| 1 | /* ------------- File format converting subroutine ------------- */ |
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| 2 | |
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| 3 | #include <stdio.h> |
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| 4 | #include <stdlib.h> |
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| 5 | #include "convert.h" |
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| 6 | #include "global.h" |
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| 7 | |
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| 8 | /* ------------------------------------------------------------- |
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| 9 | * Function convert(). |
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| 10 | * For given input file and type, convert the file |
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| 11 | * to desired out type and save the result in |
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| 12 | * the out file. |
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| 13 | */ |
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| 14 | void convert(inf, outf, intype, outype) |
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| 15 | char *inf, *outf; |
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| 16 | int intype, outype; |
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| 17 | { |
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| 18 | int dd; /* copy stdin to outfile after first line */ |
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| 19 | dd = 0; |
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| 20 | if (outype == PHYLIP2){ |
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| 21 | outype = PHYLIP; |
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| 22 | dd = 1; |
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| 23 | } |
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| 24 | |
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| 25 | if(Cmpstr(inf, outf)==EQ) |
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| 26 | error(45, "Input file and output file must be different file.\n"); |
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| 27 | if(intype==GENBANK&&outype==MACKE) { |
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| 28 | genbank_to_macke(inf, outf); |
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| 29 | } else if(intype==GENBANK&&outype==GENBANK) { |
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| 30 | genbank_to_genbank(inf, outf); |
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| 31 | } else if(intype==GENBANK&&outype==PAUP) { |
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| 32 | to_paup(inf, outf, GENBANK); |
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| 33 | } else if(intype==GENBANK&&outype==PHYLIP) { |
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| 34 | to_phylip(inf, outf, GENBANK,dd); |
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| 35 | } else if(intype==GENBANK&&outype==PROTEIN) { |
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| 36 | error(69, "Sorry, cannot convert from GENBANK to SWISSPROT, Exit"); |
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| 37 | } else if(intype==GENBANK&&outype==EMBL) { |
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| 38 | genbank_to_embl(inf, outf); |
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| 39 | } else if(intype==GENBANK&&outype==PRINTABLE) { |
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| 40 | to_printable(inf, outf, GENBANK); |
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| 41 | } else if(intype==GENBANK&&outype==ALMA) { |
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| 42 | genbank_to_alma(inf, outf); |
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| 43 | } else if(intype==MACKE&&outype==GENBANK) { |
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| 44 | macke_to_genbank(inf, outf); |
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| 45 | } else if(intype==MACKE&&outype==PAUP) { |
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| 46 | to_paup(inf, outf, MACKE); |
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| 47 | } else if(intype==MACKE&&outype==PHYLIP) { |
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| 48 | to_phylip(inf, outf, MACKE,dd); |
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| 49 | } else if(intype==MACKE&&outype==PROTEIN) { |
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| 50 | macke_to_embl(inf, outf); |
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| 51 | } else if(intype==MACKE&&outype==EMBL) { |
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| 52 | macke_to_embl(inf, outf); |
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| 53 | } else if(intype==MACKE&&outype==PRINTABLE) { |
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| 54 | to_printable(inf, outf, MACKE); |
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| 55 | } else if(intype==MACKE&&outype==ALMA) { |
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| 56 | macke_to_alma(inf, outf); |
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| 57 | } else if(intype==PAUP&&outype==GENBANK) { |
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| 58 | error(6, "Sorry, cannot convert from Paup to GENBANK, Exit.\n"); |
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| 59 | } else if(intype==PAUP&&outype==MACKE) { |
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| 60 | error(81, "Sorry, cannot convert from Paup to AE2, Exit.\n"); |
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| 61 | } else if(intype==PAUP&&outype==PHYLIP) { |
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| 62 | error(8, "Sorry, cannot convert from Paup to Phylip, Exit.\n"); |
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| 63 | } else if(intype==PAUP&&outype==PROTEIN) { |
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| 64 | error(71, "Sorry, cannot convert from Paup to SWISSPROT, Exit."); |
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| 65 | } else if(intype==PAUP&&outype==EMBL) { |
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| 66 | error(78, "Sorry, cannot convert from Paup to SWISSPROT, Exit."); |
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| 67 | } else if(intype==PHYLIP&&outype==GENBANK) { |
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| 68 | error(85, "Sorry, cannot convert from Phylip to GenBank, Exit.\n"); |
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| 69 | } else if(intype==PHYLIP&&outype==MACKE) { |
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| 70 | error(88, "Sorry, cannot convert from Phylip to AE2, Exit.\n"); |
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| 71 | } else if(intype==PHYLIP&&outype==PAUP) { |
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| 72 | error(89, "Sorry, cannot convert from Phylip to Paup, Exit.\n"); |
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| 73 | } else if(intype==PHYLIP&&outype==PROTEIN) { |
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| 74 | error(72, "Sorry, cannot convert from Phylip to SWISSPROT, Exit.\n"); |
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| 75 | } else if(intype==PHYLIP&&outype==EMBL) { |
