1 | // =============================================================== // |
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2 | // // |
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3 | // File : ED4_text_terminals.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 <ed4_extern.hxx> |
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12 | |
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13 | #include "ed4_class.hxx" |
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14 | #include "ed4_awars.hxx" |
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15 | #include "ed4_edit_string.hxx" |
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16 | #include "ed4_block.hxx" |
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17 | #include "ed4_nds.hxx" |
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18 | #include "ed4_visualizeSAI.hxx" |
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19 | #include "ed4_ProteinViewer.hxx" |
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20 | #include "ed4_protein_2nd_structure.hxx" |
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21 | #include "ed4_seq_colors.hxx" |
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22 | |
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23 | #include <aw_preset.hxx> |
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24 | #include <aw_awar.hxx> |
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25 | |
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26 | #include <AW_helix.hxx> |
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27 | #include <aw_msg.hxx> |
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28 | #include <aw_root.hxx> |
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29 | |
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30 | #include <st_window.hxx> |
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31 | #include <arbdbt.h> |
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32 | |
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33 | #include <iostream> |
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34 | |
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35 | inline void ensure_buffer(char*& buffer, size_t& buffer_size, size_t needed) { |
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36 | if (needed>buffer_size) { |
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37 | delete [] buffer; |
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38 | buffer_size = needed+10; |
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39 | buffer = new char[buffer_size]; |
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40 | |
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41 | memset(buffer, ' ', buffer_size-1); |
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42 | buffer[buffer_size-1] = 0; |
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43 | } |
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44 | } |
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45 | |
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46 | void ED4_consensus_sequence_terminal::draw() { |
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47 | static char *buffer = NULp; |
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48 | static size_t buffer_size = 0; |
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49 | |
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50 | AW_pos x, y; |
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51 | calc_world_coords(&x, &y); |
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52 | current_ed4w()->world_to_win_coords(&x, &y); |
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53 | |
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54 | PosRange index_range = calc_update_interval(); |
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55 | if (index_range.is_empty()) return; // nothing to draw |
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56 | |
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57 | AW_pos text_x = x + CHARACTEROFFSET; // don't change |
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58 | AW_pos text_y = y + SEQ_TERM_TEXT_YOFFSET; |
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59 | |
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60 | buffer_size = 0; |
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61 | |
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62 | if (index_range.is_unlimited()) { |
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63 | e4_assert(MAXSEQUENCECHARACTERLENGTH == 0); // allow missing update interval when no seqdata is present (yet) |
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64 | |
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65 | const char *no_data = "No consensus data"; |
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66 | size_t len = strlen(no_data); |
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67 | ensure_buffer(buffer, buffer_size, len+1); |
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68 | memcpy(buffer, no_data, len); |
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69 | |
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70 | index_range = ExplicitRange(index_range, buffer_size-1); |
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71 | } |
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72 | else { |
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73 | const ED4_remap *rm = ED4_ROOT->root_group_man->remap(); |
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74 | |
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75 | index_range = rm->clip_screen_range(index_range); |
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76 | if (index_range.is_empty()) return; // nothing to draw |
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77 | |
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78 | ExplicitRange seq_range = ExplicitRange(rm->screen_to_sequence(index_range), MAXSEQUENCECHARACTERLENGTH); |
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79 | index_range = rm->sequence_to_screen(seq_range); |
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80 | |
