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/dports/biology/infernal/infernal-1.1.3/easel/miniapps/
H A Dcmd_filter.md23 sequence fragments (see `--fragthresh`). These rules, and options that
116 fragthresh/symfrac rules to a sample of 10K sequences instead of
140 `--fragthresh` and `--symfrac`.
154 Do not use a statistical subsample when using the fragthresh/symfrac
157 #### `--fragthresh <x>`
167 fragthresh calculations, without affecting the alignment itself.
169 The smaller `fragthresh` is, the fewer fragments are defined.
170 `--fragthresh 0` says no sequences are fragments. `--fragthresh 1`
H A Dcmd_filter.c72 cfg->fragthresh = esl_opt_GetReal (go, "--fragthresh"); in esl_cmd_filter()
/dports/biology/hmmer/hmmer-3.3/easel/miniapps/
H A Dcmd_filter.md23 sequence fragments (see `--fragthresh`). These rules, and options that
116 fragthresh/symfrac rules to a sample of 10K sequences instead of
140 `--fragthresh` and `--symfrac`.
154 Do not use a statistical subsample when using the fragthresh/symfrac
157 #### `--fragthresh <x>`
167 fragthresh calculations, without affecting the alignment itself.
169 The smaller `fragthresh` is, the fewer fragments are defined.
170 `--fragthresh 0` says no sequences are fragments. `--fragthresh 1`
H A Dcmd_filter.c72 cfg->fragthresh = esl_opt_GetReal (go, "--fragthresh"); in esl_cmd_filter()
/dports/biology/infernal/infernal-1.1.3/easel/
H A Desl_msa.h177 extern int esl_msa_MarkFragments (const ESL_MSA *msa, float fragthresh, ESL_BITFIELD **ret_fragassi…
178 extern int esl_msa_MarkFragments_old(ESL_MSA *msa, double fragthresh);
H A Desl_msaweight.h16 …float fragthresh; // seq is a fragment if (length from 1st to last aligned residue)/alen < fra… member
H A Desl_msaweight.c313 float fragthresh = (cfg? cfg->fragthresh : eslMSAWEIGHT_FRAGTHRESH); in consensus_by_sample() local
334 …minspan = (int) ceil( fragthresh * (float) msa->alen ); // define alispan as aligned length fr… in consensus_by_sample()
426 …float fragthresh = (cfg? cfg->fragthresh : eslMSAWEIGHT_FRAGTHRESH); // seq is fragment if (l… in collect_counts() local
427 …int minspan = (int) ceil( fragthresh * (float) msa->alen ); // precalculated span le… in collect_counts()
552 cfg->fragthresh = eslMSAWEIGHT_FRAGTHRESH; in esl_msaweight_cfg_Create()
1808 cfg->fragthresh = esl_opt_GetReal (go, "--fragthresh"); in main()
1839 printf("# fragthresh: %.4f\n", cfg->fragthresh); in main()
H A Desl_msa.c2133 esl_msa_MarkFragments(const ESL_MSA *msa, float fragthresh, ESL_BITFIELD **ret_fragassign) in esl_msa_MarkFragments() argument
2136 …int minspan = (int) ceil(fragthresh * (float) msa->alen); // precalculated span lengt… in esl_msa_MarkFragments()
2205 esl_msa_MarkFragments_old(ESL_MSA *msa, double fragthresh) in esl_msa_MarkFragments_old() argument
2211 if (msa_get_rlen(msa, i) <= fragthresh * msa->alen) in esl_msa_MarkFragments_old()
/dports/biology/hmmer/hmmer-3.3/easel/
H A Desl_msa.h177 extern int esl_msa_MarkFragments (const ESL_MSA *msa, float fragthresh, ESL_BITFIELD **ret_fragassi…
178 extern int esl_msa_MarkFragments_old(ESL_MSA *msa, double fragthresh);
H A Desl_msaweight.h16 …float fragthresh; // seq is a fragment if (length from 1st to last aligned residue)/alen < fra… member
H A Desl_msaweight.c313 float fragthresh = (cfg? cfg->fragthresh : eslMSAWEIGHT_FRAGTHRESH); in consensus_by_sample() local
