| /dports/biology/hhsuite/hh-suite-3.3.0/src/ |
| H A D | hhfullalignment.h | 20 …am& out, Hit& hit, const char showconf, const char showcons, const char showdssp, const char showp…
21 …void PrintA2M(std::stringstream& out, Hit& hit, const char showcons, const char showdssp, const ch…
22 …void PrintFASTA(std::stringstream& out, Hit& hit, const char showcons, const char showdssp, const …
23 …void PrintA3M(std::stringstream& out, Hit& hit, const char showcons, const char showdssp, const ch…
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| H A D | hhhitlist.h | 47 const char showdssp, const char showpred, const float p, const int aliwidth, const int nseqdis,
50 const char showdssp, const char showpred, const float p, const int aliwidth, const int nseqdis,
54 const char showconf, const char showcons, const char showdssp, const char showpred,
58 const char showconf, const char showcons, const char showdssp, const char showpred,
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| H A D | hhfullalignment.cpp | 209 …am& out, Hit& hit, const char showconf, const char showcons, const char showdssp, const char showp… in PrintHHR() argument
234 if (k == qa->nss_dssp && !showdssp) in PrintHHR()
348 if (k == ta->nss_dssp && !showdssp) in PrintHHR()
394 …ntA2M(std::stringstream& out, Hit& hit, const char showcons, const char showdssp, const char showp… in PrintA2M() argument
402 if (k == qa->nss_dssp && !showdssp) in PrintA2M()
424 if (k == ta->nss_dssp && !showdssp) in PrintA2M()
447 …FASTA(std::stringstream& out, Hit& hit, const char showcons, const char showdssp, const char showp… in PrintFASTA() argument
451 PrintA2M(out, hit, showcons, showdssp, showpred, aliwidth); in PrintFASTA()
457 …ntA3M(std::stringstream& out, Hit& hit, const char showcons, const char showdssp, const char showp… in PrintA3M() argument
461 PrintA2M(out, hit, showcons, showdssp, showpred, aliwidth); in PrintA3M()
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| H A D | hhhitlist.cpp | 119 const char showconf, const char showcons, const char showdssp, in PrintHHR() argument
124 …PrintHHR(q, out, maxdbstrlen, showconf, showcons, showdssp, showpred, b, B, z, Z, aliwidth, nseqdi… in PrintHHR()
142 const char showdssp, const char showpred, const int b, const int B, in PrintHHR() argument
147 …PrintAlignments(q, out, showconf, showcons, showdssp, showpred, p, aliwidth, nseqdis, b, B, E, S, … in PrintHHR()
154 const char showcons, const char showdssp, const char showpred, in PrintAlignments() argument
158 …PrintAlignments(q, out, showconf, showcons, showdssp, showpred, p, aliwidth, nseqdis, b, B, E, S, … in PrintAlignments()
180 const char showconf, const char showcons, const char showdssp, in PrintAlignments() argument
206 qt_ali.PrintHHR(out, hit, showconf, showcons, showdssp, showpred, aliwidth, maxseq); in PrintAlignments()
210 qt_ali.PrintFASTA(out, hit, showcons, showdssp, showpred, aliwidth); in PrintAlignments()
214 qt_ali.PrintA2M(out, hit, showcons, showdssp, showpred, aliwidth); in PrintAlignments()
[all …]
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| H A D | hhdecl.cpp | 27 showdssp = 1; // show predicted secondary structure ss_dssp in Parameters()
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| H A D | hhdecl.h | 175 …char showdssp; // in query-template alignments 0: don't show ss_dssp lines 1:show variable
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| H A D | hhblits.cpp | 613 par.showdssp = 0; in ProcessArguments()
1819 par.showcons, par.showdssp, par.showpred, par.b, par.B, in writeHHRFile()
1853 par.showdssp, par.showpred, par.p, par.aliwidth, in writePairwiseAlisFile()
1900 hhblits.par.showdssp, hhblits.par.showpred, in writeHHRFile()
1917 par.showdssp, par.showpred, in printHHRFile()
1934 hhblits.par.showcons, hhblits.par.showdssp, in writePairwiseAlisFile()
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| H A D | hhsearch.cpp | 363 par.showdssp = 0; in ProcessArguments()
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| H A D | hhalign.cpp | 409 par.showdssp = 0; in ProcessArguments()
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| /dports/biology/clustal-omega/clustal-omega-1.2.4/src/hhalign/ |
| H A D | hhfullalignment-C.h | 373 if (k==qa->nss_dssp && !par.showdssp) continue; in PrintHHR()
453 if (k==ta->nss_dssp && !par.showdssp) continue; in PrintHHR()
489 if (k==qa->nss_dssp && !par.showdssp) continue; in PrintA2M()
536 if (k==ta->nss_dssp && !par.showdssp) continue; in PrintA2M()
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| H A D | hhdecl-C.h | 115 int showdssp; // 0: don't show consensus sequence in alignments 1:show variable
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| H A D | hhutil-C.h | 563 par.showdssp=1; // show predicted secondary structure in SetDefaults()
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| H A D | hhalign.cpp | 542 else if (!strncmp(argv[i],"-nodssp",7)) par.showdssp=0;
793 par.showdssp=0; /* -nodssp */ in hhalign()
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| H A D | hhfunc-C.h | 854 …par.altali=1;par.hitrank=0;par.showcons=1; par.showdssp=1;par.showpred=1;par.nseqdis=iN;par.cons=1; in AlnToHMM2()
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