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81 | char *cons = NULp; |
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82 | if (!seq_range.is_empty()) { |
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83 | cons = GB_give_buffer(seq_range.size()+1); |
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84 | get_char_table().build_consensus_string_to(cons, seq_range, ED4_ROOT->get_consensus_params()); |
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85 | } |
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86 | |
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87 | ensure_buffer(buffer, buffer_size, index_range.end()+1); |
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88 | |
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89 | ED4_reference *ref = ED4_ROOT->reference; |
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90 | bool only_show_diff = ref->only_show_diff_for(this); |
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91 | |
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92 | for (int pos = index_range.start(); pos <= index_range.end(); ++pos) { |
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93 | int seq_pos = rm->screen_to_sequence(pos); |
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94 | if (seq_pos<0) { |
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95 | buffer[pos] = ' '; |
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96 | } |
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97 | else { |
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98 | char c = cons[seq_pos-seq_range.start()]; |
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99 | buffer[pos] = only_show_diff ? ref->convert(c, seq_pos) : c; |
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100 | e4_assert(buffer[pos]); |
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101 | } |
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102 | } |
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103 | } |
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104 | |
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105 | if (buffer_size) { |
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106 | current_device()->set_vertical_font_overlap(true); |
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107 | current_device()->text(ED4_G_SEQUENCES, SizedCstr(buffer, index_range.end()+1), text_x, text_y, 0, AW_SCREEN); |
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108 | current_device()->set_vertical_font_overlap(false); |
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109 | } |
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110 | } |
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111 | |
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112 | struct ShowHelix_cd { |
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113 | AW_helix *helix; |
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114 | int real_sequence_length; |
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115 | }; |
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116 | |
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117 | static bool ED4_show_helix_on_device(AW_device *device, int gc, const char *helixBuffer, size_t helixStart, size_t helixLen, const AW::Position& pos, AW_CL cduser) { |
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118 | ShowHelix_cd *cd = (ShowHelix_cd*)cduser; |
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119 | AW_helix *helix = cd->helix; |
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120 | const ED4_remap *rm = ED4_ROOT->root_group_man->remap(); |
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121 | char *buffer = GB_give_buffer(helixLen+1); |
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122 | long i, j, k; |
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123 | |
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124 | helixLen = std::min(rm->get_max_screen_pos(), helixLen); |
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125 | |
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126 | for (k=0; size_t(k)<helixLen; k++) { |
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127 | i = rm->screen_to_sequence(k+helixStart); |
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128 | |
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129 | BI_PAIR_TYPE pairType = helix->pairtype(i); |
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130 | if (pairType == HELIX_NONE) { |
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131 | buffer[k] = ' '; |
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132 | } |
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133 | else { |
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134 | j = helix->opposite_position(i); |
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135 | char pairchar = j<cd->real_sequence_length ? helixBuffer[j] : '.'; |
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136 | buffer[k] = helix->get_symbol(helixBuffer[i], pairchar, pairType); |
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137 | } |
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138 | } |
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139 | buffer[helixLen] = 0; |
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140 | return device->text(gc, buffer, pos); |
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141 | } |
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142 | |
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143 | static bool ED4_show_protein_match_on_device(AW_device *device, int gc, const char *pfoldBuffer, size_t pfoldStart, size_t pfoldLen, const AW::Position& pos, AW_CL cl_protstruct) { |
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144 | /*! \brief Calls ED4_pfold_calculate_secstruct_match() for the visible area in the |
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145 | * editor to compute the protein secondary structure match and outputs the |
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146 | * result to the device. |
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147 | * \param[in] pfoldBuffer The protein structure (primary or secondary) that should be compared to \a cl_protstruct |
