1 | /* |
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2 | |
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3 | Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory. |
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4 | All rights reserved. |
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5 | */ |
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6 | |
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7 | #define TRUTH 1 |
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8 | #define JUSTICE 2 |
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9 | #define BEAUTY 3 |
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10 | |
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11 | /* |
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12 | * Cursor directions |
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13 | */ |
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14 | #define RIGHT 1 |
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15 | #define LEFT 0 |
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16 | #define UP 0 |
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17 | #define DOWN 1 |
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18 | |
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19 | #ifndef TRUE |
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20 | #define TRUE 1 |
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21 | #define FALSE 0 |
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22 | #endif |
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23 | |
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24 | #define GBUFSIZ 4096 |
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25 | #define MAX_NA_DISPLAY_WIDTH 1024 |
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26 | #define MAX_NA_DISPLAY_HEIGHT 1024 |
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27 | #define MAX_STARTUP_CANVAS_HEIGHT 512 |
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28 | #define grey_height 8 |
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29 | #define grey_width 8 |
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30 | |
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31 | #define TEXTFIELDWIDTH 15 |
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32 | |
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33 | /* |
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34 | * Definable dialog types |
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35 | */ |
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36 | #define TEXTFIELD 0x1 |
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37 | #define SLIDER 0x2 |
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38 | #define CHOOSER 0x3 |
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39 | #define CHOICE_MENU 0x4 |
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40 | #define CHOICE_LIST 0x5 |
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41 | #define CHOICE_TREE 0x6 |
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42 | #define CHOICE_SAI 0x7 |
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43 | #define CHOICE_WEIGHTS 0x8 |
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44 | |
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45 | /* |
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46 | * File Formats |
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47 | */ |
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48 | #define GDE 0x100 |
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49 | #define GENBANK 0x101 |
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50 | #define NA_FLAT 0x102 |
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51 | #define COLORMASK 0x103 |
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52 | #define STATUS_FILE 0x104 |
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53 | #define ARBDB 0x105 |
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54 | |
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55 | /* |
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56 | * Protection bits |
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57 | */ |
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58 | |
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59 | #define PROT_BASE_CHANGES 0x1 /* Allow base changes */ |
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60 | #define PROT_GREY_SPACE 0x2 /* Allow greyspace modification */ |
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61 | #define PROT_WHITE_SPACE 0x4 /* Allow whitespace modification */ |
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62 | #define PROT_TRANSLATION 0x8 /* Allow translation */ |
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63 | #define PROT_REORIENTATION 0x10 /* Allow reorientation */ |
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64 | |
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65 | |
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66 | /* |
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67 | * File loading methods (must be 'OR/AND' able) |
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68 | */ |
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69 | |
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70 | #define NONE 0x0 |
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71 | #define DESTROY 0x1 |
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72 | #define LOAD 0x2 |
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73 | #define SAVE 0x4 |
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74 | #define SELECTED 0x8 |
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75 | #define ALL 0x10 |
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76 | #define SELECT_REGION 0x20 |
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77 | #define SELECT_ONE 0x30 |
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78 | |
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79 | /* |
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80 | * Sequence DISPLAY Types |
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81 | */ |
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82 | #define NASEQ_ALIGN 0x201 |
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83 | #define NASEQ 0x202 |
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84 | |
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85 | /* |
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86 | * Sequence Data Types |
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87 | */ |
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88 | #define DNA 0x300 |
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89 | #define RNA 0x301 |
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90 | #define TEXT 0x302 |
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91 | #define MASK 0x303 |
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92 | #define PROTEIN 0x304 |
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93 | /* |
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94 | * extended sequence attributes (true/false) |
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95 | */ |
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96 | |
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97 | #define IS_5_TO_3 0x01 /* 5prime to 3 prime */ |
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98 | #define IS_3_TO_5 0x02 /* 3 prime to 5 prime */ |
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99 | #define IS_CIRCULAR 0x04 /* circular dna */ |
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100 | #define IS_PRIMARY 0x10 /* on the primary strand */ |
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101 | #define IS_SECONDARY 0x20 /* on the secondary strand */ |
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102 | #define IS_MODIFIED 0x40 /* modification flag */ |
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103 | #define IS_ORIG_PRIMARY 0x80 /* Original sequence was primary */ |
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104 | #define IS_ORIG_SECONDARY 0x100 /* Original sequence was secondary */ |
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105 | #define IS_ORIG_5_TO_3 0x200 /* Original sequence was 5_to_3 */ |
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106 | #define IS_ORIG_3_TO_5 0x400 /* Original sequence was 3_to_5 */ |
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107 | |
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108 | #ifdef HGL |
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109 | #define DEFAULT_X_ATTR 0 |
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110 | #else |
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111 | #define DEFAULT_X_ATTR IS_5_TO_3+IS_PRIMARY; |
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112 | #endif |
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113 | |
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114 | /* |
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115 | * Other display attributed |
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116 | */ |
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117 | #define INVERTED 1 |
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118 | #define VSCROLL_LOCK 2 |
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119 | #define KEYCLICKS 4 |
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120 | #define GDE_MESSAGE_PANEL 8 |
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121 | |
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122 | /* |
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123 | * Coloring Methods |
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124 | */ |
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125 | #define COLOR_MONO 0x40 /* no color, simple black and white */ |
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126 | #define COLOR_LOOKUP 0x41 /* Use a simple value->color lookup */ |
