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Searched refs:fp_in_align (Results 1 – 11 of 11) sorted by relevance

/dports/biology/phyml/phyml-3.3.20200621/src/
H A Dcl.c1267 io->fp_in_align = Openfile(io->in_align_file,0); in Read_Command_Line()
1596 if(io->print_site_lnl && io->fp_in_align != NULL) in Read_Command_Line()
1605 if(io->print_trace && io->fp_in_align != NULL) in Read_Command_Line()
1614 if(io->print_json_trace && io->fp_in_align != NULL) in Read_Command_Line()
1624 if(io->mod->s_opt->random_input_tree && io->fp_in_align != NULL) in Read_Command_Line()
1633 if((io->print_boot_trees) && (io->do_boot == YES) && (io->fp_in_align != NULL)) in Read_Command_Line()
1648 if(io->append_run_ID && io->fp_in_align != NULL) in Read_Command_Line()
1656 if(io->fp_in_align != NULL) in Read_Command_Line()
1702 if(io->fp_in_align != NULL) in Read_Command_Line()
1710 if(io->fp_in_align != NULL) io->fp_out_summary = Openfile(io->out_summary_file,writemode); in Read_Command_Line()
H A Dnexus.c88 Get_Token(io->fp_in_align,token); in Read_Nexus_Taxa()
92 fseek(io->fp_in_align,-1*sizeof(char),SEEK_CUR); in Read_Nexus_Taxa()
147 fseek(io->fp_in_align,-1*sizeof(char),SEEK_CUR); in Read_Nexus_Matrix()
H A Dmain.c387 if(io->fp_in_align) fclose(io->fp_in_align); in main()
H A Dio.c828 fgetpos(io->fp_in_align,&curr_pos); in Detect_Align_File_Format()
832 while((c=fgetc(io->fp_in_align)) != EOF) in Detect_Align_File_Format()
838 if(!fgets(s,6,io->fp_in_align)) in Detect_Align_File_Format()
845 fsetpos(io->fp_in_align,&curr_pos); in Detect_Align_File_Format()
851 fsetpos(io->fp_in_align,&curr_pos); in Detect_Align_File_Format()
901 if(!io->fp_in_align) in Get_Seq()
920 Get_Nexus_Data(io->fp_in_align,io); in Get_Seq()
1428 if(!Read_One_Line_Seq(&data,i,io->fp_in_align)) in Read_Seq_Interleaved()
1453 if(!fgets(line,T_MAX_LINE,io->fp_in_align)) break; in Read_Seq_Interleaved()
1468 fgetpos(io->fp_in_align,&curr_pos); in Read_Seq_Interleaved()
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H A Dinterface.c243 io->fp_in_align = Openfile(io->in_align_file,0); in Launch_Interface_Input()
269 io->fp_in_align = Openfile(io->in_align_file,0); in Launch_Interface_Input()
276 io->fp_in_align = Openfile(io->in_align_file,0); in Launch_Interface_Input()
1881 io->st->optionlist[set]->fp_in_align = Openfile(io->st->optionlist[set]->in_align_file,0); in Launch_Interface_Multigene()
H A Dinvitee.c253 io -> fp_in_align = Openfile(io -> in_align_file, 1); in PhyTime_XML()
699 if(io -> fp_in_align) fclose(io -> fp_in_align); in PhyTime_XML()
H A Dm4.c259 if(io->fp_in_align) fclose(io->fp_in_align); in M4_main()
H A Dmixt.c1949 io->fp_in_align = Openfile(orig_align,0); in MIXT_Bootstrap()
1953 rewind(io->fp_in_align); in MIXT_Bootstrap()
1959 fclose(io->fp_in_align); in MIXT_Bootstrap()
H A Dxml.c388 io->fp_in_align = Openfile(io->in_align_file,READ); in XML_Process_Base()
397 fclose(io->fp_in_align); in XML_Process_Base()
H A Dutilities.h1202 FILE *fp_in_align; /*! pointer to the alignment file */ member
H A Dinit.c534 io->fp_in_align = NULL; in Set_Defaults_Input()