Mercurial > repos > clustalomega > clustalomega
annotate clustalomega/clustal-omega-0.2.0/src/squid/stockholm.c @ 0:ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
author | clustalomega |
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date | Tue, 07 Jun 2011 17:04:25 -0400 |
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1 /***************************************************************** |
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2 * SQUID - a library of functions for biological sequence analysis |
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3 * Copyright (C) 1992-2002 Washington University School of Medicine |
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4 * |
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5 * This source code is freely distributed under the terms of the |
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6 * GNU General Public License. See the files COPYRIGHT and LICENSE |
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7 * for details. |
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8 *****************************************************************/ |
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9 |
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10 /* stockholm.c |
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11 * SRE, Fri May 28 15:46:41 1999 |
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12 * |
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13 * Reading/writing of Stockholm format multiple sequence alignments. |
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14 * |
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15 * example of API: |
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16 * |
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17 * MSA *msa; |
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18 * FILE *fp; -- opened for write with fopen() |
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19 * MSAFILE *afp; -- opened for read with MSAFileOpen() |
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20 * |
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21 * while ((msa = ReadStockholm(afp)) != NULL) |
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22 * { |
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23 * WriteStockholm(fp, msa); |
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24 * MSAFree(msa); |
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25 * } |
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26 * |
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27 * RCS $Id: stockholm.c 217 2011-03-19 10:27:10Z andreas $ (Original squid RCS Id: stockholm.c,v 1.7 2002/10/12 04:40:36 eddy Exp) |
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28 */ |
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29 #include <stdio.h> |
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30 #include <string.h> |
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31 #include "squid.h" |
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32 #include "msa.h" |
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33 |
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34 static int parse_gf(MSA *msa, char *buf); |
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35 static int parse_gs(MSA *msa, char *buf); |
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36 static int parse_gc(MSA *msa, char *buf); |
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37 static int parse_gr(MSA *msa, char *buf); |
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38 static int parse_comment(MSA *msa, char *buf); |
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39 static int parse_sequence(MSA *msa, char *buf); |
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40 static void actually_write_stockholm(FILE *fp, MSA *msa, int cpl); |
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41 |
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42 #ifdef TESTDRIVE_STOCKHOLM |
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43 /***************************************************************** |
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44 * stockholm.c test driver: |
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45 * cc -DTESTDRIVE_STOCKHOLM -g -O2 -Wall -o test stockholm.c msa.c gki.c sqerror.c sre_string.c file.c hsregex.c sre_math.c sre_ctype.c -lm |
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46 * |
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47 */ |
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48 int |
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49 main(int argc, char **argv) |
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50 { |
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51 MSAFILE *afp; |
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52 MSA *msa; |
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53 char *file; |
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54 |
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55 file = argv[1]; |
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56 |
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57 if ((afp = MSAFileOpen(file, MSAFILE_STOCKHOLM, NULL)) == NULL) |
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58 Die("Couldn't open %s\n", file); |
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59 |
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60 while ((msa = ReadStockholm(afp)) != NULL) |
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61 { |
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62 WriteStockholm(stdout, msa); |
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63 MSAFree(msa); |
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64 } |
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65 |
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66 MSAFileClose(afp); |
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67 exit(0); |
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68 } |
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69 /******************************************************************/ |
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70 #endif /* testdriver */ |
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71 |
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72 |
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73 /* Function: ReadStockholm() |
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74 * Date: SRE, Fri May 21 17:33:10 1999 [St. Louis] |
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75 * |
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76 * Purpose: Parse the next alignment from an open Stockholm |
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77 * format alignment file. Return the alignment, or |
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78 * NULL if there are no more alignments in the file. |
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79 * |
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80 * Args: afp - open alignment file |
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81 * |
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82 * Returns: MSA * - an alignment object. |
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83 * caller responsible for an MSAFree() |
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84 * NULL if no more alignments |