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148 | * \param[in] cl_protstruct The reference protein secondary structure SAI |
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149 | */ |
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150 | |
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151 | GB_ERROR error = NULp; |
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152 | // TODO: proper use of ED4_remap? |
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153 | const ED4_remap *rm = ED4_ROOT->root_group_man->remap(); |
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154 | char *buffer = GB_give_buffer(pfoldLen+1); |
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155 | if (!buffer) { |
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156 | error = GB_export_error("Out of memory."); |
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157 | } |
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158 | else { |
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159 | error = ED4_pfold_calculate_secstruct_match((const unsigned char *)cl_protstruct, |
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160 | (const unsigned char *)pfoldBuffer, |
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161 | rm->screen_to_sequence(pfoldStart), |
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162 | rm->screen_to_sequence(pfoldStart + pfoldLen), |
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163 | buffer, |
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164 | (PFOLD_MATCH_METHOD)ED4_ROOT->aw_root->awar(PFOLD_AWAR_MATCH_METHOD)->read_int()); |
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165 | } |
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166 | if (error) { |
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167 | aw_message(error); |
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168 | return false; |
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169 | } |
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170 | |
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171 | buffer[pfoldLen] = 0; |
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172 | return device->text(gc, buffer, pos); |
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173 | } |
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174 | |
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175 | void ED4_orf_terminal::draw() { |
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176 | // draw aminoacid ORFs below the DNA sequence |
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177 | |
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178 | static int color_is_used[ED4_G_DRAG]; |
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179 | static char **colored_strings = NULp; |
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180 | static int len_of_colored_strings = 0; |
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181 | |
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182 | AW_device *device = current_device(); |
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183 | |
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184 | // @@@ DRY calculation of index-range to-be-updated (done in several draw functions) |
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185 | AW_pos world_x, world_y; |
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186 | calc_world_coords(&world_x, &world_y); |
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187 | current_ed4w()->world_to_win_coords(&world_x, &world_y); |
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188 | |
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189 | AW_pos text_x = world_x + CHARACTEROFFSET; // don't change |
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190 | AW_pos text_y = world_y + SEQ_TERM_TEXT_YOFFSET; |
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191 | |
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192 | const ED4_remap *rm = ED4_ROOT->root_group_man->remap(); |
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193 | |
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194 | ExplicitRange index_range = rm->clip_screen_range(calc_update_interval()); |
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195 | { |
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196 | int max_seq_len = aaSeqLen; |
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197 | int max_seq_pos = rm->sequence_to_screen(max_seq_len-1); |
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198 | index_range = ExplicitRange(PosRange(index_range), max_seq_pos); |
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199 | } |
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200 | |
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201 | if (index_range.is_empty()) { |
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202 | // @@@ looks wrong (index_range is empty depending on updated area!) |
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203 | // compare to .@DRAW_WRONG_MESSAGE |
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204 | |
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205 | const char *no_data = "No sequence data"; |
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206 | |
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207 | device->text(ED4_G_STANDARD, no_data, text_x, text_y, 0, AW_SCREEN); |
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208 | return; // nothing to draw |
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209 | } |
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210 | |
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211 | if (index_range.end() >= len_of_colored_strings) { |
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212 | len_of_colored_strings = index_range.end() + 256; |
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213 | if (!colored_strings) ARB_calloc(colored_strings, ED4_G_DRAG); |
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214 | |
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215 | for (int i=0; i<ED4_G_DRAG; i++) { |
