mothurout.h

   1 #ifndef MOTHUROUT_H
   2 #define MOTHUROUT_H
   3
   4 /*
   5  *  mothurOut.h
   6  *  Mothur
   7  *
   8  *  Created by westcott on 2/25/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14
  15 /***********************************************/
  16 struct logger {
  17
  18     logger() {}
  19     ~logger() {}
  20
  21     template< class T >
  22     logger& operator <<( const T& o ) {
  23         cout << o; return *this;
  24     }
  25
  26     logger& operator<<(ostream& (*m)(ostream&) ) {
  27         cout << m; return *this;
  28     }
  29
  30 };
  31 /***********************************************/
  32
  33 class MothurOut {
  34
  35         public:
  36                 static MothurOut* getInstance();
  37                 void setFileName(string);
  38
  39                 void mothurOut(string); //writes to cout and the logfile
  40                 void mothurOutEndLine(); //writes to cout and the logfile
  41                 void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
  42                 void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
  43         void mothurOutJustToScreen(string); //writes to cout
  44                 void mothurOutJustToLog(string);
  45                 void errorOut(exception&, string, string);
  46                 void closeLog();
  47                 string getDefaultPath() { return defaultPath; }
  48                 void setDefaultPath(string);
  49                 string getOutputDir() { return outputDir; }
  50                 void setOutputDir(string);
  51
  52                 string getReleaseDate() { return releaseDate; }
  53                 void setReleaseDate(string r) { releaseDate = r; }
  54                 string getVersion() { return version; }
  55                 void setVersion(string r) { version = r; }
  56
  57                 void addGroup(string g) { Groups.push_back(g); }
  58                 void setGroups(vector<string>& g) { sort(g.begin(), g.end()); Groups = g; }
  59                 void clearGroups() { Groups.clear(); }
  60             int getNumGroups() { return Groups.size(); }
  61                 vector<string> getGroups() { sort(Groups.begin(), Groups.end()); return Groups; }
  62                 void addAllGroup(string g) { namesOfGroups.push_back(g); }
  63                 void setAllGroups(vector<string>& g) { sort(g.begin(), g.end()); namesOfGroups = g; }
  64                 void clearAllGroups() { namesOfGroups.clear(); }
  65                 int getNumAllGroups() { return namesOfGroups.size(); }
  66
  67                 vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
  68                 vector<string> Treenames;
  69                 //map<string, string> names;
  70                 vector<string> binLabelsInFile;
  71                 vector<string> currentBinLabels;
  72                 string saveNextLabel, argv, sharedHeaderMode, groupMode;
  73                 bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
  74
  75                 //functions from mothur.h
  76                 //file operations
  77         bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable.
  78                 vector<unsigned long long> divideFile(string, int&); //divides splitting unevenness by sequence
  79         vector<unsigned long long> divideFilePerLine(string, int&); //divides splitting unevenness at line breaks
  80                 int divideFile(string, int&, vector<string>&);
  81                 vector<unsigned long long> setFilePosEachLine(string, int&);
  82                 vector<unsigned long long> setFilePosFasta(string, int&);
  83                 string sortFile(string, string);
  84                 int appendFiles(string, string);
  85         int appendFilesWithoutHeaders(string, string);
  86                 int renameFile(string, string); //oldname, newname
  87                 string getFullPathName(string);
  88         string findProgramPath(string programName);
  89                 string hasPath(string);
  90                 string getExtension(string);
  91                 string getPathName(string);
  92                 string getSimpleName(string);
  93                 string getRootName(string);
  94                 bool isBlank(string);
  95                 int openOutputFile(string, ofstream&);
  96         int openOutputFileBinary(string, ofstream&);
  97                 int openOutputFileAppend(string, ofstream&);
  98         int openOutputFileBinaryAppend(string, ofstream&);
  99                 int openInputFile(string, ifstream&);
