1 | #include <sys/time.h> |
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2 | #include <stdio.h> |
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3 | #include <stdlib.h> |
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4 | // #include <malloc.h> |
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5 | #include <string.h> |
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6 | #include <time.h> |
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7 | |
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8 | //#include <xview/xview.h> |
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9 | //#include <xview/panel.h> |
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10 | |
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11 | #include <arbdb.h> |
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12 | #include <aw_root.hxx> |
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13 | #include <aw_device.hxx> |
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14 | #include <aw_window.hxx> |
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15 | #include <awt.hxx> |
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16 | |
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17 | #include "gde.hxx" |
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18 | #include "GDE_menu.h" |
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19 | #include "GDE_def.h" |
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20 | #include "GDE_extglob.h" |
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21 | |
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22 | /* |
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23 | Copyright (c) 1990,1991,1992 Steven Smith at the Harvard Genome Laboratory. |
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24 | All rights reserved. |
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25 | */ |
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26 | |
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27 | static void AdjustGroups(NA_Alignment *aln) |
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28 | { |
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29 | size_t i; |
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30 | size_t j; |
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31 | int c,done=FALSE; |
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32 | |
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33 | #ifdef HGL |
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34 | return; |
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35 | #else |
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36 | for(c=0;c<200 && !done;c++) |
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37 | { |
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38 | for(j=1;j<=aln->numgroups;j++) |
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39 | { |
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40 | done = FALSE; |
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41 | for(i=0;i<aln->numelements;i++) |
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42 | { |
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43 | if(aln->element[i].groupid == j) |
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44 | { |
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45 | if(aln->element[i].groupf!=NULL || |
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46 | aln->element[i].groupb!=NULL) |
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47 | done = TRUE; |
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48 | else |
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49 | aln->element[i].groupid = 0; |
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50 | } |
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51 | } |
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52 | if(done == FALSE) |
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53 | { |
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54 | for(i=0;i<aln->numelements;i++) |
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55 | if(aln->element[i].groupid == aln->numgroups) |
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56 | aln->element[i].groupid = j; |
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57 | aln->numgroups--; |
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58 | } |
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59 | } |
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60 | if(aln->numgroups == 0) |
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61 | done = TRUE; |
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62 | } |
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63 | return; |
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64 | #endif |
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65 | } |
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66 | |
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67 | static void StripSpecial(char *string) |
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68 | { |
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69 | int i,j,len; |
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70 | i=0; |
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71 | |
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72 | len = strlen(string); |
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73 | for(j=0;j<len;j++) |
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74 | { |
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75 | if(string[j] == '"') |
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76 | string[j] = '`'; |
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77 | else if(string[j] == '{') |
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78 | string[j] = '('; |
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79 | else if(string[j] == '}') |
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80 | string[j] = ')'; |
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81 | } |
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82 | //return; |
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83 | } |
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84 | |
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85 | |
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86 | static void RemoveQuotes(char *string) |
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87 | { |
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88 | int i, j, len; |
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89 | |
