/dports/biology/treepuzzle/tree-puzzle-5.2/src/ |
H A D | consensus.c | 639 fprintf(treefile, "("); in writenode() 648 fprintf(treefile, ","); in writenode() 653 fprintf(treefile, "\n"); in writenode() 696 fprintf(treefile, ","); in writenode() 701 fprintf(treefile, "\n"); in writenode() 706 fprintf(treefile, ")"); in writenode() 725 fprintf(treefile, "("); in writeconsensustree() 727 fprintf(treefile, ","); in writeconsensustree() 739 fprintf(treefile, "\n"); in writeconsensustree() 782 fprintf(treefile, ","); in writeconsensustree() [all …]
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/dports/sysutils/uefi-edk2-bhyve-csm/uefi-edk2-aa8d718/AppPkg/Applications/Python/Python-2.7.2/Demo/scripts/ |
H A D | newslist.py | 53 treefile = 'grouptree' variable 113 treefile = os.path.join(topdir,treefile) variable 252 def readlocallist(treefile): argument 256 treetime = time.localtime(os.stat(treefile)[ST_MTIME]) 264 with open(treefile, 'rb') as dump: 267 print 'Cannot open local group list ' + treefile 270 def writelocallist(treefile, tree): argument 272 with open(treefile, 'wb') as dump: 274 print 'Saved list to %s\n' % treefile 343 (tree, treedate) = readlocallist(treefile) [all …]
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/dports/biology/mothur/mothur-1.46.1/source/commands/ |
H A D | deuniquetreecommand.cpp | 78 treefile = validParameter.validFile(parameters, "tree"); in DeuniqueTreeCommand() 79 if (treefile == "not open") { abort = true; } in DeuniqueTreeCommand() 80 else if (treefile == "not found") { //if there is a current design file, use it in DeuniqueTreeCommand() 81 treefile = current->getTreeFile(); in DeuniqueTreeCommand() 82 …if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter.\n… in DeuniqueTreeCommand() 84 }else { current->setTreeFile(treefile); } in DeuniqueTreeCommand() 94 if (outputdir == ""){ outputdir = util.hasPath(treefile); } in DeuniqueTreeCommand() 108 current->setTreeFile(treefile); in execute() 110 TreeReader* reader = new TreeReader(treefile, "", namefile); in execute() 118 variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(treefile)); in execute()
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H A D | classifytreecommand.cpp | 95 treefile = validParameter.validFile(parameters, "tree"); in ClassifyTreeCommand() 96 if (treefile == "not open") { treefile = ""; abort = true; } in ClassifyTreeCommand() 97 else if (treefile == "not found") { treefile = ""; in ClassifyTreeCommand() 98 treefile = current->getTreeFile(); in ClassifyTreeCommand() 99 …if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter.\… in ClassifyTreeCommand() 101 }else { current->setTreeFile(treefile); } in ClassifyTreeCommand() 147 vector<string> files; files.push_back(treefile); in ClassifyTreeCommand() 172 current->setTreeFile(treefile); in execute() 195 if (treefile != "") { in execute() 222 if (outputdir == "") { thisOutputDir += util.hasPath(treefile); } in getClassifications() [all …]
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H A D | parsimonycommand.cpp | 97 treefile = validParameter.validFile(parameters, "tree"); in ParsimonyCommand() 98 if (treefile == "not open") { treefile = ""; abort = true; } in ParsimonyCommand() 99 else if (treefile == "not found") { //if there is a current design file, use it in ParsimonyCommand() 100 treefile = current->getTreeFile(); in ParsimonyCommand() 101 …if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter.\n… in ParsimonyCommand() 103 }else { current->setTreeFile(treefile); } in ParsimonyCommand() 149 vector<string> files; files.push_back(treefile); in ParsimonyCommand() 167 Treenames = util.parseTreeFile(treefile); //extract treenames in execute() 172 current->setTreeFile(treefile); in execute() 176 else { reader = new TreeReader(treefile, countfile); } in execute() [all …]
