
1217 | mark = (lowerBound <= dist_value && dist_value <= upperBound); |
---|
1218 | GB_write_flag(gb_selected, mark); |
---|
1219 | |
---|
1220 | markedSelected = true; |
---|
1221 | } |
---|
1222 | } |
---|
1223 | } |
---|
1224 | |
---|
1225 | delete phm; |
---|
1226 | if (!error) progress.inc_and_check_user_abort(error); |
---|
1227 | } |
---|
1228 | |
---|
1229 | di_assert(!GLOBAL_MATRIX.exists()); |
---|
1230 | ASSERT_RESULT(DI_MATRIX*, NULL, GLOBAL_MATRIX.swap(prev_global)); |
---|
1231 | |
---|
1232 | if (error) progress.done(); |
---|
1233 | } |
---|
1234 | |
---|
1235 | delete aliview; |
---|
1236 | free(cancel); |
---|
1237 | free(use); |
---|
1238 | } |
---|
1239 | } |
---|
1240 | |
---|
1241 | free(selected); |
---|
1242 | error = ta.close(error); |
---|
1243 | } |
---|
1244 | |
---|
1245 | if (error) { |
---|
1246 | aw_message(error); |
---|
1247 | } |
---|
1248 | } |
---|
1249 | |
---|
1250 | static void di_calculate_full_matrix_cb(AW_window *aww, const WeightedFilter *weighted_filter); |
---|
1251 | |
---|
1252 | static GB_ERROR di_recalc_matrix() { |
---|
1253 | // recalculate matrix |
---|
1254 | last_matrix_calculation_error = NULL; |
---|
1255 | if (need_recalc.matrix && GLOBAL_MATRIX.exists()) { |
---|
1256 | GLOBAL_MATRIX.forget(); |
---|
1257 | } |
---|
1258 | di_assert(recalculate_matrix_cb.isSet()); |
---|
1259 | (*recalculate_matrix_cb)(); |
---|
1260 | return last_matrix_calculation_error; |
---|
1261 | } |
---|
1262 | |
---|
1263 | static void di_view_matrix_cb(AW_window *aww, save_matrix_params *sparam) { |
---|
1264 | GB_ERROR error = di_recalc_matrix(); |
---|
1265 | if (error) return; |
---|
1266 | |
---|
1267 | if (!matrixDisplay) matrixDisplay = new MatrixDisplay; |
---|
1268 | |
---|
1269 | static AW_window *viewer = 0; |
---|
1270 | if (!viewer) viewer = DI_create_view_matrix_window(aww->get_root(), matrixDisplay, sparam); |
---|
1271 | |
---|
1272 | matrixDisplay->mark(MatrixDisplay::NEED_SETUP); |
---|
1273 | matrixDisplay->update_display(); |
---|
1274 | |
---|
1275 | GLOBAL_MATRIX.set_changed_cb(matrix_changed_cb); |
---|
1276 | |
---|
1277 | viewer->activate(); |
---|
1278 | } |
---|
1279 | |
---|
1280 | static void di_save_matrix_cb(AW_window *aww) { |
---|
1281 | // save the matrix |
---|
1282 | GB_ERROR error = di_recalc_matrix(); |
---|
1283 | if (!error) { |
---|
1284 | char *filename = aww->get_root()->awar(AWAR_DIST_SAVE_MATRIX_FILENAME)->read_string(); |
---|
1285 | enum DI_SAVE_TYPE type = (enum DI_SAVE_TYPE)aww->get_root()->awar(AWAR_DIST_SAVE_MATRIX_TYPE)->read_int(); |
---|
1286 | |
---|
1287 | GLOBAL_MATRIX.get()->save(filename, type); |
---|
1288 | free(filename); |
---|
1289 | } |
---|
1290 | AW_refresh_fileselection(aww->get_root(), AWAR_DIST_SAVE_MATRIX_BASE); |
---|
1291 | aww->hide_or_notify(error); |
---|
1292 | } |
---|
1293 | |
---|
1294 | AW_window *DI_create_save_matrix_window(AW_root *aw_root, save_matrix_params *save_params) { |
---|
1295 | static AW_window_simple *aws = 0; |
---|
1296 | if (!aws) { |
---|
1297 | aws = new AW_window_simple; |
---|
1298 | aws->init(aw_root, "SAVE_MATRIX", "Save Matrix"); |
---|
1299 | aws->load_xfig("sel_box_user.fig"); |
---|
1300 | |
---|
1301 | aws->at("close"); aws->callback((AW_CB0)AW_POPDOWN); |
---|
1302 | aws->create_button("CLOSE", "CANCEL", "C"); |
---|
1303 | |
---|
1304 | |
---|
1305 | aws->at("help"); aws->callback(makeHelpCallback("save_matrix.hlp")); |
---|
1306 | aws->create_button("HELP", "HELP", "H"); |
---|
1307 | |
---|
1308 | aws->at("user"); |
---|
1309 | aws->create_option_menu(AWAR_DIST_SAVE_MATRIX_TYPE, true); |
---|
1310 | aws->insert_default_option("Phylip Format (Lower Triangular Matrix)", "P", DI_SAVE_PHYLIP_COMP); |
---|