334 …minspan = (int) ceil( fragthresh * (float) msa->alen ); // define alispan as aligned length fr… in consensus_by_sample()
426 …float fragthresh = (cfg? cfg->fragthresh : eslMSAWEIGHT_FRAGTHRESH); // seq is fragment if (l… in collect_counts() local
427 …int minspan = (int) ceil( fragthresh * (float) msa->alen ); // precalculated span le… in collect_counts()
552 cfg->fragthresh = eslMSAWEIGHT_FRAGTHRESH; in esl_msaweight_cfg_Create()
1808 cfg->fragthresh = esl_opt_GetReal (go, "--fragthresh"); in main()
1839 printf("# fragthresh: %.4f\n", cfg->fragthresh); in main()
H A Desl_msa.c2133 esl_msa_MarkFragments(const ESL_MSA *msa, float fragthresh, ESL_BITFIELD **ret_fragassign) in esl_msa_MarkFragments() argument
2136 …int minspan = (int) ceil(fragthresh * (float) msa->alen); // precalculated span lengt… in esl_msa_MarkFragments()
2205 esl_msa_MarkFragments_old(ESL_MSA *msa, double fragthresh) in esl_msa_MarkFragments_old() argument
2211 if (msa_get_rlen(msa, i) <= fragthresh * msa->alen) in esl_msa_MarkFragments_old()
/dports/multimedia/v4l_compat/linux-5.13-rc2/drivers/net/wireless/broadcom/brcm80211/brcmsmac/
H A Dmain.h540 u16 fragthresh[NFIFO]; member
H A Dmain.c4325 wlc->fragthresh[i] = DOT11_DEFAULT_FRAG_LEN; in brcms_c_info_init()
6774 if (wlc->fragthresh[queue] != in brcms_c_d11hdrs_mac80211()
6776 wlc->fragthresh[queue] = in brcms_c_d11hdrs_mac80211()
6790 phylen, wlc->fragthresh[queue], in brcms_c_d11hdrs_mac80211()
/dports/multimedia/v4l-utils/linux-5.13-rc2/drivers/net/wireless/broadcom/brcm80211/brcmsmac/
H A Dmain.h540 u16 fragthresh[NFIFO]; member
H A Dmain.c4325 wlc->fragthresh[i] = DOT11_DEFAULT_FRAG_LEN; in brcms_c_info_init()
6774 if (wlc->fragthresh[queue] != in brcms_c_d11hdrs_mac80211()
6776 wlc->fragthresh[queue] = in brcms_c_d11hdrs_mac80211()
6790 phylen, wlc->fragthresh[queue], in brcms_c_d11hdrs_mac80211()
/dports/multimedia/libv4l/linux-5.13-rc2/drivers/net/wireless/broadcom/brcm80211/brcmsmac/
H A Dmain.h540 u16 fragthresh[NFIFO]; member
H A Dmain.c4325 wlc->fragthresh[i] = DOT11_DEFAULT_FRAG_LEN; in brcms_c_info_init()
6774 if (wlc->fragthresh[queue] != in brcms_c_d11hdrs_mac80211()
6776 wlc->fragthresh[queue] = in brcms_c_d11hdrs_mac80211()
6790 phylen, wlc->fragthresh[queue], in brcms_c_d11hdrs_mac80211()
/dports/biology/infernal/infernal-1.1.3/hmmer/src/
H A Dp7_builder.c109 bld->fragthresh = (go != NULL) ? esl_opt_GetReal (go, "--fragthresh") : 0.5; in p7_builder_Create()
427 if ((status = esl_msa_MarkFragments_old(msa, bld->fragthresh)) != eslOK) goto ERROR; in p7_Builder()
H A Dhmmer.h1269 float fragthresh; /* if L <= fragthresh*alen, seq is called a fragment */ member
/dports/biology/hmmer/hmmer-3.3/src/
H A Dp7_builder.c109 bld->fragthresh = (go != NULL) ? esl_opt_GetReal (go, "--fragthresh") : 0.5; in p7_builder_Create()
427 if ((status = esl_msa_MarkFragments_old(msa, bld->fragthresh)) != eslOK) goto ERROR; in p7_Builder()
H A Dhmmer.h1269 float fragthresh; /* if L <= fragthresh*alen, seq is called a fragment */ member
/dports/biology/infernal/infernal-1.1.3/hmmer/testsuite/
H A Dtestsuite.sqc110 1 exercise build/--fragthresh @src/hmmbuild@ --fragthresh 0.4 --EmL 10 --EvL 10 --EfL 10 %HMMB…
/dports/biology/hmmer/hmmer-3.3/testsuite/
H A Dtestsuite.sqc110 1 exercise build/--fragthresh @src/hmmbuild@ --fragthresh 0.4 --EmL 10 --EvL 10 --EfL 10 %HMMB…