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85 * |
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86 * Diagnostics: |
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87 * Will Die() here with a (potentially) useful message |
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88 * if a parsing error occurs |
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89 */ |
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90 MSA * |
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91 ReadStockholm(MSAFILE *afp) |
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92 { |
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93 MSA *msa; |
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94 char *s; |
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95 int status; |
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96 |
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97 if (feof(afp->f)) return NULL; |
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98 |
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99 /* Initialize allocation of the MSA. |
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100 */ |
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101 msa = MSAAlloc(10, 0); |
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102 |
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103 /* Check the magic Stockholm header line. |
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104 * We have to skip blank lines here, else we perceive |
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105 * trailing blank lines in a file as a format error when |
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106 * reading in multi-record mode. |
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107 */ |
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108 do { |
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109 if ((s = MSAFileGetLine(afp)) == NULL) { |
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110 MSAFree(msa); |
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111 return NULL; |
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112 } |
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113 } while (IsBlankline(s)); |
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114 |
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115 if (strncmp(s, "# STOCKHOLM 1.", 14) != 0) |
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116 Die("\ |
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117 File %s doesn't appear to be in Stockholm format.\n\ |
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118 Assuming there isn't some other problem with your file (it is an\n\ |
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119 alignment file, right?), please either:\n\ |
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120 a) use the Babelfish format autotranslator option (-B, usually);\n\ |
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121 b) specify the file's format with the --informat option; or\n\ |
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122 a) reformat the alignment to Stockholm format.\n", |
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123 afp->fname); |
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124 |
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125 /* Read the alignment file one line at a time. |
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126 */ |
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127 while ((s = MSAFileGetLine(afp)) != NULL) |
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128 { |
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129 while (*s == ' ' || *s == '\t') s++; /* skip leading whitespace */ |
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130 |
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131 if (*s == '#') { |
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132 if (strncmp(s, "#=GF", 4) == 0) status = parse_gf(msa, s); |
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133 else if (strncmp(s, "#=GS", 4) == 0) status = parse_gs(msa, s); |
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134 else if (strncmp(s, "#=GC", 4) == 0) status = parse_gc(msa, s); |
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135 else if (strncmp(s, "#=GR", 4) == 0) status = parse_gr(msa, s); |
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136 else status = parse_comment(msa, s); |
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137 } |
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138 else if (strncmp(s, "//", 2) == 0) break; |
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139 else if (*s == '\n') continue; |
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140 else status = parse_sequence(msa, s); |
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141 |
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142 if (status == 0) |
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143 Die("Stockholm format parse error: line %d of file %s while reading alignment %s", |
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144 afp->linenumber, afp->fname, msa->name == NULL? "" : msa->name); |
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145 } |
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146 |
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147 if (s == NULL && msa->nseq != 0) |
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148 Die ("Didn't find // at end of alignment %s", msa->name == NULL ? "" : msa->name); |
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149 |
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150 if (s == NULL && msa->nseq == 0) { |
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151 /* probably just some junk at end of file */ |
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152 MSAFree(msa); |
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153 return NULL; |
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154 } |
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155 |
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156 MSAVerifyParse(msa); |
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157 return msa; |
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158 } |
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159 |
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160 |
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161 /* Function: WriteStockholm() |
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162 * Date: SRE, Mon May 31 19:15:22 1999 [St. Louis] |
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163 * |
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164 * Purpose: Write an alignment in standard multi-block |
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165 * Stockholm format to an open file. A wrapper |
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166 * for actually_write_stockholm(). |
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167 * |
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168 * Args: fp - file that's open for writing |
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169 * msa - alignment to write |
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170 * |
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171 * Returns: (void) |
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172 */ |