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| 76 | error(79, "Sorry, cannot convert from Phylip to SWISSPROT, Exit.\n"); |
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| 77 | } else if(intype==PROTEIN&&outype==MACKE) { |
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| 78 | embl_to_macke(inf, outf, PROTEIN); |
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| 79 | } else if(intype==PROTEIN&&outype==GENBANK) { |
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| 80 | error(78, "GenBank doesn't maintain protein data."); |
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| 81 | /* embl_to_genbank(inf, outf, PROTEIN); */ |
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| 82 | /* protein_to_genbank(inf, outf); */ |
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| 83 | } else if(intype==PROTEIN&&outype==PAUP) { |
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| 84 | to_paup(inf, outf, PROTEIN); |
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| 85 | } else if(intype==PROTEIN&&outype==PHYLIP) { |
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| 86 | to_phylip(inf, outf, PROTEIN,dd); |
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| 87 | } else if(intype==PROTEIN&&outype==EMBL) { |
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| 88 | error(58, "EMBL doesn't maintain protein data."); |
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| 89 | /* embl_to_embl(inf, outf, PROTEIN); */ |
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| 90 | } else if(intype==PROTEIN&&outype==PRINTABLE) { |
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| 91 | to_printable(inf, outf, PROTEIN); |
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| 92 | } else if(intype==EMBL&&outype==EMBL) { |
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| 93 | embl_to_embl(inf, outf); |
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| 94 | } else if(intype==EMBL&&outype==GENBANK) { |
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| 95 | embl_to_genbank(inf, outf); |
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| 96 | } else if(intype==EMBL&&outype==MACKE) { |
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| 97 | embl_to_macke(inf, outf, EMBL); |
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| 98 | } else if(intype==EMBL&&outype==PROTEIN) { |
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| 99 | embl_to_embl(inf, outf); |
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| 100 | } else if(intype==EMBL&&outype==PAUP) { |
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| 101 | to_paup(inf, outf, EMBL); |
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| 102 | } else if(intype==EMBL&&outype==PHYLIP) { |
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| 103 | to_phylip(inf, outf, EMBL,dd); |
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| 104 | } else if(intype==EMBL&&outype==PRINTABLE) { |
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| 105 | to_printable(inf, outf, EMBL); |
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| 106 | } else if(intype==EMBL&&outype==ALMA) { |
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| 107 | embl_to_alma(inf, outf); |
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| 108 | } else if(intype==ALMA&&outype==MACKE) { |
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| 109 | alma_to_macke(inf, outf); |
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| 110 | } else if(intype==ALMA&&outype==GENBANK) { |
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| 111 | alma_to_genbank(inf, outf); |
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| 112 | } else if(intype==ALMA&&outype==PAUP) { |
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| 113 | to_paup(inf, outf, ALMA); |
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| 114 | } else if(intype==ALMA&&outype==PHYLIP) { |
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| 115 | to_phylip(inf, outf, ALMA,dd); |
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| 116 | } else if(intype==ALMA&&outype==PRINTABLE) { |
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| 117 | to_printable(inf, outf, ALMA); |
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| 118 | } else if(outype==GCG) { |
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| 119 | to_gcg(intype, inf); |
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| 120 | } else error(90, "Unidentified input type or output type, Exit\n"); |
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| 121 | } |
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| 122 | |
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| 123 | /* ------------------- COMMON SUBROUTINES ----------------------- */ |
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| 124 | |
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| 125 | /* -------------------------------------------------------------- |
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| 126 | * Function init(). |
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| 127 | * Initialize data structure at the very beginning of running |
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| 128 | * any program. |
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| 129 | */ |
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| 130 | void |
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| 131 | init() { |
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| 132 | |
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| 133 | /* initialize macke format */ |
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| 134 | data.macke.seqabbr = NULL; |
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| 135 | data.macke.name = NULL; |
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| 136 | data.macke.atcc = NULL; |
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| 137 | data.macke.rna = NULL; |
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| 138 | data.macke.date = NULL; |
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| 139 | data.macke.nbk = NULL; |
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| 140 | data.macke.acs = NULL; |
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| 141 | data.macke.who = NULL; |
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| 142 | data.macke.remarks = NULL; |
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| 143 | data.macke.numofrem = 0; |
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| 144 | data.macke.rna_or_dna = 'd'; |
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| 145 | data.macke.journal = NULL; |
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| 146 | data.macke.title = NULL; |
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| 147 | data.macke.author = NULL; |
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| 148 | data.macke.strain = NULL; |
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| 149 | data.macke.subspecies = NULL; |
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| 150 | /* initialize gnebank format */ |
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| 151 | data.gbk.locus = NULL; |
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| 152 | data.gbk.definition = NULL; |
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| 153 | data.gbk.accession = NULL; |
