Lines Matching defs:_option
403 typedef struct _option struct
405 char **buffer; //pointer to buffer when MPI-worker otherwise NULL
406 FILE *parmfile;
407 FILE *seedfile;
408 FILE *logfile;
409 FILE *mixfile;
413 long nmlength; /* length of individual names */
414 long popnmlength; /* length of population names */
415 long allelenmlength; /* length of allele names */
418 char *custm; /* custom migration matrix: theta are first */
419 char *custm2; /*custom migration matrix: theta on diagonal */
433 int menu;
434 boolean progress;
435 boolean verbose;
436 boolean writelog;
437 boolean uep;
438 MYREAL ueprate;
439 MYREAL uepmu;
440 MYREAL uepnu;
441 MYREAL uepfreq0;
442 MYREAL uepfreq1;
443 boolean movingsteps;
444 MYREAL acceptfreq;
445 boolean printdata;
446 boolean printcov;
447 boolean usertree;
448 boolean usertreewithmig;
449 boolean randomtree;
450 short treeprint;
451 long treeinc;
452 boolean usem;
453 boolean recordedusem;
454 short migvar;
455 boolean plot;
456 boolean plotnow;
457 short plotmethod;
458 short plotvar;
459 short plotscale;
460 MYREAL plotrange[4];
461 long plotintervals;
462 MYREAL *plotxvalues;
463 MYREAL *plotyvalues;
464 boolean simulation;
465 boolean mighist;
466 boolean mighist_all;
467 long mighist_counter;
468 long mighist_increment;
469 boolean skyline;
470 float eventbinsize;
471 boolean mixplot;
472 boolean dist;
473 boolean geo;
474 boolean div;
475 char *parmfilename;
476 char *infilename;
477 char *outfilename;
478 char *pdfoutfilename;
479 char *logfilename;
480 char *mathfilename;
481 char *treefilename;
482 char *utreefilename;
483 char *catfilename;
484 char *weightfilename;
485 char *sumfilename;
486 char *mighistfilename;
487 char *skylinefilename;
488 char *distfilename;
489 char *geofilename;
490 char *divfilename;
491 char *bootfilename;
492 char *seedfilename;
493 char *mixfilename;
495 char *uepfilename;
497 char *datefilename;
498 char *bayesfilename;
499 char *bayesmdimfilename;
500 boolean mdimdelete;
501 int use_compressed;
502 boolean prioralone;
504 char title[LINESIZE + 1];
505 lratio_fmt *lratio;
529 int msat_option; argument
530 pair msat_tuning;
531 MYREAL **steps;
532 boolean interleaved;
533 MYREAL seqerror;
534 MYREAL *ttratio;
535 boolean fastlike;
536 boolean freqsfrom;
537 long categs;
538 MYREAL *rate;
539 long rcategs;
540 MYREAL *rrate;
541 MYREAL *probcat;
542 long seqrate_gamma_num; /*number of loci for gamma values*/
543 MYREAL *seqrate_gamma; /* for gamma values for many loci*/
544 MYREAL probsum;
545 boolean gammarates;
546 boolean autocorr;
547 MYREAL lambda;
548 boolean weights;
549 MYREAL freqa;
550 MYREAL freqc;
551 MYREAL freqg;
552 MYREAL freqt;
554 short autoseed;
555 unsigned long inseed;
556 unsigned long saveseed;
558 boolean bayes_infer;
559 boolean integrated_like;
561 boolean slice_sampling[PRIOR_SIZE];
562 MYREAL *slice_sticksizes;
563 MYREAL updateratio;
564 int bayesprior[3];
565 int bayespretty;
566 prior_fmt *bayespriortheta;
567 prior_fmt *bayespriorm;
568 prior_fmt *bayespriorrate;
569 bayes_fmt *bayes;
570 boolean has_bayesfile;
571 boolean has_bayesmdimfile;
572 long bayesmdiminterval;
573 short thetaguess;
574 short migrguess;
575 boolean gamma;
576 boolean murates;
577 boolean murates_fromdata;
578 boolean bayesmurates;
579 MYREAL alphavalue;
580 MYREAL *mu_rates;
581 long muloci;
582 long *newpops;
583 long newpops_numalloc;
584 long newpops_numpop;
586 MYREAL *inheritance_scalars;
587 long inheritance_scalars_numalloc;
588 boolean has_datefile;
591 boolean fluctuate;
592 MYREAL *flucrates;
594 long burn_in;
595 char burnin_autostop;
596 short heating;
597 MYREAL *thetag;
598 long numthetag;
599 MYREAL *mg;
600 long nummg;
601 long schains;
602 long sincrement;
603 long ssteps;
604 long lchains;
605 long lincrement;
606 long lsteps;
607 MYREAL lcepsilon;
608 boolean gelman;
609 boolean gelmanpairs;
610 long pluschain; //how many chains are allowed , currently HARDCODED
611 boolean replicate;
612 long replicatenum;
613 long gridpoints;
614 long numpop;
615 MYREAL heat[50];
616 boolean adaptiveheat;
617 long heating_interval;
618 long heated_chains;
620 boolean readsum;
621 boolean writesum;
623 int cpu;
626 MYREAL minmigsumstat;
628 MYREAL *mutationrate_year; // keeps mutation rate per year for each locus
629 long mutationrate_year_numalloc; //
630 MYREAL generation_year;
631 long randomsubset;
632 unsigned long randomsubsetseed;
634 MYREAL *timings; // vector of time points (options)
635 long numtimings; // number of elements in the timings vector
636 MYREAL **timemodifiers; // vector of parameter modifier vectors
638 boolean heatedswap_off;
639 boolean has_autotune;
640 MYREAL autotune;
641 long totalsites; //for snp data
642 MYREAL *wattersons;
643 long *segregs;
644 boolean onlyvariable; // analyze only variable sequence loci
645 MYREAL locusweight; // use a weight to calculate the invariant locus
646 boolean has_variableandone; // use only one invariant locus and reweight
647 long firstinvariant; // locus number of first invariant locus to reweight using locusweight