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H A D | unifracunweightedcommand.cpp | 110 treefile = validParameter.validFile(parameters, "tree"); in UnifracUnweightedCommand() 111 if (treefile == "not open") { abort = true; } in UnifracUnweightedCommand() 112 else if (treefile == "not found") { //if there is a current design file, use it in UnifracUnweightedCommand() 113 treefile = current->getTreeFile(); in UnifracUnweightedCommand() 114 …if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter.\n… in UnifracUnweightedCommand() 116 }else { current->setTreeFile(treefile); } in UnifracUnweightedCommand() 142 if (outputdir == ""){ outputdir = util.hasPath(treefile); } in UnifracUnweightedCommand() 205 vector<string> files; files.push_back(treefile); in UnifracUnweightedCommand() 226 else { reader = new TreeReader(treefile, countfile); } in execute() 678 variables["[filename]"] = outputdir + util.getSimpleName(treefile); in printUnweightedFile() [all …]
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/dports/biology/seaview/seaview/csrc/ |
H A D | phylip.c | 1680 if (eoln(treefile)) in getch() 2198 c = getc(*treefile); in countcomma() 2199 if (feof(*treefile)) in countcomma() 2234 c = gettc(*treefile); in countsemic() 2267 rewind (*treefile); in countsemic() 2545 while (eoln(treefile) && !eoff(treefile)) in treeread() 2548 if (eoff(treefile)) { in treeread() 2570 while (eoln(treefile) && !eoff(treefile)); in treeread() 2721 while (eoln(treefile) && !eoff(treefile)) in treeread2() 2724 if (eoff(treefile)) { in treeread2() [all …]
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/phylip/src/ |
H A D | phylip.cpp | 1720 if (eoln(treefile)) in getch() 2247 c = getc(*treefile); in countcomma() 2248 if (feof(*treefile)) in countcomma() 2283 c = gettc(*treefile); in countsemic() 2316 rewind (*treefile); in countsemic() 2589 while (eoln(treefile) && !eoff(treefile)) in treeread() 2592 if (eoff(treefile)) { in treeread() 2614 while (eoln(treefile) && !eoff(treefile)); in treeread() 2765 while (eoln(treefile) && !eoff(treefile)) in treeread2() 2768 if (eoff(treefile)) { in treeread2() [all …]
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/dports/www/phpgroupware/phpgroupware-0.9.16.017/phpgwapi/inc/ |
H A D | class.menutree.inc.php | 44 function showtree($treefile, $expandlevels='', $num_menus = 50, $invisible_menus = Null) argument 78 $fd = fopen($treefile, 'r'); 81 die("menutree.inc : Unable to open file ".$treefile); 83 settype($treefile,'array'); 84 $treefile = array(); 87 $treefile[] = buffer; 91 if(is_array($treefile)) 93 $ta = $treefile; 95 elseif(gettype($treefile) == 'string') 97 $ta = explode("\n",$treefile);
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/dports/biology/fastdnaml/fastDNAml_1.2.2/scripts/ |
H A D | iterate_rates | 24 transition 2 < ${root}.$suf | treefile | quickadd | global 0 0 | fastDNAml >/dev/null 25 mv `ls -t treefile.*|head -1` "${root}.dummy_tree" 26 …usertree "${root}.dummy_tree" < ${root0}.$suf | n_categories 35 | treefile | DNAml_rates > /dev/n… 27 mv `ls -t treefile.*|head -1` 37 usertree $tree1 < ${root}_${v0}.$suf | n_categories 35 | treefile | frequencies | DNAml_rates > ${…
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/dports/security/libtasn1/libtasn1-4.18.0/tests/ |
H A D | strict-der.c | 39 const char *treefile = getenv ("ASN1PKIX"); in main() local 46 if (!treefile) in main() 47 treefile = "pkix.asn"; in main() 57 printf ("ASN1TREE: %s\n", treefile); in main() 65 result = asn1_parser2tree (treefile, &definitions, errorDescription); in main()
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H A D | Test_encdec.c | 52 const char *treefile = getenv ("ASN1PKIX"); in main() local 59 if (!treefile) in main() 60 treefile = "pkix.asn"; in main() 70 printf ("ASN1TREE: %s\n", treefile); in main() 78 result = asn1_parser2tree (treefile, &definitions, errorDescription); in main()
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H A D | Test_indefinite.c | 49 const char *treefile = getenv ("ASN1PKIX"); in main() local 58 if (!treefile) in main() 59 treefile = "pkix.asn"; in main() 75 printf ("ASN1TREE: %s\n", treefile); in main() 83 result = asn1_parser2tree (treefile, &definitions, errorDescription); in main()
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H A D | copynode.c | 52 const char *treefile = getenv ("ASN1PKIX"); 59 if (!treefile) 60 treefile = "pkix.asn"; 70 printf ("ASN1TREE: %s\n", treefile); 78 result = asn1_parser2tree (treefile, &definitions, errorDescription);