 100                 int openInputFile(string, ifstream&, string); //no error given
 101                 string getline(ifstream&);
 102                 string getline(istringstream&);
 103                 void gobble(istream&);
 104                 void gobble(istringstream&);
 105         vector<string> splitWhiteSpace(string& rest, char[], int);
 106         vector<string> splitWhiteSpace(string);
 107         set<string> readAccnos(string);
 108         int readAccnos(string, vector<string>&);
 109         map<string, int> readNames(string);
 110         map<string, int> readNames(string, unsigned long int&);
 111         int readTax(string, map<string, string>&);
 112         vector<consTax> readConsTax(string);
 113         int readConsTax(string, map<string, consTax2>&);
 114         int readNames(string, map<string, string>&, map<string, int>&);
 115                 int readNames(string, map<string, string>&);
 116         int readNames(string, map<string, string>&, bool);
 117         int readNames(string, map<string, string>&, int);
 118                 int readNames(string, map<string, vector<string> >&);
 119                 int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
 120                 int mothurRemove(string);
 121                 bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 122         bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 123                 bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 124                 bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 125
 126
 127                 //searchs and checks
 128                 bool checkReleaseVersion(ifstream&, string);
 129                 bool anyLabelsToProcess(string, set<string>&, string);
 130                 bool inUsersGroups(vector<string>, vector<string>);
 131         bool inUsersGroups(vector<int>, vector< vector<int> >);
 132                 bool inUsersGroups(string, vector<string>);
 133         bool inUsersGroups(int, vector<int>);
 134                 void getNumSeqs(ifstream&, int&);
 135                 int getNumSeqs(ifstream&);
 136                 int getNumNames(string);
 137                 int getNumChar(string, char);
 138                 bool isTrue(string);
 139                 bool isContainingOnlyDigits(string);
 140                 bool isNumeric1(string);
 141
 142
 143                 //string manipulation
 144                 void splitAtEquals(string&, string&);
 145                 void splitAtComma(string&, string&);
 146                 void splitAtComma(string&, vector<string>&);
 147                 void splitAtDash(string&, set<int>&);
 148                 void splitAtDash(string&, set<string>&);
 149                 void splitAtDash(string&, vector<string>&);
 150                 void splitAtChar(string&, vector<string>&, char);
 151         void splitAtChar(string&, string&, char);
 152         vector<string> splitWhiteSpaceWithQuotes(string);
 153                 int removeConfidences(string&);
 154         string removeQuotes(string);
 155         string makeList(vector<string>&);
 156         bool isSubset(vector<string>, vector<string>); //bigSet, subset
 157         int checkName(string&);
 158         map<string, vector<string> > parseClasses(string);
 159
 160                 //math operation
 161                 int factorial(int num);
 162                 vector<vector<double> > binomial(int);
 163                 float ceilDist(float, int);
 164                 float roundDist(float, int);
 165                 unsigned int fromBase36(string);
 166                 int getRandomIndex(int); //highest
 167         double getStandardDeviation(vector<int>&);
 168         vector<double> getStandardDeviation(vector< vector<double> >&);
 169         vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
 170         vector<double> getAverages(vector< vector<double> >&);
 171         double getAverage(vector<double>);
 172         vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&);
 173         vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&, vector< vector<seqDist> >&);
 174         vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&, string);
 175         vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&);
 176
 177                 int control_pressed;
 178                 bool executing, runParse, jumble, gui, mothurCalling, debug;
 179
 180                 //current files - if you add a new type you must edit optionParser->getParameters, get.current and set.current commands and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes. add a get and set function.