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216 | freeset(colored_strings[i], ARB_alloc<char>(len_of_colored_strings+1)); |
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217 | memset(colored_strings[i], ' ', len_of_colored_strings); |
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218 | colored_strings[i][len_of_colored_strings] = 0; |
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219 | } |
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220 | } |
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221 | |
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222 | int seq_end = rm->screen_to_sequence(index_range.end()); |
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223 | |
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224 | // mark all strings as unused |
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225 | memset(color_is_used, 0, sizeof(color_is_used)); |
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226 | |
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227 | int iDisplayMode = ED4_ROOT->aw_root->awar(AWAR_PROTVIEW_DISPLAY_OPTIONS)->read_int(); |
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228 | { |
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229 | const unsigned char *aaSequence_u = (const unsigned char *)aaSequence; |
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230 | const unsigned char *aaColor_u = (const unsigned char *)aaColor; |
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231 | |
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232 | if (iDisplayMode == PV_AA_NAME || iDisplayMode == PV_AA_CODE) { |
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233 | // transform strings, compress if needed |
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234 | ED4_reference *ref = ED4_ROOT->reference; |
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235 | ref->expand_to_length(seq_end); |
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236 | |
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237 | char *char_2_char = ED4_ROOT->sequence_colors->char_2_char_aa; |
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238 | char *char_2_gc = ED4_ROOT->sequence_colors->char_2_gc_aa; |
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239 | |
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240 | if (iDisplayMode == PV_AA_NAME) { |
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241 | for (int scr_pos=index_range.start(); scr_pos <= index_range.end(); scr_pos++) { |
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242 | int seq_pos = rm->screen_to_sequence(scr_pos); |
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243 | unsigned char c = aaSequence_u[seq_pos]; |
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244 | unsigned char cc = aaColor_u[seq_pos]; |
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245 | int gc = char_2_gc[safeCharIndex(cc)]; |
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246 | |
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247 | color_is_used[gc] = scr_pos+1; |
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248 | colored_strings[gc][scr_pos] = char_2_char[safeCharIndex(c)]; |
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249 | } |
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250 | } |
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251 | else { |
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252 | for (int scr_pos=index_range.start(); scr_pos <= index_range.end(); scr_pos++) { |
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253 | int seq_pos = rm->screen_to_sequence(scr_pos); |
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254 | char c = aaSequence_u[seq_pos]; |
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255 | int gc = char_2_gc[safeCharIndex(c)]; |
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256 | |
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257 | color_is_used[gc] = scr_pos+1; |
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258 | colored_strings[gc][scr_pos] = char_2_char[safeCharIndex(c)]; |
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259 | } |
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260 | } |
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261 | } |
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262 | |
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263 | // paint background |
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264 | if ((iDisplayMode == PV_AA_CODE) || (iDisplayMode == PV_AA_BOX)) { |
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265 | AW_pos width = ED4_ROOT->font_group.get_width(ED4_G_SEQUENCES); |
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266 | const int real_left = index_range.start(); |
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267 | const int real_right = index_range.end(); |
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268 | AW_pos x2 = text_x + width*real_left; |
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269 | AW_pos y1 = world_y; |
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270 | AW_pos y2 = text_y+1; |
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271 | AW_pos height = y2-y1+1; |
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272 | int color = ED4_G_STANDARD; |
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273 | char *char_2_gc_aa = ED4_ROOT->sequence_colors->char_2_gc_aa; |
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274 | |
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275 | for (int i = real_left; i <= real_right; i++, x2 += width) { |
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276 | int new_pos = rm->screen_to_sequence(i); // getting the real position of the base in the sequence |
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277 | char base = aaSequence_u[new_pos]; |
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278 | |
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279 | if (isupper(base) || (base=='*')) { |
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280 | AW_pos x1 = x2-width; // store current x pos to x1 |
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281 | x2 += width*2; // add 2 char width to x2 |
