1 | /* |
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2 | * This file is generated by aisc_mkpt. |
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3 | * Any changes you make here will be overwritten later! |
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4 | * |
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5 | */ |
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6 | |
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7 | #ifndef GDE_PROTO_H |
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8 | #define GDE_PROTO_H |
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9 | |
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10 | /* define ARB attributes: */ |
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11 | #ifndef ATTRIBUTES_H |
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12 | # include <attributes.h> |
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13 | #endif |
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14 | |
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15 | |
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16 | /* GDE_ParseMenu.cxx */ |
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17 | void ParseMenu(void); |
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18 | int Find(const char *target, const char *key); |
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19 | int Find2(const char *target, const char *key); |
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20 | void Error(const char *msg) __ATTR__NORETURN; |
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21 | void crop(char *input, char *head, char *tail); |
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22 | |
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23 | /* GDE.cxx */ |
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24 | char *GDE_makeawarname(GmenuItem *gmenuitem, long i); |
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25 | void GDE_load_menu(AW_window *awm, AW_active mask, const char *menulabel, const char *menuitemlabel); |
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26 | void create_gde_var(AW_root *aw_root, AW_default aw_def, char *(*get_sequences )(void *THIS, GBDATA **&the_species, uchar **&the_names, uchar **&the_sequences, long &numberspecies, long &maxalignlen ), gde_cgss_window_type wt, void *THIS); |
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27 | |
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28 | /* GDE_event.cxx */ |
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29 | void GDE_startaction_cb(AW_window *aw, GmenuItem *gmenuitem, AW_CL cd); |
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30 | |
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31 | /* GDE_arbdb_io.cxx */ |
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32 | void ReadArbdb_plain(char *filename, NA_Alignment *dataset, int type); |
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33 | int ReadArbdb2(NA_Alignment *dataset, AP_filter *filter, GapCompression compress, bool cutoff_stop_codon); |
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34 | int ReadArbdb(NA_Alignment *dataset, bool marked, AP_filter *filter, GapCompression compress, bool cutoff_stop_codon); |
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35 | int getelem(NA_Sequence *a, int b); |
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36 | void putelem(NA_Sequence *a, int b, NA_Base c); |
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37 | |
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38 | /* GDE_HGLfile.cxx */ |
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39 | void ReadGDE(char *filename, NA_Alignment *dataset, int type); |
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40 | int WriteGDE(NA_Alignment *aln, char *filename, int method, int maskable); |
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41 | void SeqNorm(NA_Sequence *seq); |
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42 | char *uniqueID(void); |
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43 | |
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44 | /* GDE_Genbank.cxx */ |
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45 | void ReadGen(char *filename, NA_Alignment *dataset, int type); |
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46 | int WriteGen(NA_Alignment *aln, char *filename, int method, int maskable); |
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47 | void SetTime(void *b); |
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48 | |
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49 | /* GDE_FileIO.cxx */ |
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50 | int MAX(int a, int b); |
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51 | int MIN(int a, int b); |
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52 | void Regroup(NA_Alignment *alignment); |
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53 | void ErrorOut5(int code, const char *string); |
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54 | char *Calloc(int count, int size); |
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55 | char *Realloc(char *block, int size); |
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56 | void Cfree(char *block); |
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57 | void LoadData(char *filen); |
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58 | void AppendNA(NA_Base *buffer, int len, NA_Sequence *seq); |
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59 | void Ascii2NA(char *buffer, int len, int matrix[16 ]); |
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60 | int WriteNA_Flat(NA_Alignment *aln, char *filename, int method, int maskable); |
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61 | void Warning(const char *s); |
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62 | void InitNASeq(NA_Sequence *seq, int type); |
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63 | void ReadCMask(const char *filename); |
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64 | int WriteStatus(NA_Alignment *aln, char *filename, int method); |
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65 | void ReadStatus(char *filename); |
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66 | void NormalizeOffset(NA_Alignment *aln); |
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67 | int WriteCMask(NA_Alignment *aln, char *filename, int method, int maskable); |
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68 | |
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69 | #else |
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70 | #error GDE_proto.h included twice |
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71 | #endif /* GDE_PROTO_H */ |
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