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H A D | Test_encoding.c | 43 const char *treefile = getenv ("ASN1ENCODING"); in main() local 48 if (!treefile) in main() 49 treefile = "Test_encoding.asn"; in main() 63 result = asn1_parser2tree (treefile, &definitions, errorDescription); in main()
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H A D | setof.c | 55 const char *treefile = getenv ("ASN1SETOF"); in main() local 61 if (!treefile) in main() 62 treefile = "setof.asn"; in main() 76 result = asn1_parser2tree (treefile, &definitions, errorDescription); in main()
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/dports/shells/wcd/wcd-6.0.3/src/ |
H A D | wcd.c | 1014 deleteLink(path,treefile); in deleteDir() 1020 deleteLink(path,treefile); in deleteDir() 2597 wcd_strncpy(treefile,rootdir,sizeof(treefile)); in main() 2598 wcd_strncat(treefile,TREEFILE,sizeof(treefile)); in main() 2630 wcd_strncpy(treefile,TREEFILE,sizeof(treefile)); in main() 2664 wcd_strncpy(treefile,rootdir,sizeof(treefile)); in main() 2665 wcd_strncat(treefile,TREEFILE,sizeof(treefile)); in main() 2685 create_dir_for_file(treefile); in main() 3303 wcd_strncpy(treefile,scandir,sizeof(treefile)); in main() 3304 wcd_strncat(treefile,RELTREEFILE,sizeof(treefile)); in main() [all …]
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/dports/devel/tex-kpathsea/texlive-20150521-source/texk/kpathsea/ |
H A D | mktexlsr | 76 treefile="${TMPDIR-/tmp}/mktexlsrtrees$$.tmp" 113 if echo "$1" >>"$treefile"; then :; else 114 echo "$progname: $treefile: could not append to arg file, goodbye." >&2 134 if test -s "$treefile"; then 135 set x `sort "$treefile" | uniq`
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/dports/print/tex-xdvik/xdvik-22.87/texk/kpathsea/ |
H A D | mktexlsr | 69 treefile="${TMPDIR-/tmp}/mktexlsrtrees$$.tmp" 106 if echo "$1" >>"$treefile"; then :; else 107 echo "$progname: $treefile: could not append to arg file, goodbye." >&2 127 if test -s "$treefile"; then 128 set x `sort "$treefile" | uniq`
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/dports/biology/mothur/mothur-1.46.1/source/read/ |
H A D | treereader.cpp | 14 TreeReader::TreeReader(string tf, string cf) : treefile(tf), countfile(cf) { in TreeReader() 20 Treenames = util.parseTreeFile(treefile); //fills treenames in TreeReader() 41 TreeReader::TreeReader(string tf, string gf, string nf) : treefile(tf), groupfile(gf), namefile(nf… in TreeReader() 45 Treenames = util.parseTreeFile(treefile); //fills treenames in TreeReader() 81 ReadTree* read = new ReadNewickTree(treefile, Treenames); in readTrees()
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/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/lib/Bio/Tools/Run/Phylo/Phylip/ |
H A D | ProtPars.pm | 369 my $treefile = $self->io->catfile($self->tempdir,$self->treefile); 372 unless (-e $treefile); 375 my $in = Bio::TreeIO->new(-file => $treefile, '-format' => 'newick'); 380 unlink $treefile;
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H A D | Neighbor.pm | 437 my $treefile = $self->io->catfile($self->tempdir,$self->treefile); 439 …$self->throw("neighbor did not create tree correctly (expected $treefile) ") unless (-e $treefile); 440 my $in = Bio::TreeIO->new(-file => $treefile, '-format' => 'newick'); 449 unlink $treefile;
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/dports/science/madness/madness-ebb3fd7/src/examples/compiler/ |
H A D | mra.cc | 19 std::ofstream treefile("prog.tree",std::ios_base::trunc); in main() local 20 std::ostream treeout(treefile.rdbuf()); in main() 22 treefile.close(); in main()
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/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/t/ |
H A D | DrawTree.t | 22 my $file = $treedraw->draw_tree(test_input_file('treefile.example')); 32 my $intree = Bio::TreeIO->new(-file => test_input_file('treefile.example')); 34 $file = $treedraw->draw_tree(test_input_file('treefile.example'));
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H A D | DrawGram.t | 23 my $file = $treedraw->draw_tree(test_input_file('treefile.example')); 32 my $intree = Bio::TreeIO->new(-file => test_input_file('treefile.example')); 39 $file = $treedraw->draw_tree(test_input_file('treefile.example'));
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