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127 | #define COLOR_ALN_MASK 0x42 /* The alignment has a column by column color |
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128 | mask associated with it */ |
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129 | #define COLOR_SEQ_MASK 0x43 /* Each sequence has a color mask*/ |
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130 | #define COLOR_STRAND 0x44 /* Color based on original strandedness*/ |
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131 | |
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132 | |
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133 | |
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134 | /* |
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135 | * Data types |
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136 | */ |
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137 | |
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138 | typedef struct { |
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139 | int *valu; |
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140 | } NumList; |
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141 | |
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142 | |
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143 | typedef struct { |
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144 | struct { |
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145 | int yy; |
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146 | int mm; |
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147 | int dd; |
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148 | int hr; |
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149 | int mn; |
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150 | int sc; |
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151 | } origin,modify; |
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152 | } TimeStamp; |
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153 | |
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154 | typedef unsigned char NA_Base; |
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155 | |
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156 | typedef struct { |
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157 | char *name; |
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158 | int type; |
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159 | NumList *list; |
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160 | int listlen; |
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161 | int maxlen; |
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162 | } GMask; |
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163 | |
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164 | |
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165 | typedef struct NA_SeqStruct |
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166 | { |
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167 | char id[80]; /* sequence id (ACCESSION)*/ |
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168 | char seq_name[80]; /* Sequence name (ORGANISM) */ |
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169 | char short_name[32]; /* Name (LOCUS) */ |
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170 | char barcode[80]; |
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171 | char contig[80]; |
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172 | char membrane[80]; |
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173 | char description[80]; /* Description (DEFINITION)*/ |
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174 | char authority[80]; /* Author (or creator) */ |
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175 | char *comments; /* Stuff we can't parse */ |
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176 | int comments_len, comments_maxlen; |
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177 | |
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178 | NA_Base *sequence; /* List of bases */ |
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179 | TimeStamp t_stamp; /* Time stamp of origin/modification */ |
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180 | GMask *mask; /* List of masks(analysis/display) */ |
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181 | int offset; /* offset into alignment (left white) space */ |
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182 | int seqlen; /* Number of elements in sequence[] */ |
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183 | int seqmaxlen; /* Size sequence[] (for mem alloc) */ |
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184 | unsigned int protect; /* Protection mask */ |
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185 | int attr; /* Extended attributes */ |
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186 | size_t groupid; /* group id */ |
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187 | int *col_lut; /* character to color LUT */ |
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188 | |
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189 | struct NA_SeqStruct *groupb; /* Group link backward */ |
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190 | struct NA_SeqStruct *groupf; /* Group link forward */ |
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191 | |
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192 | int *cmask; /* color mask */ |
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193 | int selected; /* Selection flag */ |
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194 | int subselected; /* Sub selection flag */ |
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195 | int format; /* default file format */ |
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196 | int elementtype; /* what type of data are being aligned*/ |
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197 | char *baggage; /* unformatted comments*/ |
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198 | int baggage_len, baggage_maxlen; |
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199 | int *tmatrix; /* translation matrix (code->char) */ |
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200 | int *rmatrix; /* reverse translation matrix (char->code)*/ |
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201 | |
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202 | GBDATA *gb_species; |
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203 | } NA_Sequence; |
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204 | |
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205 | typedef struct |
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206 | { |
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207 | char *id; /* Alignment ID */ |
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208 | char *description; /* Description of the alignment*/ |
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209 | char *authority; /* Who generated the alignment*/ |
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210 | int *cmask; /* color mask */ |
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211 | int cmask_offset; /* color mask offset */ |
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212 | int cmask_len; /* color mask length */ |
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213 | int ref; /* reference sequence */ |
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214 | size_t numelements; /* number of data elements */ |
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215 | int maxnumelements; /* maximum number of data elements */ |
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216 | int nummasks; /* number of masks */ |
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217 | int maxlen; /* Maximum length of alignment */ |
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218 | int rel_offset; /* add this to every sequence offset */ |
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219 | /* to orient it back to 0 */ |
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220 | GMask *mask; /* masks */ |
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221 | NA_Sequence *element; /* alignment elements */ |
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222 | size_t numgroups; /* number of groups */ |
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223 | NA_Sequence **group; /* link to array of pointers into |
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224 | each group */ |
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225 | char *na_ddata; /* display data */ |
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226 | int format; /* default file format */ |
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227 | char *selection_mask; /* Sub sequence selection mask */ |
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228 | int selection_mask_len; /* Sub selection mask length */ |
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229 | int min_subselect; /* Leftmost coord of selection mask */ |
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230 | |
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231 | GBDATA *gb_main; |
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232 | char *alignment_name; |
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233 | |
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234 | } NA_Alignment; |
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235 | |
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236 | extern NA_Alignment *DataSet; |
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237 | |
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238 | |
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239 | #define getcmask(a,b) (b < ((a)->offset))?0:((a)->cmask[(b-(a)->offset)]) |
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240 | |
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