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| 154 | data.gbk.keywords = NULL; |
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| 155 | data.gbk.source = NULL; |
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| 156 | data.gbk.organism = NULL; |
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| 157 | data.gbk.numofref = 0; |
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| 158 | data.gbk.reference = NULL; |
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| 159 | data.gbk.comments.orginf.exist = 0; |
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| 160 | data.gbk.comments.orginf.source = NULL; |
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| 161 | data.gbk.comments.orginf.cc = NULL; |
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| 162 | data.gbk.comments.orginf.formname = NULL; |
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| 163 | data.gbk.comments.orginf.nickname = NULL; |
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| 164 | data.gbk.comments.orginf.commname = NULL; |
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| 165 | data.gbk.comments.orginf.hostorg = NULL; |
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| 166 | data.gbk.comments.seqinf.exist = 0; |
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| 167 | data.gbk.comments.seqinf.RDPid = NULL; |
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| 168 | data.gbk.comments.seqinf.gbkentry = NULL; |
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| 169 | data.gbk.comments.seqinf.methods = NULL; |
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| 170 | data.gbk.comments.seqinf.comp5 = ' '; |
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| 171 | data.gbk.comments.seqinf.comp3 = ' '; |
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| 172 | data.gbk.comments.others = NULL; |
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| 173 | /* initialize paup format */ |
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| 174 | data.paup.ntax = 0; |
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| 175 | data.paup.equate = "~=.|><"; |
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| 176 | data.paup.gap = '-'; |
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| 177 | /* initial phylip data */ |
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| 178 | /* initial embl data */ |
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| 179 | data.embl.id = NULL; |
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| 180 | data.embl.dateu = NULL; |
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| 181 | data.embl.datec = NULL; |
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| 182 | data.embl.description = NULL; |
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| 183 | data.embl.os = NULL; |
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| 184 | data.embl.accession = NULL; |
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| 185 | data.embl.keywords = NULL; |
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| 186 | data.embl.dr = NULL; |
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| 187 | data.embl.numofref = 0; |
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| 188 | data.embl.reference = NULL; |
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| 189 | data.embl.comments.orginf.exist = 0; |
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| 190 | data.embl.comments.orginf.source = NULL; |
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| 191 | data.embl.comments.orginf.cc = NULL; |
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| 192 | data.embl.comments.orginf.formname = NULL; |
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| 193 | data.embl.comments.orginf.nickname = NULL; |
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| 194 | data.embl.comments.orginf.commname = NULL; |
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| 195 | data.embl.comments.orginf.hostorg = NULL; |
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| 196 | data.embl.comments.seqinf.exist = 0; |
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| 197 | data.embl.comments.seqinf.RDPid = NULL; |
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| 198 | data.embl.comments.seqinf.gbkentry = NULL; |
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| 199 | data.embl.comments.seqinf.methods = NULL; |
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| 200 | data.embl.comments.seqinf.comp5 = ' '; |
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| 201 | data.embl.comments.seqinf.comp3 = ' '; |
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| 202 | data.embl.comments.others = NULL; |
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| 203 | /* initial alma data */ |
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| 204 | data.alma.id = NULL; |
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| 205 | data.alma.filename = NULL; |
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| 206 | data.alma.format = UNKNOWN; |
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| 207 | data.alma.defgap = '-'; |
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| 208 | data.alma.num_of_sequence = 0; |
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| 209 | data.alma.sequence = NULL; |
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| 210 | /* inital NBRF data format */ |
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| 211 | data.nbrf.id = NULL; |
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| 212 | data.nbrf.description = NULL; |
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| 213 | /* initial sequence data */ |
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| 214 | data.numofseq = 0; |
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| 215 | data.seq_length = 0; |
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| 216 | data.max = INITSEQ; |
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| 217 | data.sequence = (char*)calloc(1,(unsigned)(sizeof(char)*INITSEQ+1)); |
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| 218 | |
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| 219 | data.ids = NULL; |
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| 220 | data.seqs = NULL; |
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| 221 | data.lengths = NULL; |
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| 222 | data.allocated = 0; |
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| 223 | } |
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| 224 | /* -------------------------------------------------------------- |
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| 225 | * Function init_seq_data(). |
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| 226 | * Init. seq. data. |
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| 227 | */ |
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| 228 | void |
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| 229 | init_seq_data() { |
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| 230 | data.numofseq = 0; |
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| 231 | data.seq_length = 0; |
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| 232 | } |
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