 181                 string getPhylipFile()          { return phylipfile;            }
 182                 string getColumnFile()          { return columnfile;            }
 183                 string getListFile()            { return listfile;                      }
 184                 string getRabundFile()          { return rabundfile;            }
 185                 string getSabundFile()          { return sabundfile;            }
 186                 string getNameFile()            { return namefile;                      }
 187                 string getGroupFile()           { return groupfile;                     }
 188                 string getOrderFile()           { return orderfile;                     }
 189                 string getOrderGroupFile()      { return ordergroupfile;        }
 190                 string getTreeFile()            { return treefile;                      }
 191                 string getSharedFile()          { return sharedfile;            }
 192                 string getRelAbundFile()        { return relabundfile;          }
 193                 string getDesignFile()          { return designfile;            }
 194                 string getFastaFile()           { return fastafile;                     }
 195                 string getSFFFile()                     { return sfffile;                       }
 196                 string getQualFile()            { return qualfile;                      }
 197                 string getOligosFile()          { return oligosfile;            }
 198                 string getAccnosFile()          { return accnosfile;            }
 199                 string getTaxonomyFile()        { return taxonomyfile;          }
 200                 string getFlowFile()            { return flowfile;                      }
 201         string getBiomFile()            { return biomfile;                      }
 202         string getCountTableFile()      { return counttablefile;        }
 203         string getSummaryFile()     { return summaryfile;       }
 204                 string getProcessors()          { return processors;            }
 205
 206                 void setListFile(string f)                      { listfile = getFullPathName(f);                        }
 207                 void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
 208                 void setGroupFile(string f)                     { groupfile = getFullPathName(f);       groupMode = "group";            }
 209                 void setPhylipFile(string f)            { phylipfile = getFullPathName(f);                      }
 210                 void setColumnFile(string f)            { columnfile = getFullPathName(f);                      }
 211                 void setNameFile(string f)                      { namefile = getFullPathName(f);                        }
 212                 void setRabundFile(string f)            { rabundfile = getFullPathName(f);                      }
 213                 void setSabundFile(string f)            { sabundfile = getFullPathName(f);                      }
 214                 void setSharedFile(string f)            { sharedfile = getFullPathName(f);                      }
 215                 void setRelAbundFile(string f)          { relabundfile = getFullPathName(f);            }
 216                 void setOrderFile(string f)                     { orderfile = getFullPathName(f);                       }
 217                 void setOrderGroupFile(string f)        { ordergroupfile = getFullPathName(f);          }
 218                 void setDesignFile(string f)            { designfile = getFullPathName(f);                      }
 219                 void setFastaFile(string f)                     { fastafile = getFullPathName(f);                       }
 220                 void setSFFFile(string f)                       { sfffile = getFullPathName(f);                         }
 221                 void setQualFile(string f)                      { qualfile = getFullPathName(f);                        }
 222                 void setOligosFile(string f)            { oligosfile = getFullPathName(f);                      }
 223                 void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
 224                 void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
 225                 void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
 226         void setBiomFile(string f)                      { biomfile = getFullPathName(f);                        }
 227         void setSummaryFile(string f)           { summaryfile = getFullPathName(f);                     }
 228         void setCountTableFile(string f)        { counttablefile = getFullPathName(f);  groupMode = "count";    }
 229         void setProcessors(string p)            { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");       }
 230
 231                 void printCurrentFiles();
 232                 bool hasCurrentFiles();
 233                 void clearCurrentFiles();
 234         set<string> getCurrentTypes();
 235
 236         private:
 237                 static MothurOut* _uniqueInstance;
 238                 MothurOut( const MothurOut& ); // Disable copy constructor
 239                 void operator=( const MothurOut& ); // Disable assignment operator
 240                 MothurOut() {
 241                         control_pressed = false; defaultPath="";
 242                         phylipfile = "";
 243                         columnfile = "";
 244                         listfile = "";
 245                         rabundfile = "";
 246                         sabundfile = "";
 247                         namefile = "";
 248                         groupfile = "";
 249                         designfile = "";
 250                         orderfile = "";
 251                         treefile = "";
 252                         sharedfile = "";
 253                         ordergroupfile = "";
 254                         relabundfile = "";
 255                         fastafile = "";
 256                         qualfile = "";
 257                         sfffile = "";
 258                         oligosfile = "";
 259                         accnosfile = "";
 260                         taxonomyfile = "";
 261                         processors = "1";
 262                         flowfile = "";
 263             biomfile = "";
 264             counttablefile = "";
 265             summaryfile = "";
 266                         gui = false;
 267                         printedHeaders = false;
 268                         commandInputsConvertError = false;
 269             mothurCalling = false;
 270             debug = false;
 271                         sharedHeaderMode = "";
 272             groupMode = "group";
 273             changedSeqNames = false;
 274             modifyNames = true;
 275                 }
 276                 ~MothurOut();
 277
 278                 string logFileName;
 279                 string defaultPath, outputDir;
 280                 string releaseDate, version;
 281
 282                 string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
 283                 string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile;
 284
 285                 vector<string> Groups;
 286                 vector<string> namesOfGroups;
 287                 ofstream out;
 288
 289                 int mem_usage(double&, double&);
 290
 291 };
 292 /***********************************************/
 293
 294 #endif
 295