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90 | len = strlen(string); |
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91 | for(j=0;j<len;j++) { |
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92 | if(string[j] == '"') string[j] = ' '; |
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93 | } |
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94 | |
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95 | for(j=0;string[j]==' ' && j<(int)strlen(string);j++) ; |
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96 | |
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97 | len = strlen(string); |
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98 | for(i=0;i<len - j;i++) string[i] = string[i+j]; |
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99 | |
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100 | for(j=strlen(string)-1; j>=0 && (string[j]=='\n'||string[j]==' '); j--) { |
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101 | string[j] = '\0'; |
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102 | } |
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103 | |
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104 | //return; |
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105 | } |
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106 | |
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107 | /* |
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108 | * OverWrite(), overwrite all non-default data from a sequence entry |
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109 | * onto any entry with the same ID or short name. |
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110 | */ |
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111 | static int OverWrite(NA_Sequence *thiss,NA_Alignment *aln) |
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112 | { |
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113 | size_t j; |
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114 | int indx = -1; |
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115 | NA_Sequence *that; |
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116 | for(j=0;j<aln->numelements;j++) |
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117 | { |
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118 | if(Find2(thiss->id,aln->element[j].id) != -1) |
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119 | if(Find2(aln->element[j].id,thiss->id) != -1) |
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120 | indx = j; |
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121 | } |
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122 | if(indx == -1) |
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123 | for(j=0;j<aln->numelements;j++) |
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124 | { |
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125 | if(Find2(thiss->short_name,aln->element[j].short_name)!= -1) |
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126 | if(Find2(aln->element[j].short_name,thiss->short_name)!= -1) |
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127 | indx = j; |
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128 | } |
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129 | if(indx != -1) |
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130 | { |
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131 | that = &(aln->element[indx]); |
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132 | if(thiss->seq_name[0]) |
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133 | strcpy(that->seq_name,thiss->seq_name); |
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134 | if(thiss->barcode[0]) |
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135 | strcpy(that->barcode,thiss->barcode); |
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136 | if(thiss->contig[0]) |
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137 | strcpy(that->contig,thiss->contig); |
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138 | if(thiss->membrane[0]) |
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139 | strcpy(that->membrane,thiss->membrane); |
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140 | if(thiss->authority[0]) |
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141 | strcpy(that->authority,thiss->authority); |
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142 | if(thiss->short_name[0]) |
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143 | strcpy(that->short_name,thiss->short_name); |
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144 | if(thiss->description[0]) |
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145 | strcpy(that->description,thiss->description); |
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146 | if(thiss->sequence) |
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147 | { |
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148 | free((char*)that->sequence); |
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149 | that->sequence = thiss->sequence; |
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150 | that->seqlen = thiss->seqlen; |
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151 | that->seqmaxlen = thiss->seqmaxlen; |
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152 | } |
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153 | if(thiss->baggage) |
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154 | { |
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155 | that->baggage_len += thiss->baggage_len; |
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156 | that->baggage_maxlen += thiss->baggage_maxlen; |
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157 | if(that->baggage) |
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158 | that->baggage = |
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159 | Realloc(that->baggage,that->baggage_maxlen*sizeof(char)); |
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160 | else |
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161 | that->baggage = Calloc(that->baggage_maxlen,sizeof(char)); |
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162 | strncat(that->baggage,thiss->baggage,that->baggage_maxlen); |
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163 | } |
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164 | if(thiss->comments) |
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165 | { |
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166 | that->comments_len += thiss->comments_len; |
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167 | that->comments_maxlen += thiss->comments_maxlen; |
