| /dports/biology/mothur/mothur-1.46.1/source/ |
| H A D | mothurout.cpp | 16 MothurOut* MothurOut::getInstance() { in getInstance()
18 _uniqueInstance = new MothurOut(); in getInstance()
23 void MothurOut::appendLogBuffer(string partialLog) { in appendLogBuffer()
61 void MothurOut::closeLog() { in closeLog()
114 void MothurOut::mothurOutClearBuffer() { in mothurOutClearBuffer()
124 MothurOut::~MothurOut() { in ~MothurOut()
134 void MothurOut::mothurOut(string output) { in mothurOut()
178 void MothurOut::mothurOutJustToScreen(string output) { in mothurOutJustToScreen()
213 void MothurOut::mothurOutEndLine() { in mothurOutEndLine()
288 void MothurOut::mothurOutJustToLog(string output) { in mothurOutJustToLog()
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| H A D | mothurout.h | 36 class MothurOut {
39 static MothurOut* getInstance();
77 static MothurOut* _uniqueInstance;
78 MothurOut( const MothurOut& ); // Disable copy constructor
79 void operator=( const MothurOut& ); // Disable assignment operator
80 MothurOut() { in MothurOut() function
96 ~MothurOut();
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| H A D | mothur.cpp | 18 MothurOut* MothurOut::_uniqueInstance = 0;
23 MothurOut* m = MothurOut::getInstance(); in ctrlc_handler()
36 MothurOut* m = MothurOut::getInstance(); in main()
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| H A D | collect.h | 15 …mSeqs()), order(order), displays(disp), label(order->getLabel()) { m = MothurOut::getInstance(); … in Collect()
17 …der(sharedorder), displays(disp), label(sharedorder->getLabel()) { m = MothurOut::getInstance(); } in Collect()
24 MothurOut* m;
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| H A D | rarefact.h | 15 …eqs()), order(o), displays(disp), label(o.getLabel()), ends(en) { m = MothurOut::getInstance(); … in Rarefact()
18 … lookup(shared), displays(disp), jumble(j) { m = MothurOut::getInstance(); processors = proc; } in Rarefact()
33 MothurOut* m;
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| H A D | summary.hpp | 24 …Summary(int p) { processors = p; m = MothurOut::getInstance(); total = 0; numUniques = 0; hasNameO… in Summary()
73 MothurOut* m;
129 MothurOut* m;
139 m = MothurOut::getInstance(); in seqSumData()
152 m = MothurOut::getInstance(); in seqSumData()
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| H A D | opticluster.h | 38 …OptiCluster() : Cluster() { m = MothurOut::getInstance(); truePositives = 0; trueNegatives = 0; fa… in OptiCluster()
43 …m = MothurOut::getInstance(); matrix = mt; metric = met; truePositives = 0; trueNegatives = 0; fal… in OptiCluster()
56 MothurOut* m;
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| H A D | wilcox.h | 17 PWilcox() { mout = MothurOut::getInstance();} in PWilcox()
24 MothurOut* mout;
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| H A D | myseqdist.cpp | 16 m = MothurOut::getInstance(); in correctDist()
26 m = MothurOut::getInstance(); in correctDist()
110 MothurOut* m;
118 m = MothurOut::getInstance(); in correctData()
145 …ctor<vector<char> >& alignMoves, int i, int j, vector<int>& seqA, vector<int>& seqB, MothurOut* m){ in getLastMatch()
173 …etDist(vector<int>& seqA, vector<int>& seqB, vector<vector<double> >& correctMatrix, MothurOut* m){ in getDist()
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| /dports/biology/mothur/mothur-1.46.1/TestMothur/ |
| H A D | testoptirefmatrix.cpp | 14 m = MothurOut::getInstance(); in TestOptiRefMatrix()
27 MothurOut* m; m = MothurOut::getInstance(); in TEST()
51 MothurOut* m; m = MothurOut::getInstance(); in TEST()
103 MothurOut* m; m = MothurOut::getInstance(); in TEST()
129 MothurOut* m; m = MothurOut::getInstance(); in TEST()
172 MothurOut* m; m = MothurOut::getInstance(); in TEST()
222 MothurOut* m; m = MothurOut::getInstance(); in TEST()
234 MothurOut* m; m = MothurOut::getInstance(); in TEST()
250 MothurOut* m; m = MothurOut::getInstance(); in TEST()
277 MothurOut* m; m = MothurOut::getInstance(); in TEST()
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| H A D | main.cpp | 38 MothurOut* MothurOut::_uniqueInstance;
43 MothurOut* m; m = MothurOut::getInstance(); in main()
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| /dports/biology/mothur/mothur-1.46.1/source/datastructures/ |
| H A D | datavector.hpp | 25 DataVector(){ m = MothurOut::getInstance(); } in DataVector()
26 DataVector(string l) : label(l) { m = MothurOut::getInstance();}; in DataVector()