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173 void |
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174 WriteStockholm(FILE *fp, MSA *msa) |
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175 { |
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176 actually_write_stockholm(fp, msa, 50); /* 50 char per block */ |
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177 } |
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178 |
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179 /* Function: WriteStockholmOneBlock() |
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180 * Date: SRE, Mon May 31 19:15:22 1999 [St. Louis] |
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181 * |
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182 * Purpose: Write an alignment in Pfam's single-block |
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183 * Stockholm format to an open file. A wrapper |
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184 * for actually_write_stockholm(). |
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185 * |
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186 * Args: fp - file that's open for writing |
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187 * msa - alignment to write |
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188 * |
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189 * Returns: (void) |
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190 */ |
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191 void |
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192 WriteStockholmOneBlock(FILE *fp, MSA *msa) |
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193 { |
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194 actually_write_stockholm(fp, msa, msa->alen); /* one big block */ |
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195 } |
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196 |
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197 |
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198 /* Function: actually_write_stockholm() |
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199 * Date: SRE, Fri May 21 17:39:22 1999 [St. Louis] |
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200 * |
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201 * Purpose: Write an alignment in Stockholm format to |
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202 * an open file. This is the function that actually |
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203 * does the work. The API's WriteStockholm() |
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204 * and WriteStockholmOneBlock() are wrappers. |
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205 * |
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206 * Args: fp - file that's open for writing |
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207 * msa - alignment to write |
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208 * cpl - characters to write per line in alignment block |
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209 * |
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210 * Returns: (void) |
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211 */ |
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212 static void |
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213 actually_write_stockholm(FILE *fp, MSA *msa, int cpl) |
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214 { |
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215 int i, j; |
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216 int len = 0; |
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217 int namewidth; |
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218 int typewidth = 0; /* markup tags are up to 5 chars long */ |
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219 int markupwidth = 0; /* #=GR, #=GC are four char wide + 1 space */ |
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220 char *buf; |
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221 int currpos; |
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222 char *s, *tok; |
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223 |
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224 /* Figure out how much space we need for name + markup |
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225 * to keep the alignment in register. Required by Stockholm |
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226 * spec, even though our Stockholm parser doesn't care (Erik's does). |
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227 */ |
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228 namewidth = 0; |
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229 for (i = 0; i < msa->nseq; i++) |
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230 if ((len = strlen(msa->sqname[i])) > namewidth) |
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231 namewidth = len; |
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232 |
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233 /* Figure out how much space we need for markup tags |
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234 * markupwidth = always 4 if we're doing markup: strlen("#=GR") |
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235 * typewidth = longest markup tag |
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236 */ |
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237 if (msa->ss != NULL) { markupwidth = 4; typewidth = 2; } |
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238 if (msa->sa != NULL) { markupwidth = 4; typewidth = 2; } |
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239 for (i = 0; i < msa->ngr; i++) |
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240 if ((len = strlen(msa->gr_tag[i])) > typewidth) typewidth = len; |
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241 |
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242 if (msa->rf != NULL) { markupwidth = 4; if (typewidth < 2) typewidth = 2; } |
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243 if (msa->ss_cons != NULL) { markupwidth = 4; if (typewidth < 7) typewidth = 7; } |
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244 if (msa->sa_cons != NULL) { markupwidth = 4; if (typewidth < 7) typewidth = 7; } |
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245 for (i = 0; i < msa->ngc; i++) |
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246 if ((len = strlen(msa->gc_tag[i])) > typewidth) typewidth = len; |
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247 |
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248 buf = MallocOrDie(sizeof(char) * (cpl+namewidth+typewidth+markupwidth+61)); |
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249 |
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250 /* Magic Stockholm header |
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251 */ |
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252 fprintf(fp, "# STOCKHOLM 1.0\n"); |
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253 |
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254 /* Free text comments |
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255 */ |
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256 for (i = 0; i < msa->ncomment; i++) |
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257 fprintf(fp, "# %s\n", msa->comment[i]); |
