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Searched refs:treefile (Results 1 – 25 of 243) sorted by relevance

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/dports/biology/treepuzzle/tree-puzzle-5.2/src/
H A Dconsensus.c639 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 …]
/dports/sysutils/uefi-edk2-bhyve-csm/uefi-edk2-aa8d718/AppPkg/Applications/Python/Python-2.7.2/Demo/scripts/
H A Dnewslist.py53 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 …]
/dports/biology/mothur/mothur-1.46.1/source/commands/
H A Ddeuniquetreecommand.cpp78 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()
H A Dclassifytreecommand.cpp95 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 …]
H A Dparsimonycommand.cpp97 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 …]
H A Dunifracunweightedcommand.cpp110 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()
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/dports/biology/seaview/seaview/csrc/
H A Dphylip.c1680 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()
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/phylip/src/
H A Dphylip.cpp1720 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()
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/dports/www/phpgroupware/phpgroupware-0.9.16.017/phpgwapi/inc/
H A Dclass.menutree.inc.php44 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);
/dports/biology/fastdnaml/fastDNAml_1.2.2/scripts/
H A Diterate_rates24 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 > ${…
/dports/security/libtasn1/libtasn1-4.18.0/tests/
H A Dstrict-der.c39 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()
H A DTest_encdec.c52 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()
H A DTest_indefinite.c49 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()
H A Dcopynode.c52 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);
H A DTest_encoding.c43 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()
H A Dsetof.c55 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()
/dports/shells/wcd/wcd-6.0.3/src/
H A Dwcd.c1014 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()
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/dports/devel/tex-kpathsea/texlive-20150521-source/texk/kpathsea/
H A Dmktexlsr76 treefile="${TMPDIR-/tmp}/mktexlsrtrees$$.tmp"
113 if echo "$1" >>"$treefile"; then :; else
114 echo "$progname: $treefile: could not append to arg file, goodbye." >&2
134 if test -s "$treefile"; then
135 set x `sort "$treefile" | uniq`
/dports/print/tex-xdvik/xdvik-22.87/texk/kpathsea/
H A Dmktexlsr69 treefile="${TMPDIR-/tmp}/mktexlsrtrees$$.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`
/dports/biology/mothur/mothur-1.46.1/source/read/
H A Dtreereader.cpp14 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()
/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/lib/Bio/Tools/Run/Phylo/Phylip/
H A DProtPars.pm369 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;
H A DNeighbor.pm437 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;
/dports/science/madness/madness-ebb3fd7/src/examples/compiler/
H A Dmra.cc19 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()
/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/t/
H A DDrawTree.t22 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'));
H A DDrawGram.t23 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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