27 DataVector(const DataVector& dv) : label(dv.label){ m = MothurOut::getInstance();} in DataVector()
28 DataVector(ifstream&) {m = MothurOut::getInstance();} in DataVector()
29 DataVector(ifstream&, GroupMap*){m = MothurOut::getInstance();} in DataVector()
52 MothurOut* m;
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| H A D | fastqread.cpp | 15 m = MothurOut::getInstance(); in FastqRead()
32 m = MothurOut::getInstance(); format = "illumina1.8+"; in FastqRead()
60 m = MothurOut::getInstance(); format = f; in FastqRead()
88 m = MothurOut::getInstance(); in FastqRead()
106 m = MothurOut::getInstance(); in FastqRead()
124 m = MothurOut::getInstance(); in FastqRead()
179 m = MothurOut::getInstance(); in FastqRead()
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| H A D | taxonomy.cpp | 13 m = MothurOut::getInstance(); in Taxonomy()
19 m = MothurOut::getInstance(); in Taxonomy()
35 m = MothurOut::getInstance(); in Taxonomy()
51 m = MothurOut::getInstance(); in Taxonomy()
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| H A D | report.hpp | 21 Report() { m = MothurOut::getInstance(); } in Report()
35 MothurOut* m;
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| H A D | storagedatabase.hpp | 20 StorageDatabase() { m = MothurOut::getInstance(); length = 0; samelength = true; } in StorageDatabase()
35 MothurOut* m;
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| /dports/biology/mothur/mothur-1.46.1/source/calculators/ |
| H A D | calculator.h | 24 Calculator(){ m = MothurOut::getInstance(); needsAll = false; } in Calculator()
25 …Calculator(string n, int c, bool f) : name(n), cols(c), multiple(f) { m = MothurOut::getInstance()… in Calculator()
26 …t c, bool f, bool a) : name(n), cols(c), multiple(f), needsAll(a) { m = MothurOut::getInstance(); … in Calculator()
46 MothurOut* m;
64 ClusterMetric(){ m = MothurOut::getInstance(); } in ClusterMetric()
65 ClusterMetric(string n){ m = MothurOut::getInstance(); name = n; } in ClusterMetric()
75 MothurOut* m;
88 DistCalc(double c){ name = "unknown"; dist = 0; cutoff = c; m = MothurOut::getInstance(); } in DistCalc()
103 MothurOut* m;
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| H A D | metrolognormal.cpp | 22 MothurOut* m = MothurOut::getInstance(); in nLogLikelihood1()
67 MothurOut* m = MothurOut::getInstance(); in negLogLikelihood1()
113 MothurOut* m = MothurOut::getInstance(); in metropolis1()
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| H A D | uvest.h | 24 UVEst() { m = MothurOut::getInstance(); } in UVEst()
30 MothurOut* m;
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| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | filterseqscommand.h | 66 MothurOut* m;
76 m = MothurOut::getInstance(); in filterData()
96 MothurOut* m;
107 m = MothurOut::getInstance(); in filterRunData()
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| H A D | distancecommand.h | 36 MothurOut* m;
45 m = MothurOut::getInstance(); in distanceData()
50 m = MothurOut::getInstance(); in distanceData()
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| H A D | nocommands.cpp | 19 MothurOut* m = MothurOut::getInstance(); in execute()
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| H A D | listseqscommand.cpp | 160 void readFastq(set<string>& names, ifstream& in, MothurOut*& m){ in readFastq()
185 void readFasta(set<string>& names, ifstream& in, MothurOut*& m){ in readFasta()
209 void readList(set<string>& names, ifstream& in, MothurOut*& m){ in readList()
239 void readNameTaxGroup(set<string>& names, ifstream& in, MothurOut*& m){ in readNameTaxGroup()
264 void readCount(set<string>& names, ifstream& in, MothurOut*& m){ in readCount()
286 void readAlignContigs(set<string>& names, ifstream& in, MothurOut*& m){ in readAlignContigs()
362 …d::process(vector<string> files, set<string>& names, void f(set<string>&, ifstream&, MothurOut*&)){ in process() argument
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| /dports/biology/mothur/mothur-1.46.1/source/read/ |
| H A D | readmatrix.hpp | 24 ReadMatrix(){ DMatrix = new SparseDistanceMatrix(); m = MothurOut::getInstance(); } in ReadMatrix()
39 MothurOut* m;
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| /dports/biology/mothur/mothur-1.46.1/source/metastats/ |
| H A D | mothurfisher.h | 20 MothurFisher(){otuLabel = ""; m = MothurOut::getInstance(); } in MothurFisher()
26 MothurOut* m;
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