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168 | if(that->comments) |
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169 | that->comments = |
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170 | Realloc(that->comments,that->comments_maxlen*sizeof(char)); |
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171 | else |
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172 | that->comments = Calloc(that->comments_maxlen,sizeof(char)); |
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173 | strncat(that->comments,thiss->comments,that->comments_maxlen); |
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174 | } |
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175 | if(thiss->cmask) |
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176 | { |
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177 | free((char*)that->cmask); |
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178 | that->cmask = thiss->cmask; |
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179 | } |
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180 | if(thiss->offset != that->offset) |
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181 | that->offset = thiss->offset; |
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182 | if(thiss->attr != 0) |
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183 | that->attr = thiss->attr; |
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184 | if(thiss->groupid != 0) |
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185 | { |
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186 | that->groupid = thiss->groupid; |
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187 | } |
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188 | that->groupb = NULL; |
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189 | that->groupf = NULL; |
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190 | } |
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191 | |
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192 | return(indx); |
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193 | } |
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194 | |
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195 | void ReadGDE(char *filename,NA_Alignment *dataset,int type) |
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196 | { |
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197 | int done = FALSE; |
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198 | size_t len = 0, j=0; |
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199 | int success,count,temp = 0; |
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200 | char in_line[GBUFSIZ],c; |
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201 | char *buffer,*line; |
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202 | size_t buflen = GBUFSIZ; |
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203 | int genclen = 0,curelem = 0; |
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204 | NA_Sequence *this_elem = NULL,temp_elem; |
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205 | FILE *file; |
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206 | |
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207 | type=0;count=0;c=0; |
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208 | |
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209 | ErrorOut5(0!=(file = fopen(filename,"r")),"No such file"); |
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210 | |
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211 | for(;fgets(in_line,GBUFSIZ,file) != 0;) |
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212 | { |
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213 | for(line = in_line;line[0]==' ' || line[0] == '\t';line++) ; |
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214 | |
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215 | if(Find2(line,"{")==0) |
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216 | { |
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217 | this_elem = &temp_elem; |
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218 | InitNASeq(this_elem,DNA); |
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219 | this_elem->offset = -(dataset->rel_offset); |
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220 | } |
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221 | else if(Find2(line,"type")==0) |
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222 | { |
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223 | if(Find(line,"DNA")) |
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224 | { |
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225 | this_elem->elementtype = DNA; |
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226 | this_elem->tmatrix = Default_DNA_Trans; |
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227 | this_elem->rmatrix = Default_NA_RTrans; |
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228 | } |
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229 | else if(Find(line,"RNA")) |
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230 | { |
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231 | this_elem->elementtype = RNA; |
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232 | this_elem->tmatrix = Default_RNA_Trans; |
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233 | this_elem->rmatrix = Default_NA_RTrans; |
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234 | } |
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235 | else if(Find(line,"MASK")) |
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236 | { |
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237 | this_elem->elementtype = MASK; |
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238 | this_elem->rmatrix = NULL; |
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239 | this_elem->tmatrix = NULL; |
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240 | this_elem->col_lut = NULL; |
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241 | } |
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242 | else if(Find(line,"TEXT")) |
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243 | { |
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244 | this_elem->elementtype = TEXT; |
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245 | this_elem->rmatrix = NULL; |
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246 | this_elem->tmatrix = NULL; |
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247 | this_elem->col_lut = NULL; |