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282 | i += 2; // jump two pos |
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283 | |
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284 | int gcChar = char_2_gc_aa[safeCharIndex(base)]; |
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285 | if ((gcChar>=0) && (gcChar<ED4_G_DRAG)) { |
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286 | color = gcChar; |
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287 | if (iDisplayMode == PV_AA_BOX) { |
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288 | device->box(color, AW::FillStyle::SOLID, x1, y1, width*3, height); |
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289 | } |
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290 | else { |
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291 | double rad_x = width*1.5; |
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292 | double rad_y = height*0.7; |
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293 | double center_x = x1+rad_x; |
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294 | const int DRAW_DEG = 62; |
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295 | |
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296 | device->arc(ED4_G_SEQUENCES, AW::FillStyle::EMPTY, center_x, y1, rad_x, rad_y, 0, DRAW_DEG); |
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297 | device->arc(ED4_G_SEQUENCES, AW::FillStyle::EMPTY, center_x, y1, rad_x, rad_y, 180, -DRAW_DEG); |
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298 | } |
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299 | } |
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300 | } |
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301 | } |
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302 | } |
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303 | } |
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304 | |
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305 | if ((iDisplayMode == PV_AA_NAME) || (iDisplayMode == PV_AA_CODE)) { |
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306 | device->set_vertical_font_overlap(true); |
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307 | // output strings |
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308 | for (int gc = 0; gc < ED4_G_DRAG; gc++) { |
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309 | if (color_is_used[gc] && (int)strlen(colored_strings[gc]) >= color_is_used[gc]) { |
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310 | device->text(gc, SizedCstr(colored_strings[gc], color_is_used[gc]), text_x, text_y, 0, AW_SCREEN); |
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311 | memset(colored_strings[gc] + index_range.start(), ' ', index_range.size()); // clear string |
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312 | } |
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313 | } |
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314 | device->set_vertical_font_overlap(false); |
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315 | } |
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316 | } |
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317 | |
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318 | void ED4_sequence_terminal::draw() { |
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319 | static int color_is_used[ED4_G_DRAG]; |
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320 | static char **colored_strings = NULp; |
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321 | static int len_of_colored_strings = 0; |
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322 | |
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323 | #if defined(TRACE_REFRESH) |
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324 | fprintf(stderr, "ED4_sequence_terminal::draw for id='%s'\n", id); fflush(stderr); |
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325 | #endif |
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326 | |
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327 | AW_device *device = current_device(); |
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328 | |
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329 | int max_seq_len; |
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330 | resolve_pointer_to_char_pntr(&max_seq_len); |
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331 | e4_assert(max_seq_len>0); |
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332 | |
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333 | AW_pos world_x, world_y; |
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334 | calc_world_coords(&world_x, &world_y); |
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335 | current_ed4w()->world_to_win_coords(&world_x, &world_y); |
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336 | |
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337 | AW_pos text_x = world_x + CHARACTEROFFSET; // don't change |
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338 | AW_pos text_y = world_y + SEQ_TERM_TEXT_YOFFSET; |
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339 | |
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340 | const ED4_remap *rm = ED4_ROOT->root_group_man->remap(); |
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341 | |
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342 | ExplicitRange index_range = rm->clip_screen_range(calc_update_interval()); |
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343 | if (index_range.is_empty()) return; // nothing to draw |
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344 | |
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345 | int left = index_range.start(); // @@@ do similar to ED4_orf_terminal::draw here |
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346 | int right = index_range.end(); |
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347 | |
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348 | { |
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349 | int max_seq_pos = rm->sequence_to_screen(max_seq_len-1); |
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350 | |