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258 if (msa->ncomment > 0) fprintf(fp, "\n"); |
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259 |
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260 /* GF section: per-file annotation |
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261 */ |
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262 if (msa->name != NULL) fprintf(fp, "#=GF ID %s\n", msa->name); |
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263 if (msa->acc != NULL) fprintf(fp, "#=GF AC %s\n", msa->acc); |
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264 if (msa->desc != NULL) fprintf(fp, "#=GF DE %s\n", msa->desc); |
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265 if (msa->au != NULL) fprintf(fp, "#=GF AU %s\n", msa->au); |
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266 |
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clustalomega
parents:
diff
changeset
|
267 /* Thresholds are hacky. Pfam has two. Rfam has one. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
268 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
269 if (msa->cutoff_is_set[MSA_CUTOFF_GA1] && msa->cutoff_is_set[MSA_CUTOFF_GA2]) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
270 fprintf(fp, "#=GF GA %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_GA1], msa->cutoff[MSA_CUTOFF_GA2]); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
271 else if (msa->cutoff_is_set[MSA_CUTOFF_GA1]) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
272 fprintf(fp, "#=GF GA %.1f\n", msa->cutoff[MSA_CUTOFF_GA1]); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
273 if (msa->cutoff_is_set[MSA_CUTOFF_NC1] && msa->cutoff_is_set[MSA_CUTOFF_NC2]) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
274 fprintf(fp, "#=GF NC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_NC1], msa->cutoff[MSA_CUTOFF_NC2]); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
275 else if (msa->cutoff_is_set[MSA_CUTOFF_NC1]) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
276 fprintf(fp, "#=GF NC %.1f\n", msa->cutoff[MSA_CUTOFF_NC1]); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
277 if (msa->cutoff_is_set[MSA_CUTOFF_TC1] && msa->cutoff_is_set[MSA_CUTOFF_TC2]) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
278 fprintf(fp, "#=GF TC %.1f %.1f\n", msa->cutoff[MSA_CUTOFF_TC1], msa->cutoff[MSA_CUTOFF_TC2]); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
279 else if (msa->cutoff_is_set[MSA_CUTOFF_TC1]) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
280 fprintf(fp, "#=GF TC %.1f\n", msa->cutoff[MSA_CUTOFF_TC1]); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
281 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
282 for (i = 0; i < msa->ngf; i++) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
283 fprintf(fp, "#=GF %-5s %s\n", msa->gf_tag[i], msa->gf[i]); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
284 fprintf(fp, "\n"); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
285 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
286 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
287 /* GS section: per-sequence annotation |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
288 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
289 if (msa->flags & MSA_SET_WGT) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
290 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
291 for (i = 0; i < msa->nseq; i++) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
292 fprintf(fp, "#=GS %-*.*s WT %.2f\n", namewidth, namewidth, msa->sqname[i], msa->wgt[i]); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
293 fprintf(fp, "\n"); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
294 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
295 if (msa->sqacc != NULL) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
296 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
297 for (i = 0; i < msa->nseq; i++) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
298 if (msa->sqacc[i] != NULL) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
299 fprintf(fp, "#=GS %-*.*s AC %s\n", namewidth, namewidth, msa->sqname[i], msa->sqacc[i]); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
300 fprintf(fp, "\n"); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
301 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
302 if (msa->sqdesc != NULL) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
303 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
304 for (i = 0; i < msa->nseq; i++) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
305 if (msa->sqdesc[i] != NULL) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
306 fprintf(fp, "#=GS %*.*s DE %s\n", namewidth, namewidth, msa->sqname[i], msa->sqdesc[i]); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
307 fprintf(fp, "\n"); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
308 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
309 for (i = 0; i < msa->ngs; i++) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
310 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
311 /* Multiannotated GS tags are possible; for example, |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
312 * #=GS foo DR PDB; 1xxx; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
313 * #=GS foo DR PDB; 2yyy; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
314 * These are stored, for example, as: |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
315 * msa->gs[0][0] = "PDB; 1xxx;\nPDB; 2yyy;" |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
316 * and must be decomposed. |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
317 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
318 for (j = 0; j < msa->nseq; j++) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
319 if (msa->gs[i][j] != NULL) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
320 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
321 s = msa->gs[i][j]; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
322 while ((tok = sre_strtok(&s, "\n", NULL)) != NULL) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
323 fprintf(fp, "#=GS %*.*s %5s %s\n", namewidth, namewidth, |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
324 msa->sqname[j], msa->gs_tag[i], tok); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
325 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
326 fprintf(fp, "\n"); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
327 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
328 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
329 /* Alignment section: |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
330 * contains aligned sequence, #=GR annotation, and #=GC annotation |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
331 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
332 for (currpos = 0; currpos < msa->alen; currpos += cpl) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
333 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
334 if (currpos > 0) fprintf(fp, "\n"); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
335 for (i = 0; i < msa->nseq; i++) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
336 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
337 strncpy(buf, msa->aseq[i] + currpos, cpl); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
338 buf[cpl] = '\0'; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