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248 | } |
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249 | else if(Find(line,"PROT")) |
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250 | { |
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251 | this_elem->elementtype = PROTEIN; |
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252 | this_elem->rmatrix = NULL; |
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253 | this_elem->tmatrix = NULL; |
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254 | this_elem->col_lut = Default_PROColor_LKUP; |
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255 | } |
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256 | /* |
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257 | this_elem->attr = DEFAULT_X_ATTR; |
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258 | */ |
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259 | } |
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260 | else if(Find2(line,"circular")==0) |
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261 | { |
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262 | sscanf(line,"%*s %d",&temp); |
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263 | if(temp == 1) |
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264 | { |
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265 | this_elem->attr |= IS_CIRCULAR; |
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266 | } |
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267 | else |
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268 | { |
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269 | this_elem->attr &= ~IS_CIRCULAR; |
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270 | } |
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271 | } |
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272 | else if(Find2(line,"orig_direction")==0) |
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273 | { |
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274 | sscanf(line,"%*s %d",&temp); |
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275 | if(temp == 1) |
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276 | { |
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277 | this_elem->attr |= IS_ORIG_5_TO_3; |
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278 | this_elem->attr &= ~IS_ORIG_3_TO_5; |
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279 | } |
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280 | else |
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281 | { |
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282 | this_elem->attr |= IS_ORIG_3_TO_5; |
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283 | this_elem->attr &= ~IS_ORIG_5_TO_3; |
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284 | } |
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285 | } |
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286 | else if(Find2(line,"direction")==0) |
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287 | { |
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288 | sscanf(line,"%*s %d",&temp); |
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289 | if(temp == 1) |
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290 | { |
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291 | this_elem->attr |= IS_5_TO_3; |
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292 | this_elem->attr &= ~IS_3_TO_5; |
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293 | } |
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294 | else |
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295 | { |
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296 | this_elem->attr |= IS_3_TO_5; |
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297 | this_elem->attr &= ~IS_5_TO_3; |
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298 | } |
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299 | } |
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300 | else if(Find2(line,"orig_strand")==0) |
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301 | { |
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302 | sscanf(line,"%*s %d",&temp); |
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303 | if(temp == 1) |
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304 | { |
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305 | this_elem->attr |= IS_ORIG_PRIMARY; |
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306 | this_elem->attr &= ~IS_ORIG_SECONDARY; |
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307 | } |
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308 | else |
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309 | { |
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310 | this_elem->attr |= IS_ORIG_SECONDARY; |
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311 | this_elem->attr &= ~IS_ORIG_PRIMARY; |
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312 | } |
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313 | } |
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314 | else if(Find2(line,"strandedness")==0) |
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315 | { |
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316 | sscanf(line,"%*s %d",&temp); |
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317 | if(temp == 1) |
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318 | { |
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319 | this_elem->attr |= IS_PRIMARY; |
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320 | this_elem->attr &= ~IS_SECONDARY; |
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321 | } |
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322 | else |
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323 | { |
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324 | this_elem->attr |= IS_SECONDARY; |
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325 | this_elem->attr &= ~IS_PRIMARY; |
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326 | } |
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327 | } |
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328 | else if(Find2(line,"creator")==0) |
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329 | { |
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330 | sscanf(line,"%*s %[^\n]",this_elem->authority); |
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331 | RemoveQuotes(this_elem->authority); |
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332 | } |