1311 | aws->insert_option("Readable (using NDS)", "R", DI_SAVE_READABLE); |
---|
1312 | aws->insert_option("Tabbed (using NDS)", "R", DI_SAVE_TABBED); |
---|
1313 | aws->update_option_menu(); |
---|
1314 | |
---|
1315 | AW_create_standard_fileselection(aws, save_params->awar_base); |
---|
1316 | |
---|
1317 | aws->at("save2"); |
---|
1318 | aws->callback(makeWindowCallback(di_save_matrix_cb)); |
---|
1319 | aws->create_button("SAVE", "SAVE", "S"); |
---|
1320 | |
---|
1321 | aws->callback((AW_CB0)AW_POPDOWN); |
---|
1322 | aws->at("cancel2"); |
---|
1323 | aws->create_button("CLOSE", "CANCEL", "C"); |
---|
1324 | } |
---|
1325 | return aws; |
---|
1326 | } |
---|
1327 | |
---|
1328 | static AW_window *awt_create_select_cancel_window(AW_root *aw_root) { |
---|
1329 | AW_window_simple *aws = new AW_window_simple; |
---|
1330 | aws->init(aw_root, "SELECT_CHARS_TO_CANCEL_COLUMN", "CANCEL SELECT"); |
---|
1331 | aws->load_xfig("di_cancel.fig"); |
---|
1332 | |
---|
1333 | aws->at("close"); aws->callback((AW_CB0)AW_POPDOWN); |
---|
1334 | aws->create_button("CLOSE", "CLOSE", "C"); |
---|
1335 | |
---|
1336 | aws->at("cancel"); |
---|
1337 | aws->create_input_field(AWAR_DIST_CANCEL_CHARS, 12); |
---|
1338 | |
---|
1339 | return (AW_window *)aws; |
---|
1340 | } |
---|
1341 | |
---|
1342 | static const char *enum_trans_to_string[] = { |
---|
1343 | "none", |
---|
1344 | "similarity", |
---|
1345 | "jukes_cantor", |
---|
1346 | "felsenstein", |
---|
1347 | |
---|
1348 | "pam", |
---|
1349 | "hall", |
---|
1350 | "barker", |
---|
1351 | "chemical", |
---|
1352 | |
---|
1353 | "haesch", |
---|
1354 | "kimura", |
---|
1355 | "olsen", |
---|
1356 | "felsenstein voigt", |
---|
1357 | "olsen voigt", |
---|
1358 | "max ml", |
---|
1359 | |
---|
1360 | NULL, // treedist |
---|
1361 | }; |
---|
1362 | |
---|
1363 | STATIC_ASSERT(ARRAY_ELEMS(enum_trans_to_string) == DI_TRANSFORMATION_COUNT); |
---|
1364 | |
---|
1365 | static void di_calculate_tree_cb(AW_window *aww, WeightedFilter *weighted_filter, bool bootstrap_flag) { |
---|
1366 | recalculate_tree_cb = new BoundWindowCallback(aww, makeWindowCallback(di_calculate_tree_cb, weighted_filter, bootstrap_flag)); |
---|
1367 | |
---|
1368 | AW_root *aw_root = aww->get_root(); |
---|
1369 | GB_ERROR error = 0; |
---|
1370 | StrArray *all_names = 0; |
---|
1371 | |
---|
1372 | int loop_count = 0; |
---|
1373 | int bootstrap_count = aw_root->awar(AWAR_DIST_BOOTSTRAP_COUNT)->read_int(); |
---|
1374 | |
---|
1375 | { |
---|
1376 | char *tree_name = aw_root->awar(AWAR_DIST_TREE_STD_NAME)->read_string(); |
---|
1377 | error = GBT_check_tree_name(tree_name); |
---|
1378 | free(tree_name); |
---|
1379 | } |
---|
1380 | |
---|
1381 | SmartPtr<arb_progress> progress; |
---|
1382 | SmartPtr<ConsensusTree> ctree; |
---|
1383 | |
---|
1384 | if (!error) { |
---|
1385 | if (bootstrap_flag) { |
---|
1386 | if (bootstrap_count) { |
---|
1387 | progress = new arb_progress("Calculating bootstrap trees", bootstrap_count+1); |
---|
1388 | } |
---|
1389 | else { |
---|
1390 | progress = new arb_progress("Calculating bootstrap trees (KILL to stop)", INT_MAX); |
---|
1391 | } |
---|
1392 | progress->auto_subtitles("tree"); |
---|
1393 | } |
---|
1394 | else { |
---|
1395 | progress = new arb_progress("Calculating tree"); |
---|
1396 | } |
---|
1397 | |
---|
1398 | if (bootstrap_flag) { |
---|
1399 | GLOBAL_MATRIX.forget(); |
---|
1400 | GLOBAL_MATRIX.set_changed_cb(NULL); // otherwise matrix window will repeatedly pop up/down |
---|
1401 | |
---|
1402 | error = di_calculate_matrix(aw_root, weighted_filter, bootstrap_flag, true, NULL); |
---|
1403 | if (!error) { |
---|
1404 | DI_MATRIX *matr = GLOBAL_MATRIX.get(); |
---|
1405 | if (!matr) { |
---|
