| /dports/biology/fasta3/fasta-36.3.8/src/ |
| H A D | url_subs.c | 133 if (m_msp->lname[0]!='%') { in do_url1()
134 SAFE_STRNCPY(lib,m_msp->lname,sizeof(lib)); in do_url1()
138 SAFE_STRNCAT(lib,&m_msp->lname[1],sizeof(lib)); in do_url1()
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| /dports/biology/hhsuite/hh-suite-3.3.0/scripts/hhpred/dependencies/modeller_cuser/ |
| H A D | cuser_form52_wrap.c | 682 size_t lname = (name ? strlen(name) : 0); in SWIG_PackDataName() local
683 if ((2*sz + 2 + lname) > bsz) return 0; in SWIG_PackDataName()
686 if (lname) { in SWIG_PackDataName()
687 strncpy(r,name,lname+1); in SWIG_PackDataName()
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| H A D | cuser_form54_wrap.c | 682 size_t lname = (name ? strlen(name) : 0); in SWIG_PackDataName() local
683 if ((2*sz + 2 + lname) > bsz) return 0; in SWIG_PackDataName()
686 if (lname) { in SWIG_PackDataName()
687 strncpy(r,name,lname+1); in SWIG_PackDataName()
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| H A D | cuser_form56_wrap.c | 682 size_t lname = (name ? strlen(name) : 0); in SWIG_PackDataName() local
683 if ((2*sz + 2 + lname) > bsz) return 0; in SWIG_PackDataName()
686 if (lname) { in SWIG_PackDataName()
687 strncpy(r,name,lname+1); in SWIG_PackDataName()
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| H A D | cuser_form_wrap.c | 660 size_t lname = (name ? strlen(name) : 0); in SWIG_PackDataName() local
661 if ((2*sz + 2 + lname) > bsz) return 0; in SWIG_PackDataName()
664 if (lname) { in SWIG_PackDataName()
665 strncpy(r,name,lname+1); in SWIG_PackDataName()
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| /dports/biology/hhsuite/hh-suite-3.3.0/scripts/ |
| H A D | reformat.pl | 113 my $lname; # length of sequence name in clustal, stockholm, psi format
141 if ($options=~s/ -lname\s+(\S+) / /) {$lname=$1;}
747 if (!$lname) {$lname=32;}
749 printf(OUTFILE "%-$lname.$lname"."s %s\n","#=GF DE",$1);
752 printf(OUTFILE "%-$lname.$lname"."s %s\n","#=GC RF",$refline);
769 if (!$lname) {$lname=32;}
770 printf(OUTFILE "%-$lname.$lname"."s %s\n",$1,$seqs[$k]);
788 if (!$lname) {$lname=18;}
789 printf(OUTFILE "%-$lname.$lname"."s %s\n",$names[$k],$1); # and print them after the sequence name
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| /dports/biology/jalview/jalview/getdown/src/getdown/core/src/main/java/com/threerings/getdown/data/ |
| H A D | Resource.java | 150 String dotJar = ".jar", lname = _local.getName(); in Resource() local
151 String uname = lname.substring(0, lname.lastIndexOf(dotJar) + dotJar.length()); in Resource()
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| /dports/biology/jellyfish/jellyfish-2.3.0/swig/perl5/ |
| H A D | swig_wrap.cpp | 710 size_t lname = (name ? strlen(name) : 0); in SWIG_PackDataName() local
711 if ((2*sz + 2 + lname) > bsz) return 0; in SWIG_PackDataName()
714 if (lname) { in SWIG_PackDataName()
715 strncpy(r,name,lname+1); in SWIG_PackDataName()
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| /dports/biology/jellyfish/jellyfish-2.3.0/swig/python/ |
| H A D | swig_wrap.cpp | 720 size_t lname = (name ? strlen(name) : 0); in SWIG_PackDataName() local
721 if ((2*sz + 2 + lname) > bsz) return 0; in SWIG_PackDataName()
724 if (lname) { in SWIG_PackDataName()
725 strncpy(r,name,lname+1); in SWIG_PackDataName()
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| /dports/biology/jellyfish/jellyfish-2.3.0/swig/ruby/ |
| H A D | swig_wrap.cpp | 833 size_t lname = (name ? strlen(name) : 0); in SWIG_PackDataName() local
834 if ((2*sz + 2 + lname) > bsz) return 0; in SWIG_PackDataName()
837 if (lname) { in SWIG_PackDataName()
838 strncpy(r,name,lname+1); in SWIG_PackDataName()