339 fprintf(fp, "%-*.*s %s\n", namewidth+typewidth+markupwidth, namewidth+typewidth+markupwidth, |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
340 msa->sqname[i], buf); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
341 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
342 if (msa->ss != NULL && msa->ss[i] != NULL) { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
343 strncpy(buf, msa->ss[i] + currpos, cpl); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
344 buf[cpl] = '\0'; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
345 fprintf(fp, "#=GR %-*.*s SS %s\n", namewidth, namewidth, msa->sqname[i], buf); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
346 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
347 if (msa->sa != NULL && msa->sa[i] != NULL) { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
348 strncpy(buf, msa->sa[i] + currpos, cpl); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
349 buf[cpl] = '\0'; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
350 fprintf(fp, "#=GR %-*.*s SA %s\n", namewidth, namewidth, msa->sqname[i], buf); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
351 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
352 for (j = 0; j < msa->ngr; j++) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
353 if (msa->gr[j][i] != NULL) { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
354 strncpy(buf, msa->gr[j][i] + currpos, cpl); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
355 buf[cpl] = '\0'; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
356 fprintf(fp, "#=GR %-*.*s %5s %s\n", |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
357 namewidth, namewidth, msa->sqname[i], msa->gr_tag[j], buf); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
358 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
359 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
360 if (msa->ss_cons != NULL) { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
361 strncpy(buf, msa->ss_cons + currpos, cpl); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
362 buf[cpl] = '\0'; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
363 fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, "SS_cons", buf); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
364 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
365 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
366 if (msa->sa_cons != NULL) { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
367 strncpy(buf, msa->sa_cons + currpos, cpl); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
368 buf[cpl] = '\0'; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
369 fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, "SA_cons", buf); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
370 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
371 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
372 if (msa->rf != NULL) { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
373 strncpy(buf, msa->rf + currpos, cpl); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
374 buf[cpl] = '\0'; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
375 fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, "RF", buf); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
376 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
377 for (j = 0; j < msa->ngc; j++) { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
378 strncpy(buf, msa->gc[j] + currpos, cpl); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
379 buf[cpl] = '\0'; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
380 fprintf(fp, "#=GC %-*.*s %s\n", namewidth+typewidth, namewidth+typewidth, |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
381 msa->gc_tag[j], buf); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
382 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
383 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
384 fprintf(fp, "//\n"); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
385 free(buf); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
386 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
387 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
388 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
389 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
390 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
391 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
392 /* Format of a GF line: |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
393 * #=GF <featurename> <text> |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
394 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
395 static int |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
396 parse_gf(MSA *msa, char *buf) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
397 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
398 char *gf; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
399 char *featurename; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
400 char *text; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
401 char *s; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
402 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
403 s = buf; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
404 if ((gf = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
405 if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
406 if ((text = sre_strtok(&s, "\n", NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
407 while (*text && (*text == ' ' || *text == '\t')) text++; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
408 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
409 if (strcmp(featurename, "ID") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
410 msa->name = sre_strdup(text, -1); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
411 else if (strcmp(featurename, "AC") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
412 msa->acc = sre_strdup(text, -1); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
413 else if (strcmp(featurename, "DE") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
414 msa->desc = sre_strdup(text, -1); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
415 else if (strcmp(featurename, "AU") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
416 msa->au = sre_strdup(text, -1); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
417 else if (strcmp(featurename, "GA") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
418 { /* Pfam has GA1, GA2. Rfam just has GA1. */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
419 s = text; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
420 if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
421 msa->cutoff[MSA_CUTOFF_GA1] = atof(text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
422 msa->cutoff_is_set[MSA_CUTOFF_GA1] = TRUE; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
423 if ((text = sre_strtok(&s, WHITESPACE, NULL)) != NULL) { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
424 msa->cutoff[MSA_CUTOFF_GA2] = atof(text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
425 msa->cutoff_is_set[MSA_CUTOFF_GA2] = TRUE; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
426 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
427 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
428 else if (strcmp(featurename, "NC") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
429 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