1406 | error = "unexpected error in di_calculate_matrix_cb (data missing)"; |
---|
1407 | } |
---|
1408 | else { |
---|
1409 | all_names = new StrArray; |
---|
1410 | all_names->reserve(matr->nentries+2); |
---|
1411 | |
---|
1412 | for (size_t i=0; i<matr->nentries; i++) { |
---|
1413 | all_names->put(strdup(matr->entries[i]->name)); |
---|
1414 | } |
---|
1415 | ctree = new ConsensusTree(*all_names); |
---|
1416 | } |
---|
1417 | } |
---|
1418 | } |
---|
1419 | } |
---|
1420 | |
---|
1421 | GBT_TREE *tree = 0; |
---|
1422 | do { |
---|
1423 | if (error) break; |
---|
1424 | |
---|
1425 | bool aborted = false; |
---|
1426 | |
---|
1427 | if (bootstrap_flag) { |
---|
1428 | if (loop_count>0) { // in first loop we already have a valid matrix -> no need to recalculate |
---|
1429 | GLOBAL_MATRIX.forget(); |
---|
1430 | } |
---|
1431 | } |
---|
1432 | else if (need_recalc.matrix) { |
---|
1433 | GLOBAL_MATRIX.forget(); |
---|
1434 | } |
---|
1435 | |
---|
1436 | error = di_calculate_matrix(aw_root, weighted_filter, bootstrap_flag, !bootstrap_flag, &aborted); |
---|
1437 | if (error && aborted) { |
---|
1438 | error = 0; // clear error (otherwise no tree will be read below) |
---|
1439 | break; // end of bootstrap |
---|
1440 | } |
---|
1441 | |
---|
1442 | if (!GLOBAL_MATRIX.exists()) { |
---|
1443 | error = "unexpected error in di_calculate_matrix_cb (data missing)"; |
---|
1444 | break; |
---|
1445 | } |
---|
1446 | |
---|
1447 | DI_MATRIX *matr = GLOBAL_MATRIX.get(); |
---|
1448 | char **names = (char **)calloc(sizeof(char *), (size_t)matr->nentries+2); |
---|
1449 | |
---|
1450 | for (size_t i=0; i<matr->nentries; i++) { |
---|
1451 | names[i] = matr->entries[i]->name; |
---|
1452 | } |
---|
1453 | di_assert(matr->nentries == matr->matrix->size()); |
---|
1454 | tree = neighbourjoining(names, *matr->matrix); |
---|
1455 | |
---|
1456 | if (bootstrap_flag) { |
---|
1457 | error = ctree->insert_tree_weighted(tree, matr->nentries, 1, false); |
---|
1458 | delete tree; tree = NULL; |
---|
1459 | loop_count++; |
---|
1460 | progress->inc(); |
---|
1461 | if (!bootstrap_count) { // when waiting for kill |
---|
1462 | int t = time(0); |
---|
1463 | static int tlast = 0; |
---|
1464 | |
---|
1465 | if (t>tlast) { |
---|
1466 | progress->force_update(); |
---|
1467 | tlast = t; |
---|
1468 | } |
---|
1469 | } |
---|
1470 | } |
---|
1471 | free(names); |
---|
1472 | } while (bootstrap_flag && loop_count != bootstrap_count); |
---|
1473 | |
---|
1474 | if (!error) { |
---|
1475 | if (bootstrap_flag) { |
---|
1476 | tree = ctree->get_consensus_tree(error); |
---|
1477 | progress->inc(); |
---|
1478 | if (!error) { |
---|
1479 | error = GBT_is_invalid(tree); |
---|
1480 | di_assert(!error); |
---|
1481 | } |
---|
1482 | } |
---|
1483 | |
---|
1484 | if (!error) { |
---|
1485 | char *tree_name = aw_root->awar(AWAR_DIST_TREE_STD_NAME)->read_string(); |
---|
1486 | GB_begin_transaction(GLOBAL_gb_main); |
---|
1487 | error = GBT_write_tree(GLOBAL_gb_main, tree_name, tree); |
---|
1488 | |
---|
1489 | if (!error) { |
---|
1490 | char *filter_name = AWT_get_combined_filter_name(aw_root, "dist"); |
---|
1491 | int transr = aw_root->awar(AWAR_DIST_CORR_TRANS)->read_int(); |
---|
1492 | |
---|
1493 | const char *comment; |
---|
1494 | if (enum_trans_to_string[transr]) { |
---|
1495 | comment = GBS_global_string("PRG=dnadist CORR=%s FILTER=%s PKG=ARB", enum_trans_to_string[transr], filter_name); |
---|
1496 | } |
---|
1497 | else { |
---|
1498 | di_assert(transr == DI_TRANSFORMATION_FROM_TREE); |
---|
1499 | const char *treename = aw_root->awar(AWAR_DIST_TREE_CURR_NAME)->read_char_pntr(); |
---|
1500 | comment = GBS_global_string("PRG=treedist (from '%s') PKG=ARB", treename); |
---|
1501 | } |
---|
1502 | |
---|