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351 | if (right>max_seq_len) right = max_seq_pos; |
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352 | if (left>right) { |
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353 | // @@@ may be correct here |
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354 | // compare to .@DRAW_WRONG_MESSAGE |
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355 | |
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356 | const char *no_data = "No sequence data"; |
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357 | |
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358 | device->text(ED4_G_STANDARD, no_data, text_x, text_y, 0, AW_SCREEN); |
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359 | return; // nothing to draw |
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360 | } |
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361 | } |
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362 | |
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363 | if (right >= len_of_colored_strings) { |
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364 | len_of_colored_strings = right + 256; |
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365 | if (!colored_strings) ARB_calloc(colored_strings, ED4_G_DRAG); |
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366 | |
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367 | for (int i=0; i<ED4_G_DRAG; i++) { |
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368 | freeset(colored_strings[i], (char *)malloc(sizeof(char) * (len_of_colored_strings+1))); |
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369 | memset(colored_strings[i], ' ', len_of_colored_strings); |
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370 | colored_strings[i][len_of_colored_strings] = 0; |
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371 | } |
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372 | } |
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373 | |
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374 | int seq_start = rm->screen_to_sequence(left); // real start of sequence |
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375 | int seq_end = rm->screen_to_sequence(right); |
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376 | |
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377 | // mark all strings as unused |
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378 | memset(color_is_used, 0, sizeof(color_is_used)); |
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379 | |
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380 | // transform strings, compress if needed |
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381 | { |
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382 | ED4_reference *ref = ED4_ROOT->reference; |
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383 | unsigned char *db_pointer = (unsigned char *)resolve_pointer_to_string_copy(); |
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384 | |
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385 | ref->expand_to_length(seq_end); |
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386 | |
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387 | GB_alignment_type aliType = GetAliType(); |
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388 | char *char_2_char = (aliType && (aliType==GB_AT_AA)) ? ED4_ROOT->sequence_colors->char_2_char_aa : ED4_ROOT->sequence_colors->char_2_char; |
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389 | char *char_2_gc = (aliType && (aliType==GB_AT_AA)) ? ED4_ROOT->sequence_colors->char_2_gc_aa : ED4_ROOT->sequence_colors->char_2_gc; |
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390 | |
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391 | bool only_show_diff = ref->only_show_diff_for(this); |
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392 | for (int scr_pos=left; scr_pos <= right; scr_pos++) { |
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393 | int seq_pos = rm->screen_to_sequence(scr_pos); |
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394 | int c = db_pointer[seq_pos]; |
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395 | int gc = char_2_gc[c]; |
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396 | |
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397 | color_is_used[gc] = scr_pos+1; |
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398 | colored_strings[gc][scr_pos] = char_2_char[only_show_diff ? ref->convert(c, seq_pos) : c]; |
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399 | } |
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400 | |
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401 | free(db_pointer); |
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402 | } |
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403 | |
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404 | // Set background |
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405 | |
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406 | { |
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407 | GB_transaction ta(ED4_ROOT->get_gb_main()); |
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408 | ST_ML_Color *statColors = NULp; |
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409 | char *searchColors = results().buildColorString(this, seq_start, seq_end); // defined in ED4_SearchResults class : ED4_search.cxx |
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410 | ED4_species_manager *spec_man = get_parent(LEV_SPECIES)->to_species_manager(); |
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411 | int color_group = AW_color_groups_active() ? GBT_get_color_group(spec_man->get_species_pointer()) : 0; |
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412 | |
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413 | PosRange selection; |
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414 | int is_selected = ED4_get_selected_range(this, selection); |
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415 | int is_marked = GB_read_flag(spec_man->get_species_pointer()); |