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| /dports/biology/lamarc/lamarc-2.1.8/src/convModel/ |
| H A D | gc_datastore_writebatch.cpp | 151 TiXmlText * lname = new TiXmlText(locNames[0].c_str()); in CmdExportInfile() local
152 lMatch->LinkEndChild(lname); in CmdExportInfile()
162 TiXmlText * lname = new TiXmlText(locNames[i].c_str()); in CmdExportInfile() local
163 locName->LinkEndChild(lname); in CmdExportInfile()
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| /dports/biology/lamarc/lamarc-2.1.8/src/datalike/ |
| H A D | haplotypes.cpp | 31 Haplotypes::Haplotypes(long regnum, string lname) in Haplotypes() argument
33 m_locusname(lname), in Haplotypes()
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| H A D | haplotypes.h | 39 Haplotypes(long regnum, string lname);
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| H A D | phenotypes.cpp | 31 Phenotypes::Phenotypes(long regnum, string lname) in Phenotypes() argument
33 m_locusname(lname), in Phenotypes()
42 Phenotypes::Phenotypes(string lname) in Phenotypes() argument
44 m_locusname(lname), in Phenotypes()
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| H A D | phenotypes.h | 47 Phenotypes(long regionnum, string lname);
48 Phenotypes(string lname); //A blank copy.
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| H A D | region.cpp | 338 bool Region::HasLocus(string lname) const in HasLocus()
342 if (m_loci[locus].GetName() == lname) return true; in HasLocus()
346 if (m_movingloci[locus].GetName() == lname) return true; in HasLocus()
372 long Region::GetLocusIndex(string lname) const in GetLocusIndex()
376 if (m_loci[locus].GetName() == lname) return locus; in GetLocusIndex()
378 if (HasLocus(lname)) in GetLocusIndex()
388 const Locus& Region::GetLocus(string lname) const in GetLocus()
392 if (m_movingloci[locus].GetName() == lname) return m_movingloci[locus]; in GetLocus()
396 if (m_loci[locus].GetName() == lname) return m_loci[locus]; in GetLocus()
843 void Region::CopyTipDataForLocus(const string& lname) in CopyTipDataForLocus() argument
[all …]
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| H A D | region.h | 129 bool HasLocus(string lname)const;
130 const Locus& GetLocus(string lname)const;
131 long GetLocusIndex(string lname) const;
177 void CopyTipDataForLocus(const string& lname);
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| /dports/biology/lamarc/lamarc-2.1.8/src/tree/ |
| H A D | individual.cpp | 163 hap = m_haplotypesmap.find(make_pair(lname, marker)); in AddHaplotype()
166 Haplotypes haplo(regnum, lname); in AddHaplotype()
178 hap = m_haplotypesmap.find(make_pair(lname, marker)); in GetAllelesFor()
212 hap = m_haplotypesmap.find(make_pair(lname, marker)); in GetHaplotypesFor()
230 hap = m_haplotypesmap.find(make_pair(lname, marker)); in GetMarkerDataFor()
243 pair<string, long> tag = make_pair(lname, marker); in ChooseNewHaplotypesFor()
249 lname + "."); in ChooseNewHaplotypesFor()
272 pair<string, long> tag = make_pair(lname, marker); in ChooseRandomHaplotypesFor()
309 pair<string, long> tag = make_pair(lname, marker); in ChooseFirstHaplotypeFor()
325 pair<string, long> tag = make_pair(lname, marker); in ChooseNextHaplotypeFor()
[all …]
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| H A D | individual.h | 68 …void AddHaplotype(long regnum, string lname, long marker, const StringVec1d& alleles, double penet…
69 StringVec1d GetAllelesFor(string lname, long marker) const; //phase 1
70 vector<LocusCell> GetLocusCellsFor(string lname, long marker) const; //phase 2
71 Haplotypes GetHaplotypesFor(string lname, long marker) const;
72 string GetMarkerDataFor(string lname, long marker) const; //phase 3/Output.