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333 | else if(Find2(line,"longname")==0) |
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334 | { |
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335 | sscanf(line,"%*s %[^\n]",this_elem->seq_name); |
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336 | RemoveQuotes(this_elem->seq_name); |
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337 | } |
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338 | else if(Find2(line,"descrip")==0) |
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339 | { |
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340 | sscanf(line,"%*s %[^\n]",this_elem->description); |
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341 | RemoveQuotes(this_elem->description); |
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342 | } |
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343 | else if(Find2(line,"name")==0) |
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344 | { |
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345 | sscanf(line,"%*s %[^\n]",this_elem->short_name); |
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346 | RemoveQuotes(this_elem->short_name); |
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347 | } |
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348 | else if(Find2(line,"group-ID")==0) |
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349 | { |
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350 | sscanf(line,"%*s %zu",&(this_elem->groupid)); |
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351 | dataset->numgroups = |
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352 | MAX(this_elem->groupid, dataset->numgroups); |
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353 | } |
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354 | else if(Find2(line,"sequence-ID")==0) |
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355 | { |
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356 | sscanf(line,"%*s %[^\n]",this_elem->id); |
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357 | RemoveQuotes(this_elem->id); |
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358 | } |
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359 | else if(Find2(line,"barcode")==0) |
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360 | { |
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361 | sscanf(line,"%*s %[^\n]",this_elem->barcode); |
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362 | RemoveQuotes(this_elem->barcode); |
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363 | } |
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364 | else if(Find2(line,"membrane")==0) |
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365 | { |
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366 | sscanf(line,"%*s %[^\n]",this_elem->membrane); |
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367 | RemoveQuotes(this_elem->membrane); |
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368 | } |
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369 | else if(Find2(line,"contig")==0) |
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370 | { |
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371 | sscanf(line,"%*s %[^\n]",this_elem->contig); |
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372 | RemoveQuotes(this_elem->contig); |
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373 | } |
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374 | else if(Find2(line,"creation-date")==0) |
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375 | { |
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376 | sscanf(line,"%*s %2d%*c%2d%*c%2d%*c%2d%*c%2d%*c%2d\n", |
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377 | &(this_elem->t_stamp.origin.mm), |
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378 | &(this_elem->t_stamp.origin.dd), |
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379 | &(this_elem->t_stamp.origin.yy), |
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380 | &(this_elem->t_stamp.origin.hr), |
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381 | &(this_elem->t_stamp.origin.mn), |
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382 | &(this_elem->t_stamp.origin.sc)); |
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383 | } |
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384 | else if(Find2(line,"offset")==0) |
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385 | { |
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386 | sscanf(line,"%*s %d",&(this_elem->offset)); |
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387 | this_elem->offset -= dataset->rel_offset; |
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388 | } |
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389 | else if(Find2(line,"comments")==0) |
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390 | { |
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391 | if(this_elem->comments_maxlen ==0) |
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392 | buflen = 2048; |
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393 | else |
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394 | buflen = this_elem->comments_maxlen; |
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395 | |
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396 | done = FALSE; |
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397 | len = this_elem->comments_len; |
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398 | |
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399 | for(;line[0] != '"';line++) |
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400 | if(line[0] == '\0') |
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401 | ErrorOut5(0,"Error in input file"); |
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402 | line++; |
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403 | buffer = Calloc(buflen,sizeof(char)); |
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404 | for(;!done;) |
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405 | { |
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406 | for(j=0;j<strlen(line);j++) |
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407 | { |
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408 | if(len+strlen(line) >= buflen) |
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409 | { |
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410 | buflen *=2; |
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411 | buffer = Realloc(buffer, |