430 s = text; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
431 if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
432 msa->cutoff[MSA_CUTOFF_NC1] = atof(text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
433 msa->cutoff_is_set[MSA_CUTOFF_NC1] = TRUE; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
434 if ((text = sre_strtok(&s, WHITESPACE, NULL)) != NULL) { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
435 msa->cutoff[MSA_CUTOFF_NC2] = atof(text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
436 msa->cutoff_is_set[MSA_CUTOFF_NC2] = TRUE; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
437 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
438 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
439 else if (strcmp(featurename, "TC") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
440 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
441 s = text; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
442 if ((text = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
443 msa->cutoff[MSA_CUTOFF_TC1] = atof(text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
444 msa->cutoff_is_set[MSA_CUTOFF_TC1] = TRUE; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
445 if ((text = sre_strtok(&s, WHITESPACE, NULL)) != NULL) { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
446 msa->cutoff[MSA_CUTOFF_TC2] = atof(text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
447 msa->cutoff_is_set[MSA_CUTOFF_TC2] = TRUE; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
448 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
449 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
450 else |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
451 MSAAddGF(msa, featurename, text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
452 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
453 return 1; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
454 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
455 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
456 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
457 /* Format of a GS line: |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
458 * #=GS <seqname> <featurename> <text> |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
459 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
460 static int |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
461 parse_gs(MSA *msa, char *buf) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
462 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
463 char *gs; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
464 char *seqname; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
465 char *featurename; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
466 char *text; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
467 int seqidx; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
468 char *s; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
469 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
470 s = buf; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
471 if ((gs = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
472 if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
473 if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
474 if ((text = sre_strtok(&s, "\n", NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
475 while (*text && (*text == ' ' || *text == '\t')) text++; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
476 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
477 /* GS usually follows another GS; guess lastidx+1 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
478 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
479 seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx+1); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
480 msa->lastidx = seqidx; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
481 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
482 if (strcmp(featurename, "WT") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
483 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
484 msa->wgt[seqidx] = atof(text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
485 msa->flags |= MSA_SET_WGT; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
486 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
487 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
488 else if (strcmp(featurename, "AC") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
489 MSASetSeqAccession(msa, seqidx, text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
490 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
491 else if (strcmp(featurename, "DE") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
492 MSASetSeqDescription(msa, seqidx, text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
493 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
494 else |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
495 MSAAddGS(msa, featurename, seqidx, text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
496 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
497 return 1; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
498 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
499 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
500 /* Format of a GC line: |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
501 * #=GC <featurename> <text> |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
502 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
503 static int |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
504 parse_gc(MSA *msa, char *buf) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
505 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
506 char *gc; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
507 char *featurename; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
508 char *text; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
509 char *s; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
510 int len; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
511 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
512 s = buf; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
513 if ((gc = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
514 if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
515 if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
516 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
517 if (strcmp(featurename, "SS_cons") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
518 sre_strcat(&(msa->ss_cons), -1, text, len); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
519 else if (strcmp(featurename, "SA_cons") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
520 sre_strcat(&(msa->sa_cons), -1, text, len); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
521 else if (strcmp(featurename, "RF") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
522 sre_strcat(&(msa->rf), -1, text, len); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
523 else |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
524 MSAAppendGC(msa, featurename, text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
525 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
526 return 1; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
527 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
528 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
529 /* Format of a GR line: |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