73 void ChooseNewHaplotypesFor(string lname, long marker);
74 bool ChooseRandomHaplotypesFor(string lname, long marker);
77 void ChooseFirstHaplotypeFor(string lname, long marker);
78 bool ChooseNextHaplotypeFor(string lname, long marker);
81 void SetHaplotypes(string lname, long marker, Haplotypes haps);
[all …]
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| H A D | parameter.cpp | 136 const string lname, in Parameter() argument
146 m_name(lname), in Parameter()
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| H A D | parameter.h | 145 const string lname,
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| H A D | rectree.cpp | 361 void RecTree::ReassignDLsFor(string lname, long marker, long ind) in ReassignDLsFor() argument
368 if ((*m_pMovingLocusVec)[lnum].GetName() == lname) in ReassignDLsFor()
376 return Tree::ReassignDLsFor(lname, marker, ind); in ReassignDLsFor()
380 vector<LocusCell> cells = m_individuals[ind].GetLocusCellsFor(lname, marker); in ReassignDLsFor()
791 string lname = (*m_pMovingLocusVec)[mloc].GetName(); in UpdateDataLikesForIndividualsFrom() local
798 for (m_individuals[ind].ChooseFirstHaplotypeFor(lname, marker); in UpdateDataLikesForIndividualsFrom()
800 newhaps = m_individuals[ind].ChooseNextHaplotypeFor(lname, marker)) in UpdateDataLikesForIndividualsFrom()
802 ReassignDLsFor(lname, marker, ind); in UpdateDataLikesForIndividualsFrom()
893 string lname = (*m_pMovingLocusVec)[mlocus].GetName(); in RandomizeMovingHaplotypes() local
899 if (m_individuals[ind].ChooseRandomHaplotypesFor(lname, marker)) in RandomizeMovingHaplotypes()
[all …]
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| H A D | tree.cpp | 830 string lname = locusmarker.first; in PickNewSiteDLs() local
834 m_individuals[ind].ChooseNewHaplotypesFor(lname, marker); in PickNewSiteDLs()
839 ReassignDLsFor(lname, marker, ind); in PickNewSiteDLs()
846 void Tree::ReassignDLsFor(string lname, long marker, long ind) in ReassignDLsFor() argument
853 if ((*m_pLocusVec)[lnum].GetName() == lname) in ReassignDLsFor()
860 throw implementation_error("We have the segment name " + lname in ReassignDLsFor()
866 vector<LocusCell> cells = m_individuals[ind].GetLocusCellsFor(lname, marker); in ReassignDLsFor()
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| H A D | tree.h | 165 virtual void ReassignDLsFor(std::string lname, long marker, long ind);
320 virtual void ReassignDLsFor(std::string lname, long marker, long ind);
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| /dports/biology/lamarc/lamarc-2.1.8/src/ui_vars/ |
| H A D | ui_vars_datapackplus.cpp | 97 long UIVarsDataPackPlus::GetNumIndividualsWithMultipleHaplotypes(long region, string lname) const in GetNumIndividualsWithMultipleHaplotypes()
103 if (individuals[ind].GetHaplotypesFor(lname, 0).MultipleHaplotypes()) in GetNumIndividualsWithMultipleHaplotypes()
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