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416 | |
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417 | if (species_name && |
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418 | ED4_ROOT->column_stat_activated && |
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419 | (st_ml_node || (st_ml_node = STAT_find_node_by_name(ED4_ROOT->st_ml, this->species_name)))) |
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420 | { |
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421 | statColors = STAT_get_color_string(ED4_ROOT->st_ml, NULp, st_ml_node, seq_start, seq_end); |
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422 | } |
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423 | |
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424 | const char *saiColors = NULp; |
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425 | |
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426 | if (species_name && |
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427 | ED4_ROOT->visualizeSAI && |
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428 | spec_man->get_type() != ED4_SP_SAI && |
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429 | (is_marked || ED4_ROOT->visualizeSAI_allSpecies)) |
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430 | { |
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431 | saiColors = ED4_getSaiColorString(ED4_ROOT->aw_root, seq_start, seq_end); |
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432 | } |
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433 | |
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434 | if (statColors || searchColors || is_marked || is_selected || color_group || saiColors) { |
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435 | int i; |
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436 | AW_pos width = ED4_ROOT->font_group.get_width(ED4_G_SEQUENCES); |
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437 | int real_left = left; |
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438 | int real_right = right; |
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439 | AW_pos x2 = text_x + width*real_left; |
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440 | AW_pos old_x = x2; |
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441 | AW_pos y1 = world_y; |
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442 | AW_pos y2 = text_y+1; |
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443 | AW_pos height = y2-y1+1; |
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444 | int old_color = ED4_G_STANDARD; |
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445 | int color = ED4_G_STANDARD; |
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446 | |
---|
447 | int back_color; |
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448 | if (is_marked) back_color = ED4_G_MARKED; |
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449 | else if (color_group) back_color = ED4_G_FIRST_COLOR_GROUP+color_group-1; |
---|
450 | else back_color = ED4_G_STANDARD; |
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451 | |
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452 | if (is_selected && selection.is_unlimited()) { |
---|
453 | selection = ExplicitRange(selection, rm->screen_to_sequence(real_right)); |
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454 | } |
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455 | |
---|
456 | for (i = real_left; i <= real_right; i++, x2 += width) { |
---|
457 | int new_pos = rm->screen_to_sequence(i); // getting the real position of the base in the sequence |
---|
458 | |
---|
459 | // Note: if you change background color priorities, |
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460 | // please update help in ../HELP_SOURCE/source/e4_background_priority.hlp@COLOR_PRIORITY |
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461 | |
---|
462 | if (searchColors && searchColors[new_pos]) { |
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463 | color = searchColors[new_pos]; |
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464 | } |
---|
465 | else if (is_selected && selection.contains(new_pos)) { |
---|
466 | color = ED4_G_SELECTED; |
---|
467 | } |
---|
468 | else if (statColors) { |
---|
469 | color = statColors[new_pos] + ED4_G_CBACK_0; |
---|
470 | if (color > ED4_G_CBACK_9) color = ED4_G_CBACK_9; |
---|
471 | } |
---|
472 | else if (saiColors) { |
---|
473 | color = saiColors[new_pos]; |
---|
474 | if (color < ED4_G_CBACK_0 || color > ED4_G_CBACK_9) color = back_color; |
---|
475 | } |
---|
476 | else { |
---|
477 | color = back_color; |
---|
478 | } |
---|
479 | |
---|
480 | if (color != old_color) { // draw till oldcolor |
---|
481 | if (x2>old_x) { |
---|
482 | if (old_color!=ED4_G_STANDARD) { |
---|
483 | device->box(old_color, AW::FillStyle::SOLID, old_x, y1, x2-old_x, height); // paints the search pattern background |
---|
484 | } |
---|
485 | } |
---|
486 | old_x = x2; |
---|
487 | old_color = color; |
---|
488 | } |
---|
489 | } |
---|
490 | |
---|
491 | if (x2>old_x) { |
---|
492 | if (color!=ED4_G_STANDARD) { |
---|
493 | device->box(color, AW::FillStyle::SOLID, old_x, y1, x2-old_x, height); |
---|
494 | } |
---|
495 | } |
---|
496 | } |
---|
497 | } |
---|
498 | |
---|
499 | device->set_vertical_font_overlap(true); |
---|
500 | |
---|
501 | if (shall_display_secstruct_info) { |
---|
502 | if (ED4_ROOT->helix->is_enabled()) { |
---|
503 | // output helix |
---|
504 | int db_len; |
---|
505 | char *db_pointer = resolve_pointer_to_string_copy(&db_len); |
---|
506 | |
---|
507 | e4_assert(size_t(db_len) == ED4_ROOT->helix->size()); |
---|
508 | ShowHelix_cd cd = { ED4_ROOT->helix, max_seq_len }; |
---|
509 | device->text_overlay(ED4_G_HELIX, |
---|
510 | SizedCstr(db_pointer, db_len), |
---|
511 | AW::Position(text_x, text_y + ED4_ROOT->helix_spacing), 0.0, AW_ALL_DEVICES_UNSCALED, |
---|
512 | ED4_show_helix_on_device, (AW_CL)&cd); |
---|
513 | free(db_pointer); |
---|
514 | } |
---|
515 | |
---|
516 | if (ED4_ROOT->protstruct) { |
---|
517 | // output protein structure match |
---|
518 | ED4_species_manager *spec_man = get_parent(LEV_SPECIES)->to_species_manager(); |
---|