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412 | buflen*sizeof(char)); |
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413 | } |
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414 | if(line[j] == '"') done = TRUE; |
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415 | |
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416 | else |
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417 | buffer[len++] = line[j]; |
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418 | } |
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419 | /* |
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420 | * Check pad with null |
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421 | */ |
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422 | buffer[len] = '\0'; |
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423 | if(!done) |
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424 | { |
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425 | if(fgets(in_line,GBUFSIZ,file) == 0) |
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426 | done = TRUE; |
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427 | line = in_line; |
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428 | } |
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429 | } |
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430 | this_elem->comments = buffer; |
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431 | this_elem->comments_len = strlen(buffer); |
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432 | this_elem->comments_maxlen = buflen; |
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433 | RemoveQuotes(this_elem->comments); |
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434 | } |
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435 | else if(Find2(line,"sequence")==0) |
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436 | { |
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437 | buflen = GBUFSIZ; |
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438 | done = FALSE; |
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439 | len = 0; |
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440 | |
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441 | buffer = Calloc(buflen,sizeof(char)); |
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442 | for(;line[0] != '"';line++) |
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443 | if(line[0] == '\0') |
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444 | ErrorOut5(0,"Error in input file"); |
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445 | |
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446 | line++; |
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447 | for(;!done;) |
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448 | { |
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449 | for(j=0;j<strlen(line);j++) |
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450 | { |
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451 | if(len+strlen(line) >= buflen) |
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452 | { |
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453 | buflen *=2; |
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454 | buffer = Realloc(buffer, |
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455 | buflen*sizeof(char)); |
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456 | } |
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457 | if(line[j] == '"') done = TRUE; |
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458 | |
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459 | else |
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460 | { |
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461 | /* |
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462 | * If not text, ignore spaces... |
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463 | */ |
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464 | if(this_elem->elementtype !=TEXT) |
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465 | { |
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466 | if(line[j]!=' ' && line[j] != |
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467 | '\t' && line[j] != '\n') |
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468 | buffer[len++] = line[j]; |
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469 | } |
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470 | else |
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471 | if(line[j] != '\t' && line[j] != '\n') |
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472 | buffer[len++] = line[j]; |
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473 | } |
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474 | } |
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475 | if(!done) |
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476 | { |
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477 | if(fgets(in_line,GBUFSIZ,file) == 0) |
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478 | done = TRUE; |
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479 | line = in_line; |
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480 | } |
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481 | } |
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482 | if(this_elem->rmatrix) { |
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483 | for(j=0;j<len;j++) { |
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484 | buffer[j]=this_elem->rmatrix[(unsigned char)buffer[j]]; |
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485 | } |
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486 | } |
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487 | this_elem->sequence =(NA_Base*)buffer; |
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488 | this_elem->seqlen = len; |
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489 | this_elem->seqmaxlen = buflen; |
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490 | } |
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491 | |
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492 | else if (Find2(line,"}")==0) |
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493 | { |
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494 | if(this_elem->id[0] == '\0') |
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495 | strncpy(this_elem->id,uniqueID(),79); |
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496 | if(this_elem->short_name[0] == '\0') |
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497 | strncpy(this_elem->short_name,this_elem->id,79); |