1503 | error = GBT_write_tree_remark(GLOBAL_gb_main, tree_name, comment); |
---|
1504 | free(filter_name); |
---|
1505 | } |
---|
1506 | error = GB_end_transaction(GLOBAL_gb_main, error); |
---|
1507 | free(tree_name); |
---|
1508 | } |
---|
1509 | } |
---|
1510 | |
---|
1511 | delete tree; |
---|
1512 | |
---|
1513 | // aw_status(); // remove 'abort' flag (@@@ got no equiv for arb_progress yet. really needed?) |
---|
1514 | |
---|
1515 | if (bootstrap_flag) { |
---|
1516 | if (all_names) delete all_names; |
---|
1517 | GLOBAL_MATRIX.forget(); |
---|
1518 | } |
---|
1519 | #if defined(DEBUG) |
---|
1520 | else { |
---|
1521 | di_assert(all_names == 0); |
---|
1522 | } |
---|
1523 | #endif // DEBUG |
---|
1524 | |
---|
1525 | progress->done(); |
---|
1526 | if (error) { |
---|
1527 | aw_message(error); |
---|
1528 | } |
---|
1529 | else { |
---|
1530 | need_recalc.tree = false; |
---|
1531 | aw_root->awar(AWAR_TREE_REFRESH)->touch(); |
---|
1532 | } |
---|
1533 | } |
---|
1534 | |
---|
1535 | |
---|
1536 | static void di_autodetect_callback(AW_window *aww) { |
---|
1537 | GB_push_transaction(GLOBAL_gb_main); |
---|
1538 | |
---|
1539 | GLOBAL_MATRIX.forget(); |
---|
1540 | |
---|
1541 | AW_root *aw_root = aww->get_root(); |
---|
1542 | char *use = aw_root->awar(AWAR_DIST_ALIGNMENT)->read_string(); |
---|
1543 | long ali_len = GBT_get_alignment_len(GLOBAL_gb_main, use); |
---|
1544 | GB_ERROR error = NULL; |
---|
1545 | |
---|
1546 | if (ali_len<=0) { |
---|
1547 | GB_pop_transaction(GLOBAL_gb_main); |
---|
1548 | error = "Please select a valid alignment"; |
---|
1549 | GB_clear_error(); |
---|
1550 | } |
---|
1551 | else { |
---|
1552 | arb_progress progress("Analyzing data"); |
---|
1553 | |
---|
1554 | char *filter_str = aw_root->awar(AWAR_DIST_FILTER_FILTER)->read_string(); |
---|
1555 | char *cancel = aw_root->awar(AWAR_DIST_CANCEL_CHARS)->read_string(); |
---|
1556 | |
---|
1557 | AliView *aliview = NULL; |
---|
1558 | { |
---|
1559 | AP_filter *ap_filter = NULL; |
---|
1560 | long flen = strlen(filter_str); |
---|
1561 | |
---|
1562 | if (flen == ali_len) { |
---|
1563 | ap_filter = new AP_filter(filter_str, "0", ali_len); |
---|
1564 | } |
---|
1565 | else { |
---|
1566 | if (flen) { |
---|
1567 | aw_message("Warning: your filter len is not equal to the alignment len\nfilter got truncated with zeros or cutted"); |
---|
1568 | ap_filter = new AP_filter(filter_str, "0", ali_len); |
---|
1569 | } |
---|
1570 | else { |
---|
1571 | ap_filter = new AP_filter(ali_len); // unfiltered |
---|
1572 | } |
---|
1573 | } |
---|
1574 | |
---|
1575 | error = ap_filter->is_invalid(); |
---|
1576 | if (!error) { |
---|
1577 | AP_weights ap_weights(ap_filter); |
---|
1578 | aliview = new AliView(GLOBAL_gb_main, *ap_filter, ap_weights, use); |
---|
1579 | } |
---|
1580 | delete ap_filter; |
---|
1581 | } |
---|
1582 | |
---|
1583 | if (error) { |
---|
1584 | GB_pop_transaction(GLOBAL_gb_main); |
---|
1585 | } |
---|
1586 | else { |
---|
1587 | DI_MATRIX phm(*aliview, aw_root); |
---|
1588 | |
---|
1589 | { |
---|
1590 | char *load_what = aw_root->awar(AWAR_DIST_WHICH_SPECIES)->read_string(); |
---|
1591 | char *sort_tree_name = aw_root->awar(AWAR_DIST_TREE_SORT_NAME)->read_string(); |
---|
1592 | |
---|
1593 | LoadWhat all_flag = (strcmp(load_what, "all") == 0) ? DI_LOAD_ALL : DI_LOAD_MARKED; |
---|
1594 | |
---|
1595 | GLOBAL_MATRIX.forget(); |
---|
1596 | |
---|
1597 | MatrixOrder order(GLOBAL_gb_main, sort_tree_name); |
---|
1598 | error = phm.load(all_flag, order, true, NULL); |
---|
1599 | |
---|
1600 | free(sort_tree_name); |
---|
1601 | free(load_what); |
---|
1602 | } |
---|
1603 | |
---|
1604 | GB_pop_transaction(GLOBAL_gb_main); |
---|
1605 | |
---|
1606 | if (!error) { |