519 | if (spec_man->get_type() != ED4_SP_SAI && ED4_ROOT->aw_root->awar(PFOLD_AWAR_ENABLE)->read_int()) { // should do a remap |
---|
520 | int db_len; |
---|
521 | char *protstruct = resolve_pointer_to_string_copy(&db_len); |
---|
522 | |
---|
523 | if (protstruct) { |
---|
524 | device->text_overlay(ED4_G_HELIX, |
---|
525 | SizedCstr(protstruct, db_len), |
---|
526 | AW::Position(text_x, text_y + ED4_ROOT->helix_spacing), 0.0, AW_ALL_DEVICES_UNSCALED, |
---|
527 | ED4_show_protein_match_on_device, (AW_CL)ED4_ROOT->protstruct); |
---|
528 | free(protstruct); |
---|
529 | } |
---|
530 | } |
---|
531 | } |
---|
532 | } |
---|
533 | // output strings |
---|
534 | { |
---|
535 | int gc; |
---|
536 | for (gc = 0; gc < ED4_G_DRAG; gc++) { |
---|
537 | if (!color_is_used[gc]) continue; |
---|
538 | device->text(gc, SizedCstr(colored_strings[gc], color_is_used[gc]), text_x, text_y, 0, AW_SCREEN); |
---|
539 | memset(colored_strings[gc] + left, ' ', right-left+1); // clear string |
---|
540 | } |
---|
541 | } |
---|
542 | |
---|
543 | device->set_vertical_font_overlap(false); |
---|
544 | } |
---|
545 | |
---|
546 | |
---|
547 | void ED4_sequence_info_terminal::draw() { |
---|
548 | AW_pos x, y; |
---|
549 | calc_world_coords(&x, &y); |
---|
550 | current_ed4w()->world_to_win_coords(&x, &y); |
---|
551 | |
---|
552 | AW_pos text_x = x + CHARACTEROFFSET; // don't change |
---|
553 | AW_pos text_y = y+INFO_TERM_TEXT_YOFFSET; |
---|
554 | |
---|
555 | char buffer[10]; |
---|
556 | GBDATA *gbdata = data(); |
---|
557 | |
---|
558 | if (gbdata) { |
---|
559 | GB_push_transaction(gbdata); |
---|
560 | buffer[0] = '0' + GB_read_security_write(gbdata); |
---|
561 | GB_pop_transaction(gbdata); |
---|
562 | } |
---|
563 | else { |
---|
564 | buffer[0] = ' '; |
---|
565 | } |
---|
566 | strncpy(&buffer[1], this->id, 8); |
---|
567 | buffer[9] = 0; |
---|
568 | |
---|
569 | if (containing_species_manager()->is_selected()) { |
---|
570 | current_device()->box(ED4_G_SELECTED, AW::FillStyle::SOLID, x, y, extension.size[WIDTH], text_y-y+1); |
---|
571 | } |
---|
572 | |
---|
573 | current_device()->set_vertical_font_overlap(true); |
---|
574 | current_device()->text(ED4_G_STANDARD, buffer, text_x, text_y, 0, AW_SCREEN); |
---|
575 | current_device()->set_vertical_font_overlap(false); |
---|
576 | } |
---|
577 | |
---|
578 | // --------------------------- |
---|
579 | // ED4_text_terminal |
---|
580 | |
---|
581 | void ED4_text_terminal::draw() { |
---|
582 | AW_pos x, y; |
---|
583 | calc_world_coords(&x, &y); |
---|
584 | current_ed4w()->world_to_win_coords(&x, &y); |
---|
585 | |
---|
586 | AW_pos text_x = x + CHARACTEROFFSET; // don't change |
---|
587 | AW_pos text_y = y + INFO_TERM_TEXT_YOFFSET; |
---|
588 | |
---|
589 | current_device()->set_vertical_font_overlap(true); |
---|
590 | |
---|
591 | if (is_species_name_terminal()) { // @@@ handle by virtual method (eg. draw_text()) |
---|
592 | GB_CSTR real_name = to_species_name_terminal()->get_displayed_text(); |
---|
593 | int width_of_char; |
---|
594 | int height_of_char = -1; |
---|
595 | bool paint_box = inside_species_seq_manager(); |
---|
596 | bool is_marked = false; |
---|
597 | |
---|
598 | if (paint_box) { |
---|
599 | ED4_species_manager *species_man = get_parent(LEV_SPECIES)->to_species_manager(); |
---|
600 | GBDATA *gbd = species_man->get_species_pointer(); |
---|
601 | |
---|
602 | if (gbd) { |
---|
603 | GB_transaction ta(gbd); |
---|
604 | is_marked = GB_read_flag(gbd); |
---|
605 | } |
---|
606 | |
---|
607 | width_of_char = ED4_ROOT->font_group.get_width(ED4_G_STANDARD); |
---|
608 | height_of_char = ED4_ROOT->font_group.get_height(ED4_G_STANDARD); |
---|
609 | #define MIN_MARK_BOX_SIZE 8 |
---|
610 | if (width_of_char<MIN_MARK_BOX_SIZE) width_of_char = MIN_MARK_BOX_SIZE; |
---|
611 | if (height_of_char<MIN_MARK_BOX_SIZE) height_of_char = MIN_MARK_BOX_SIZE; |
---|
612 | #undef MIN_MARK_BOX_SIZE |
---|
613 | } |
---|
614 | else { |
---|
615 | width_of_char = 0; |
---|
616 | } |
---|
617 | |
---|
618 | if (containing_species_manager()->is_selected()) { |
---|
619 | current_device()->box(ED4_G_SELECTED, AW::FillStyle::SOLID, x, y, extension.size[WIDTH], text_y-y+1); |
---|
620 | } |
---|
621 | current_device()->text(ED4_G_STANDARD, real_name, text_x+width_of_char, text_y, 0, AW_SCREEN); |
---|
622 | |
---|
623 | if (paint_box) { |
---|
624 | int xsize = (width_of_char*6)/10; |
---|
625 | int ysize = (height_of_char*6)/10; |
---|
626 | int xoff = xsize>>1; |
---|
627 | int yoff = 0; |
---|
628 | int bx = int(text_x+xoff); |
---|
629 | int by = int(text_y-(yoff+ysize)); |
---|
630 | |
---|
631 | current_device()->box(ED4_G_STANDARD, AW::FillStyle::SOLID, bx, by, xsize, ysize); |
---|
632 | if (!is_marked && xsize>2 && ysize>2) { |
---|
633 | current_device()->clear_part(bx+1, by+1, xsize-2, ysize-2, AW_ALL_DEVICES); |
---|
634 | } |
---|
635 | } |
---|
636 | } |
---|
637 | else if (is_flag_header_terminal()) { // @@@ handle by virtual method (eg. draw_text()) |
---|
638 | ED4_flag_header_terminal *header_term = to_flag_header_terminal(); |
---|
639 | const char *header_text = header_term->get_displayed_text(); |
---|
640 | |
---|
641 | text_y += (SEQ_TERM_TEXT_YOFFSET-INFO_TERM_TEXT_YOFFSET); // @@@ wrong vertical shift? (change fontsize to examine) |
---|
642 | current_device()->text(ED4_G_FLAG_INFO, SizedCstr(header_text, header_term->get_length()), text_x, text_y, 0, AW_SCREEN); |
---|
643 | } |
---|
644 | else { |
---|
645 | e4_assert(is_pure_text_terminal()); // unhandled terminal type that does not overload draw() |
---|
646 | |
---|
647 | char *db_pointer = resolve_pointer_to_string_copy(); |
---|
648 | |
---|
649 | text_y += (SEQ_TERM_TEXT_YOFFSET-INFO_TERM_TEXT_YOFFSET); |
---|
650 | current_device()->text(ED4_G_SEQUENCES, db_pointer, text_x, text_y, 0, AW_SCREEN); |
---|
651 | |
---|
652 | free(db_pointer); |
---|
653 | } |
---|
654 | current_device()->set_vertical_font_overlap(false); |
---|
655 | } |
---|
656 | |
---|
657 | ED4_text_terminal::ED4_text_terminal(const ED4_objspec& spec_, GB_CSTR temp_id, AW_pos width, AW_pos height, ED4_manager *temp_parent) : |
---|
658 | ED4_terminal(spec_, temp_id, width, height, temp_parent) |
---|
659 | {} |
---|
660 | |
---|