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498 | if(this_elem->seqlen == 0) |
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499 | this_elem->protect= |
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500 | PROT_BASE_CHANGES+ |
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501 | PROT_GREY_SPACE+ |
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502 | PROT_WHITE_SPACE+ |
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503 | PROT_TRANSLATION; |
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504 | genclen = 0; |
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505 | /* |
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506 | * Make a new sequence entry... |
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507 | */ |
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508 | |
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509 | success = -1; |
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510 | if(OVERWRITE) |
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511 | success = OverWrite(this_elem,dataset); |
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512 | |
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513 | if(success == -1) |
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514 | { |
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515 | curelem = dataset->numelements++; |
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516 | if(curelem == 0) |
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517 | { |
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518 | dataset->element=(NA_Sequence*) |
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519 | Calloc(5,sizeof(NA_Sequence)); |
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520 | dataset->maxnumelements = 5; |
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521 | } |
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522 | else if (curelem==dataset->maxnumelements) |
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523 | { |
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524 | (dataset->maxnumelements) *= 2; |
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525 | dataset->element =(NA_Sequence*) |
---|
526 | Realloc((char*)dataset->element, |
---|
527 | dataset->maxnumelements * sizeof(NA_Sequence)); |
---|
528 | } |
---|
529 | dataset->element[curelem] = *this_elem; |
---|
530 | } |
---|
531 | } |
---|
532 | else if(this_elem != NULL) |
---|
533 | { |
---|
534 | if (this_elem->baggage == NULL) |
---|
535 | { |
---|
536 | this_elem->baggage = strdup(line); |
---|
537 | this_elem->baggage_maxlen = |
---|
538 | this_elem->baggage_len = |
---|
539 | strlen(this_elem->baggage)+1; |
---|
540 | } |
---|
541 | else |
---|
542 | { |
---|
543 | this_elem->baggage_len += strlen(line)+1; |
---|
544 | this_elem->baggage = Realloc( |
---|
545 | this_elem->baggage,this_elem->baggage_len * |
---|
546 | sizeof(char)); |
---|
547 | this_elem->baggage_maxlen = |
---|
548 | this_elem->baggage_len; |
---|
549 | |
---|
550 | strncat(this_elem->baggage,line,GBUFSIZ); |
---|
551 | } |
---|
552 | } |
---|
553 | } |
---|
554 | |
---|
555 | fclose(file); |
---|
556 | NormalizeOffset(dataset); |
---|
557 | Regroup(dataset); |
---|
558 | AdjustGroups(dataset); |
---|
559 | return; |
---|
560 | } |
---|
561 | |
---|
562 | |
---|
563 | int WriteGDE(NA_Alignment *aln,char *filename,int method,int maskable) |
---|
564 | { |
---|
565 | int i; |
---|
566 | size_t j; |
---|
567 | int k,mask = -1; |
---|
568 | FILE *file; |
---|
569 | NA_Sequence *this_elem; |
---|
570 | //extern char month[12][6]; |
---|
571 | |
---|
572 | if(aln == NULL) |
---|
573 | return(1); |
---|
574 | //ARB |
---|
575 | //if(aln->na_ddata == NULL) |
---|
576 | // return(1); |
---|
577 | //ARB END |
---|
578 | file = fopen(filename,"w"); |
---|
579 | if(file == NULL) |
---|
580 | { |
---|
581 | Warning("Cannot open file for output"); |
---|
582 | return(1); |
---|
583 | } |
---|
584 | |
---|
585 | if(maskable && method != SELECT_REGION) |
---|
586 | for(j=0;j<aln->numelements;j++) |
---|
587 | if(aln->element[j].elementtype == MASK && |
---|
588 | aln->element[j].selected) |
---|
589 | mask = j; |
---|
590 | |
---|
591 | for(j=0;j<aln->numelements;j++) |
---|
592 | { |
---|
593 | if((aln->element[j].selected && (int)j!=mask && method!=SELECT_REGION) |
---|
594 | || (method == ALL) |
---|
595 | || (aln->element[j].subselected && method == SELECT_REGION)) |
---|
596 | { |
---|
597 | this_elem = &(aln->element[j]); |
---|
598 | /*SeqNorm(this_elem);*/ |
---|
599 | fprintf(file,"{\n"); |
---|
600 | if(this_elem->short_name[0]) |
---|
601 | fprintf(file,"name \"%s\"\n",this_elem->short_name); |
---|
602 | switch(this_elem->elementtype) |
---|
603 | { |
---|
604 | case DNA: |
---|
605 | fprintf(file,"type \"DNA\"\n"); |
---|
606 | break; |
---|
607 | case RNA: |
---|
608 | fprintf(file,"type \"RNA\"\n"); |
---|
609 | break; |
---|
610 | case PROTEIN: |
---|
611 | fprintf(file,"type \"PROTEIN\"\n"); |
---|
612 | break; |
---|
613 | case MASK: |
---|
614 | fprintf(file,"type \"MASK\"\n"); |
---|
615 | break; |
---|
616 | case TEXT: |
---|
617 | fprintf(file,"type \"TEXT\"\n"); |
---|
618 | break; |
---|
619 | } |
---|
620 | if(this_elem->seq_name[0]) |
---|
621 | fprintf(file,"longname %s\n",this_elem->seq_name); |
---|
622 | |
---|
623 | if(this_elem->id[0]) |
---|
624 | fprintf(file,"sequence-ID \"%s\"\n",this_elem->id); |
---|
625 | RemoveQuotes(this_elem->barcode); |
---|
626 | RemoveQuotes(this_elem->contig); |
---|
627 | |
---|
628 | if(this_elem->barcode[0]) |
---|
629 | fprintf(file,"barcode \"%s\"\n",this_elem->barcode); |
---|
630 | if(this_elem->membrane[0]) |
---|
631 | fprintf(file,"membrane \"%s\"\n",this_elem->membrane); |
---|
632 | if(this_elem->contig[0]) |
---|
633 | fprintf(file,"contig \"%s\"\n",this_elem->contig); |
---|
634 | if(this_elem->description[0]) |
---|
635 | fprintf(file,"descrip \"%s\"\n",this_elem->description); |
---|
636 | if(this_elem->authority[0]) |
---|
637 | fprintf(file,"creator \"%s\"\n",this_elem->authority); |
---|
638 | if(this_elem->groupid) |
---|
639 | fprintf(file,"group-ID %zu\n", this_elem->groupid); |
---|
640 | if(this_elem->offset+aln->rel_offset && method!=SELECT_REGION) |
---|
641 | fprintf(file,"offset %d\n",this_elem->offset+aln->rel_offset); |
---|
642 | if(method == SELECT_REGION) |
---|
643 | { |
---|
644 | /* |
---|
645 | * If selecting a region, the offset should be moved to the first |
---|
646 | * non-'0' space in the mask. |
---|
647 | */ |
---|
648 | for(k=this_elem->offset;k<aln->selection_mask_len && aln->selection_mask[k] == '0';k++) ; |