---|
1607 | progress.subtitle("Search Correction"); |
---|
1608 | phm.analyse(); |
---|
1609 | } |
---|
1610 | } |
---|
1611 | |
---|
1612 | free(cancel); |
---|
1613 | delete aliview; |
---|
1614 | |
---|
1615 | free(filter_str); |
---|
1616 | } |
---|
1617 | |
---|
1618 | if (error) aw_message(error); |
---|
1619 | |
---|
1620 | free(use); |
---|
1621 | } |
---|
1622 | |
---|
1623 | __ATTR__NORETURN static void di_exit(AW_window *aww) { |
---|
1624 | if (GLOBAL_gb_main) { |
---|
1625 | AW_root *aw_root = aww->get_root(); |
---|
1626 | shutdown_macro_recording(aw_root); |
---|
1627 | aw_root->unlink_awars_from_DB(GLOBAL_gb_main); |
---|
1628 | GB_close(GLOBAL_gb_main); |
---|
1629 | } |
---|
1630 | GLOBAL_MATRIX.set_changed_cb(NULL); |
---|
1631 | exit(EXIT_SUCCESS); |
---|
1632 | } |
---|
1633 | |
---|
1634 | static void di_calculate_full_matrix_cb(AW_window *aww, const WeightedFilter *weighted_filter) { |
---|
1635 | recalculate_matrix_cb = new BoundWindowCallback(aww, makeWindowCallback(di_calculate_full_matrix_cb, weighted_filter)); |
---|
1636 | |
---|
1637 | GLOBAL_MATRIX.forget_if_not_has_type(DI_MATRIX_FULL); |
---|
1638 | GB_ERROR error = di_calculate_matrix(aww->get_root(), weighted_filter, 0, true, NULL); |
---|
1639 | aw_message_if(error); |
---|
1640 | last_matrix_calculation_error = error; |
---|
1641 | if (!error) tree_needs_recalc_cb(); |
---|
1642 | } |
---|
1643 | |
---|
1644 | static void di_calculate_compressed_matrix_cb(AW_window *aww, WeightedFilter *weighted_filter) { |
---|
1645 | recalculate_matrix_cb = new BoundWindowCallback(aww, makeWindowCallback(di_calculate_compressed_matrix_cb, weighted_filter)); |
---|
1646 | |
---|
1647 | GB_transaction ta(GLOBAL_gb_main); |
---|
1648 | |
---|
1649 | AW_root *aw_root = aww->get_root(); |
---|
1650 | char *treename = aw_root->awar(AWAR_DIST_TREE_COMP_NAME)->read_string(); |
---|
1651 | GB_ERROR error = 0; |
---|
1652 | GBT_TREE *tree = GBT_read_tree(GLOBAL_gb_main, treename, GBT_TREE_NodeFactory()); |
---|
1653 | |
---|
1654 | if (!tree) { |
---|
1655 | error = GB_await_error(); |
---|
1656 | } |
---|
1657 | else { |
---|
1658 | { |
---|
1659 | LocallyModify<MatrixDisplay*> skipRefresh(matrixDisplay, NULL); // skip refresh, until matrix has been compressed |
---|
1660 | |
---|
1661 | GLOBAL_MATRIX.forget(); // always forget (as tree might have changed) |
---|
1662 | error = di_calculate_matrix(aw_root, weighted_filter, 0, true, NULL); |
---|
1663 | if (!error && !GLOBAL_MATRIX.exists()) { |
---|
1664 | error = "Failed to calculate your matrix (bug?)"; |
---|
1665 | } |
---|
1666 | if (!error) { |
---|
1667 | error = GLOBAL_MATRIX.get()->compress(tree); |
---|
1668 | } |
---|
1669 | } |
---|
1670 | delete tree; |
---|
1671 | |
---|
1672 | // now force refresh |
---|
1673 | if (matrixDisplay) { |
---|
1674 | matrixDisplay->mark(MatrixDisplay::NEED_SETUP); |
---|
1675 | matrixDisplay->update_display(); |
---|
1676 | } |
---|
1677 | } |
---|
1678 | free(treename); |
---|
1679 | aw_message_if(error); |
---|
1680 | last_matrix_calculation_error = error; |
---|
1681 | if (!error) tree_needs_recalc_cb(); |
---|
1682 | } |
---|
1683 | |
---|
1684 | static void di_define_sort_tree_name_cb(AW_window *aww) { |
---|
1685 | AW_root *aw_root = aww->get_root(); |
---|
1686 | char *tree_name = aw_root->awar(AWAR_DIST_TREE_CURR_NAME)->read_string(); |
---|
1687 | aw_root->awar(AWAR_DIST_TREE_SORT_NAME)->write_string(tree_name); |
---|
1688 | free(tree_name); |
---|
1689 | } |
---|
1690 | static void di_define_compression_tree_name_cb(AW_window *aww) { |
---|
1691 | AW_root *aw_root = aww->get_root(); |
---|
1692 | char *tree_name = aw_root->awar(AWAR_DIST_TREE_CURR_NAME)->read_string(); |
---|