530 * #=GR <seqname> <featurename> <text> |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
531 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
532 static int |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
533 parse_gr(MSA *msa, char *buf) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
534 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
535 char *gr; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
536 char *seqname; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
537 char *featurename; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
538 char *text; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
539 int seqidx; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
540 int len; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
541 int j; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
542 char *s; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
543 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
544 s = buf; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
545 if ((gr = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
546 if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
547 if ((featurename = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
548 if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
549 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
550 /* GR usually follows sequence it refers to; guess msa->lastidx */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
551 seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
552 msa->lastidx = seqidx; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
553 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
554 if (strcmp(featurename, "SS") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
555 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
556 if (msa->ss == NULL) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
557 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
558 msa->ss = MallocOrDie(sizeof(char *) * msa->nseqalloc); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
559 msa->sslen = MallocOrDie(sizeof(int) * msa->nseqalloc); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
560 for (j = 0; j < msa->nseqalloc; j++) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
561 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
562 msa->ss[j] = NULL; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
563 msa->sslen[j] = 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
564 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
565 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
566 msa->sslen[seqidx] = sre_strcat(&(msa->ss[seqidx]), msa->sslen[seqidx], text, len); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
567 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
568 else if (strcmp(featurename, "SA") == 0) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
569 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
570 if (msa->sa == NULL) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
571 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
572 msa->sa = MallocOrDie(sizeof(char *) * msa->nseqalloc); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
573 msa->salen = MallocOrDie(sizeof(int) * msa->nseqalloc); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
574 for (j = 0; j < msa->nseqalloc; j++) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
575 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
576 msa->sa[j] = NULL; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
577 msa->salen[j] = 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
578 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
579 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
580 msa->salen[seqidx] = sre_strcat(&(msa->sa[seqidx]), msa->salen[seqidx], text, len); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
581 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
582 else |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
583 MSAAppendGR(msa, featurename, seqidx, text); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
584 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
585 return 1; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
586 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
587 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
588 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
589 /* comments are simply stored verbatim, not parsed |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
590 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
591 static int |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
592 parse_comment(MSA *msa, char *buf) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
593 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
594 char *s; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
595 char *comment; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
596 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
597 s = buf + 1; /* skip leading '#' */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
598 if (*s == '\n') { *s = '\0'; comment = s; } /* deal with blank comment */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
599 else if ((comment = sre_strtok(&s, "\n", NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
600 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
601 MSAAddComment(msa, comment); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
602 return 1; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
603 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
604 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
605 static int |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
606 parse_sequence(MSA *msa, char *buf) |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
607 { |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
608 char *s; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
609 char *seqname; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
610 char *text; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
611 int seqidx; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
612 int len; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
613 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
614 s = buf; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
615 if ((seqname = sre_strtok(&s, WHITESPACE, NULL)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
616 if ((text = sre_strtok(&s, WHITESPACE, &len)) == NULL) return 0; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
617 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
618 /* seq usually follows another seq; guess msa->lastidx +1 */ |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
619 seqidx = MSAGetSeqidx(msa, seqname, msa->lastidx+1); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
620 msa->lastidx = seqidx; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
621 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
622 msa->sqlen[seqidx] = sre_strcat(&(msa->aseq[seqidx]), msa->sqlen[seqidx], text, len); |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
623 return 1; |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
624 } |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
625 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
626 |
ff1768533a07
Migrated tool version 0.2 from old tool shed archive to new tool shed repository
clustalomega
parents:
diff
changeset
|
627 |