---|
649 | fprintf(file,"offset %d\n", aln->rel_offset+k); |
---|
650 | } |
---|
651 | if(this_elem->t_stamp.origin.mm != 0) |
---|
652 | fprintf(file, |
---|
653 | "creation-date %2d/%2d/%2d %2d:%2d:%2d\n", |
---|
654 | this_elem->t_stamp.origin.mm, |
---|
655 | this_elem->t_stamp.origin.dd, |
---|
656 | (this_elem->t_stamp.origin.yy)>1900? |
---|
657 | (this_elem->t_stamp.origin.yy-1900): |
---|
658 | (this_elem->t_stamp.origin.yy), |
---|
659 | this_elem->t_stamp.origin.hr, |
---|
660 | this_elem->t_stamp.origin.mn, |
---|
661 | this_elem->t_stamp.origin.sc); |
---|
662 | if((this_elem->attr & IS_ORIG_5_TO_3) && |
---|
663 | ((this_elem->attr & IS_ORIG_3_TO_5) == 0)) |
---|
664 | fprintf(file,"orig_direction 1\n"); |
---|
665 | |
---|
666 | if((this_elem->attr & IS_CIRCULAR) ) |
---|
667 | fprintf(file,"circular 1\n"); |
---|
668 | |
---|
669 | if((this_elem->attr & IS_5_TO_3) && |
---|
670 | ((this_elem->attr & IS_3_TO_5) == 0)) |
---|
671 | fprintf(file,"direction 1\n"); |
---|
672 | |
---|
673 | if((this_elem->attr & IS_ORIG_3_TO_5) && |
---|
674 | ((this_elem->attr & IS_ORIG_5_TO_3) == 0)) |
---|
675 | fprintf(file,"orig_direction -1\n"); |
---|
676 | |
---|
677 | if((this_elem->attr & IS_3_TO_5) && |
---|
678 | ((this_elem->attr & IS_5_TO_3) == 0)) |
---|
679 | fprintf(file,"direction -1\n"); |
---|
680 | |
---|
681 | if((this_elem->attr & IS_ORIG_PRIMARY) && |
---|
682 | ((this_elem->attr & IS_ORIG_SECONDARY) == 0)) |
---|
683 | fprintf(file,"orig_strand 1\n"); |
---|
684 | |
---|
685 | if((this_elem->attr & IS_PRIMARY) && |
---|
686 | ((this_elem->attr & IS_SECONDARY) == 0)) |
---|
687 | fprintf(file,"strandedness 1\n"); |
---|
688 | |
---|
689 | if(((this_elem->attr & IS_ORIG_PRIMARY) == 0) && |
---|
690 | (this_elem->attr & IS_ORIG_SECONDARY)) |
---|
691 | fprintf(file,"orig_strand 2\n"); |
---|
692 | |
---|
693 | if(((this_elem->attr & IS_PRIMARY) == 0) && |
---|
694 | (this_elem->attr & IS_SECONDARY)) |
---|
695 | fprintf(file,"strandedness 2\n"); |
---|
696 | |
---|
697 | if(this_elem->comments != NULL) |
---|
698 | { |
---|
699 | StripSpecial(this_elem->comments); |
---|
700 | fprintf(file,"comments \"%s\"\n",this_elem->comments); |
---|
701 | } |
---|
702 | if(this_elem->baggage != NULL) |
---|
703 | { |
---|
704 | if(this_elem-> |
---|
705 | baggage[strlen(this_elem->baggage)-1] == '\n') |
---|
706 | fprintf(file,"%s",this_elem->baggage); |
---|
707 | else |
---|
708 | fprintf(file,"%s\n",this_elem->baggage); |
---|
709 | } |
---|
710 | fprintf(file,"sequence \""); |
---|
711 | if(this_elem->tmatrix) |
---|
712 | { |
---|
713 | if(mask == -1) |
---|
714 | { |
---|
715 | for(k=this_elem->offset;k<this_elem->seqlen+this_elem->offset;k++) |
---|
716 | { |
---|
717 | if(k%60 == 0) |
---|
718 | putc('\n',file); |
---|
719 | if(method == SELECT_REGION) |
---|
720 | { |
---|
721 | if(aln->selection_mask[k] == '1') |
---|
722 | putc(this_elem->tmatrix[getelem(this_elem,k)], |
---|
723 | file); |
---|
724 | } |
---|
725 | else |
---|
726 | putc(this_elem->tmatrix[getelem(this_elem,k)], |
---|
727 | file); |
---|
728 | } |
---|
729 | } |
---|
730 | else |
---|
731 | { |
---|
732 | for(i=0,k=this_elem->offset;k<this_elem->seqlen+this_elem->offset;k++) |
---|
733 | if(aln->element[mask].seqlen+this_elem->offset>k) |
---|
734 | if((char)getelem(&(aln->element[mask]),k) != '0' |
---|
735 | && ((char)getelem(&(aln->element[mask]),k) != '-')) |
---|
736 | { |
---|
737 | if(i%60 == 0) |
---|
738 | putc('\n',file); |
---|
739 | putc(this_elem->tmatrix[getelem(this_elem,k)], |
---|
740 | file); |
---|
741 | i++; |
---|
742 | } |
---|
743 | } |
---|
744 | fprintf(file,"\"\n"); |
---|
745 | } |
---|
746 | else |
---|
747 | { |
---|
748 | if(mask == -1) |
---|
749 | { |
---|
750 | for(k=this_elem->offset;k<this_elem->seqlen+this_elem->offset;k++) |
---|
751 | { |
---|
752 | if(k%60 == 0) |
---|
753 | putc('\n',file); |
---|
754 | if(method == SELECT_REGION) |
---|
755 | { |
---|
756 | if(aln->selection_mask[k] == '1') |
---|
757 | putc(getelem(this_elem,k),file); |
---|
758 | } |
---|
759 | else |
---|
760 | putc(getelem(this_elem,k),file); |
---|
761 | } |
---|
762 | } |
---|
763 | else |
---|
764 | { |
---|
765 | for(i=0,k=this_elem->offset;k<this_elem->seqlen+this_elem->offset;k++) |
---|
766 | if(((aln->element[mask].seqlen)+(aln->element[mask]. |
---|
767 | offset)) > k) |
---|
768 | if((char)getelem(&(aln->element[mask]),k) == '1') |
---|
769 | { |
---|
770 | if(i%60 == 0) |
---|
771 | putc('\n',file); |
---|
772 | putc(getelem(this_elem,k),file); |
---|
773 | i++; |
---|
774 | } |
---|
775 | } |
---|
776 | fprintf(file,"\"\n"); |
---|
777 | } |
---|
778 | fprintf(file,"}\n"); |
---|
779 | } |
---|
780 | } |
---|
781 | fclose(file); |
---|
782 | return(0); |
---|
783 | } |
---|
784 | |
---|
785 | |
---|
786 | |
---|
787 | /* |
---|
788 | * Normalize seq (remove leading indels in the sequence; |
---|
789 | */ |
---|
790 | void SeqNorm(NA_Sequence *seq) |
---|
791 | { |
---|
792 | int len,j,shift_width,trailer; |
---|
793 | char *sequence; |
---|
794 | len = seq->seqlen; |
---|
795 | |
---|
796 | sequence =(char*)seq->sequence; |
---|
797 | |
---|
798 | if(len == 0) return; |
---|
799 | |
---|
800 | if(seq->tmatrix) { |
---|
801 | for(shift_width=0; (shift_width<len) && ((sequence[shift_width]&15) == '\0'); shift_width++) ; |
---|
802 | } |
---|
803 | else { |
---|
804 | for(shift_width=0; (shift_width<len) && (sequence[shift_width] == '-'); shift_width++) ; |
---|
805 | } |
---|
806 | |
---|
807 | for(j=0;j<len-shift_width;j++) { |
---|
808 | sequence[j] = sequence[j+shift_width]; |
---|
809 | } |
---|
810 | |
---|
811 | seq->seqlen -= shift_width; |
---|
812 | seq->offset += shift_width; |
---|
813 | for (trailer=seq->seqlen-1; |
---|
814 | (sequence[trailer] =='-' || sequence[trailer] == '\0') && trailer>=0; |
---|
815 | trailer--) |
---|
816 | { |
---|
817 | sequence[trailer] = '\0'; |
---|
818 | } |
---|
819 | seq->seqlen = trailer+1; |
---|
820 | return; |
---|
821 | } |
---|
822 | |
---|
823 | /* ALWAYS COPY the result from uniqueID() to a char[32], |
---|
824 | * (strlen(hostname)+1+10). Memory is lost when the function |
---|
825 | * is finished. |
---|
826 | */ |
---|
827 | |
---|
828 | char *uniqueID() |
---|
829 | { |
---|
830 | static char vname[32]; |
---|
831 | time_t *tp; |
---|
832 | static int cnt = 0; |
---|
833 | |
---|
834 | tp = (time_t *)Calloc(1, sizeof(time_t)); |
---|
835 | |
---|
836 | time(tp); |
---|
837 | sprintf(vname, "host:%d:%ld", cnt, *tp); |
---|
838 | cnt++; |
---|
839 | Cfree((char*)tp); |
---|
840 | return(vname); |
---|
841 | } |
---|
842 | |
---|