1693 | aw_root->awar(AWAR_DIST_TREE_COMP_NAME)->write_string(tree_name); |
---|
1694 | free(tree_name); |
---|
1695 | } |
---|
1696 | |
---|
1697 | static void di_define_save_tree_name_cb(AW_window *aww) { |
---|
1698 | AW_root *aw_root = aww->get_root(); |
---|
1699 | char *tree_name = aw_root->awar(AWAR_DIST_TREE_CURR_NAME)->read_string(); |
---|
1700 | aw_root->awar(AWAR_DIST_TREE_STD_NAME)->write_string(tree_name); |
---|
1701 | free(tree_name); |
---|
1702 | } |
---|
1703 | |
---|
1704 | |
---|
1705 | AW_window *DI_create_matrix_window(AW_root *aw_root) { |
---|
1706 | AW_window_simple_menu *aws = new AW_window_simple_menu; |
---|
1707 | aws->init(aw_root, "NEIGHBOUR JOINING", "NEIGHBOUR JOINING [ARB_DIST]"); |
---|
1708 | aws->load_xfig("di_ge_ma.fig"); |
---|
1709 | aws->button_length(10); |
---|
1710 | |
---|
1711 | aws->at("close"); |
---|
1712 | aws->callback(di_exit); |
---|
1713 | aws->create_button("CLOSE", "CLOSE", "C"); |
---|
1714 | |
---|
1715 | aws->at("help"); |
---|
1716 | aws->callback(makeHelpCallback("dist.hlp")); |
---|
1717 | aws->create_button("HELP", "HELP", "H"); |
---|
1718 | |
---|
1719 | |
---|
1720 | GB_push_transaction(GLOBAL_gb_main); |
---|
1721 | |
---|
1722 | #if defined(DEBUG) |
---|
1723 | AWT_create_debug_menu(aws); |
---|
1724 | #endif // DEBUG |
---|
1725 | |
---|
1726 | aws->create_menu("File", "F", AWM_ALL); |
---|
1727 | insert_macro_menu_entry(aws, false); |
---|
1728 | aws->insert_menu_topic("quit", "Quit", "Q", "quit.hlp", AWM_ALL, di_exit); |
---|
1729 | |
---|
1730 | aws->create_menu("Properties", "P", AWM_ALL); |
---|
1731 | aws->insert_menu_topic("frame_props", "Frame ...", "F", "props_frame.hlp", AWM_ALL, AW_preset_window); |
---|
1732 | aws->sep______________(); |
---|
1733 | AW_insert_common_property_menu_entries(aws); |
---|
1734 | aws->sep______________(); |
---|
1735 | aws->insert_menu_topic("save_props", "Save Properties (dist.arb)", "S", "savedef.hlp", AWM_ALL, AW_save_properties); |
---|
1736 | |
---|
1737 | aws->insert_help_topic("ARB_DIST help", "D", "dist.hlp", AWM_ALL, makeHelpCallback("dist.hlp")); |
---|
1738 | |
---|
1739 | // ------------------ |
---|
1740 | // left side |
---|
1741 | |
---|
1742 | aws->at("which_species"); |
---|
1743 | aws->create_option_menu(AWAR_DIST_WHICH_SPECIES, true); |
---|
1744 | aws->insert_option("all", "a", "all"); |
---|
1745 | aws->insert_default_option("marked", "m", "marked"); |
---|
1746 | aws->update_option_menu(); |
---|
1747 | |
---|
1748 | aws->at("which_alignment"); |
---|
1749 | awt_create_selection_list_on_alignments(GLOBAL_gb_main, (AW_window *)aws, AWAR_DIST_ALIGNMENT, "*="); |
---|
1750 | |
---|
1751 | // filter & weights |
---|
1752 | |
---|
1753 | AW_awar *awar_dist_alignment = aws->get_root()->awar_string(AWAR_DIST_ALIGNMENT); |
---|
1754 | WeightedFilter *weighted_filter = // do NOT free (bound to callbacks) |
---|
1755 | new WeightedFilter(GLOBAL_gb_main, aws->get_root(), AWAR_DIST_FILTER_NAME, AWAR_DIST_COLUMN_STAT_NAME, awar_dist_alignment); |
---|
1756 | |
---|
1757 | aws->at("filter_select"); |
---|
1758 | aws->callback(makeCreateWindowCallback(awt_create_select_filter_win, weighted_filter->get_adfiltercbstruct())); |
---|
1759 | aws->create_button("SELECT_FILTER", AWAR_DIST_FILTER_NAME); |
---|
1760 | |
---|
1761 | aws->at("weights_select"); |
---|
1762 | aws->sens_mask(AWM_EXP); |
---|
1763 | aws->callback(makeCreateWindowCallback(COLSTAT_create_selection_window, weighted_filter->get_column_stat())); |
---|
1764 | aws->create_button("SELECT_COL_STAT", AWAR_DIST_COLUMN_STAT_NAME); |
---|
1765 | aws->sens_mask(AWM_ALL); |
---|
1766 | |
---|
1767 | aws->at("which_cancel"); |
---|
1768 | aws->create_input_field(AWAR_DIST_CANCEL_CHARS, 12); |
---|
1769 | |
---|
1770 | aws->at("cancel_select"); |
---|
1771 | aws->callback(awt_create_select_cancel_window); |
---|
1772 | aws->create_button("SELECT_CANCEL_CHARS", "Info", "C"); |
---|
1773 | |
---|
1774 | aws->at("change_matrix"); |
---|
1775 | aws->callback(create_dna_matrix_window); |
---|
1776 | aws->create_button("EDIT_MATRIX", "Edit Matrix"); |
---|
1777 | |
---|
1778 | aws->at("enable"); |
---|
1779 | aws->create_toggle(AWAR_DIST_MATRIX_DNA_ENABLED); |
---|
1780 | |
---|
1781 | aws->at("which_correction"); |
---|
1782 | aws->create_option_menu(AWAR_DIST_CORR_TRANS, true); |
---|
1783 | aws->insert_option("none", "n", (int)DI_TRANSFORMATION_NONE); |
---|
1784 | aws->insert_option("similarity", "n", (int)DI_TRANSFORMATION_SIMILARITY); |
---|
1785 | aws->insert_option("jukes-cantor (dna)", "c", (int)DI_TRANSFORMATION_JUKES_CANTOR); |
---|
1786 | aws->insert_option("felsenstein (dna)", "f", (int)DI_TRANSFORMATION_FELSENSTEIN); |
---|
1787 | aws->insert_option("olsen (dna)", "o", (int)DI_TRANSFORMATION_OLSEN); |
---|
1788 | aws->insert_option("felsenstein/voigt (exp)", "1", (int)DI_TRANSFORMATION_FELSENSTEIN_VOIGT); |
---|
1789 | aws->insert_option("olsen/voigt (exp)", "2", (int)DI_TRANSFORMATION_OLSEN_VOIGT); |
---|
1790 | aws->insert_option("haesch (exp)", "f", (int)DI_TRANSFORMATION_HAESCH); |
---|
1791 | aws->insert_option("kimura (pro)", "k", (int)DI_TRANSFORMATION_KIMURA); |
---|
1792 | aws->insert_option("PAM (protein)", "c", (int)DI_TRANSFORMATION_PAM); |
---|
1793 | aws->insert_option("Cat. Hall(exp)", "c", (int)DI_TRANSFORMATION_CATEGORIES_HALL); |
---|
1794 | aws->insert_option("Cat. Barker(exp)", "c", (int)DI_TRANSFORMATION_CATEGORIES_BARKER); |
---|
1795 | aws->insert_option("Cat.Chem (exp)", "c", (int)DI_TRANSFORMATION_CATEGORIES_CHEMICAL); |
---|
1796 | aws->insert_option("from selected tree", "t", (int)DI_TRANSFORMATION_FROM_TREE); |
---|
1797 | aws->insert_default_option("unknown", "u", (int)DI_TRANSFORMATION_NONE); |
---|
1798 | |
---|
1799 | aws->update_option_menu(); |
---|
1800 | |
---|
1801 | aws->at("autodetect"); // auto |
---|
1802 | aws->callback(di_autodetect_callback); |
---|
1803 | aws->sens_mask(AWM_EXP); |
---|
1804 | aws->create_button("AUTODETECT_CORRECTION", "AUTODETECT", "A"); |
---|
1805 | aws->sens_mask(AWM_ALL); |
---|
1806 | |
---|
1807 | // ------------------- |
---|
1808 | // right side |
---|
1809 | |
---|
1810 | |
---|
1811 | aws->at("mark_distance"); |
---|
1812 | aws->callback(makeWindowCallback(di_mark_by_distance, weighted_filter)); |
---|
1813 | aws->create_autosize_button("MARK_BY_DIST", "Mark all species"); |
---|
1814 | |
---|
1815 | aws->at("mark_lower"); |
---|
1816 | aws->create_input_field(AWAR_DIST_MIN_DIST, 5); |
---|
1817 | |
---|
1818 | aws->at("mark_upper"); |
---|
1819 | aws->create_input_field(AWAR_DIST_MAX_DIST, 5); |
---|
1820 | |
---|
1821 | // ----------------- |
---|
1822 | |
---|
1823 | // tree selection |
---|
1824 | |
---|
1825 | aws->at("tree_list"); |
---|
1826 | awt_create_selection_list_on_trees(GLOBAL_gb_main, aws, AWAR_DIST_TREE_CURR_NAME, true); |
---|
1827 | |
---|
1828 | aws->at("detect_clusters"); |
---|
1829 | aws->callback(makeCreateWindowCallback(DI_create_cluster_detection_window, weighted_filter)); |
---|
1830 | aws->create_autosize_button("DETECT_CLUSTERS", "Detect homogenous clusters in tree", "D"); |
---|
1831 | |
---|
1832 | // matrix calculation |
---|
1833 | |
---|
1834 | aws->button_length(18); |
---|
1835 | |
---|
1836 | aws->at("calculate"); |
---|
1837 | aws->callback(makeWindowCallback(di_calculate_full_matrix_cb, weighted_filter)); |
---|
1838 | aws->create_button("CALC_FULL_MATRIX", "Calculate\nFull Matrix", "F"); |
---|
1839 | |
---|
1840 | aws->at("compress"); |
---|
1841 | aws->callback(makeWindowCallback(di_calculate_compressed_matrix_cb, weighted_filter)); |
---|
1842 | aws->create_button("CALC_COMPRESSED_MATRIX", "Calculate\nCompressed Matrix", "C"); |
---|
1843 | |
---|
1844 | recalculate_matrix_cb = new BoundWindowCallback(aws, makeWindowCallback(di_calculate_full_matrix_cb, weighted_filter)); |
---|
1845 | |
---|
1846 | aws->button_length(13); |
---|
1847 | |
---|
1848 | { |
---|
1849 | save_matrix_params *sparams = new save_matrix_params; // do not free (bound to callbacks) |
---|
1850 | |
---|
1851 | sparams->awar_base = AWAR_DIST_SAVE_MATRIX_BASE; |
---|
1852 | sparams->weighted_filter = weighted_filter; |
---|
1853 | |
---|
1854 | aws->at("save_matrix"); |
---|
1855 | aws->callback(makeCreateWindowCallback(DI_create_save_matrix_window, sparams)); |
---|
1856 | aws->create_button("SAVE_MATRIX", "Save matrix", "M"); |
---|
1857 | |
---|
1858 | aws->at("view_matrix"); |
---|
1859 | aws->callback(makeWindowCallback(di_view_matrix_cb, sparams)); |
---|
1860 | aws->create_button("VIEW_MATRIX", "View matrix", "V"); |
---|
1861 | } |
---|
1862 | |
---|
1863 | aws->button_length(22); |
---|
1864 | aws->at("use_compr_tree"); |
---|
1865 | aws->callback(di_define_compression_tree_name_cb); |
---|
1866 | aws->create_button("USE_COMPRESSION_TREE", "Use to compress", ""); |
---|
1867 | aws->at("use_sort_tree"); |
---|
1868 | aws->callback(di_define_sort_tree_name_cb); |
---|
1869 | aws->create_button("USE_SORT_TREE", "Use to sort", ""); |
---|
1870 | |
---|
1871 | aws->at("compr_tree_name"); aws->create_input_field(AWAR_DIST_TREE_COMP_NAME, 12); |
---|
1872 | aws->at("sort_tree_name"); aws->create_input_field(AWAR_DIST_TREE_SORT_NAME, 12); |
---|
1873 | |
---|
1874 | // tree calculation |
---|
1875 | |
---|
1876 | aws->button_length(18); |
---|
1877 | |
---|
1878 | aws->at("t_calculate"); |
---|
1879 | aws->callback(makeWindowCallback(di_calculate_tree_cb, weighted_filter, false)); |
---|
1880 | aws->create_button("CALC_TREE", "Calculate \ntree", "C"); |
---|
1881 | |
---|
1882 | aws->at("bootstrap"); |
---|
1883 | aws->callback(makeWindowCallback(di_calculate_tree_cb, weighted_filter, true)); |
---|
1884 | aws->create_button("CALC_BOOTSTRAP_TREE", "Calculate \nbootstrap tree"); |
---|
1885 | |
---|
1886 | recalculate_tree_cb = new BoundWindowCallback(aws, makeWindowCallback(di_calculate_tree_cb, weighted_filter, false)); |
---|
1887 | |
---|
1888 | aws->button_length(22); |
---|
1889 | aws->at("use_existing"); |
---|
1890 | aws->callback(di_define_save_tree_name_cb); |
---|
1891 | aws->create_button("USE_NAME", "Use as new tree name", ""); |
---|
1892 | |
---|
1893 | aws->at("calc_tree_name"); |
---|
1894 | aws->create_input_field(AWAR_DIST_TREE_STD_NAME, 12); |
---|
1895 | |
---|
1896 | aws->at("bcount"); |
---|
1897 | aws->create_input_field(AWAR_DIST_BOOTSTRAP_COUNT, 7); |
---|
1898 | |
---|
1899 | { |
---|
1900 | aws->sens_mask(AWM_EXP); |
---|
1901 | |
---|
1902 | aws->at("auto_calc_tree"); |
---|
1903 | aws->label("Auto calculate tree"); |
---|
1904 | aws->create_toggle(AWAR_DIST_MATRIX_AUTO_CALC_TREE); |
---|
1905 | |
---|
1906 | aws->at("auto_recalc"); |
---|
1907 | aws->label("Auto recalculate"); |
---|
1908 | aws->create_toggle(AWAR_DIST_MATRIX_AUTO_RECALC); |
---|
1909 | |
---|
1910 | aws->sens_mask(AWM_ALL); |
---|
1911 | } |
---|
1912 | |
---|
1913 | bool disable_autocalc = !ARB_in_expert_mode(aw_root); |
---|
1914 | if (disable_autocalc) { |
---|
1915 | aw_root->awar(AWAR_DIST_MATRIX_AUTO_RECALC)->write_int(0); |
---|
1916 | aw_root->awar(AWAR_DIST_MATRIX_AUTO_CALC_TREE)->write_int(0); |
---|
1917 | } |
---|
1918 | |
---|
1919 | GB_pop_transaction(GLOBAL_gb_main); |
---|
1920 | return aws; |
---|
1921 | } |
---|
1922 | |
---|