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> sharedBinLabelsInFile;
  71                 vector<string> currentSharedBinLabels;
  72         vector<string> listBinLabelsInFile;
  73         //vector<string> currentListBinLabels;
  74                 string saveNextLabel, argv, sharedHeaderMode, groupMode;
  75                 bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
  76
  77                 //functions from mothur.h
  78                 //file operations
  79         bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable.
  80                 vector<unsigned long long> divideFile(string, int&); //divides splitting unevenness by sequence
  81         vector<unsigned long long> divideFilePerLine(string, int&); //divides splitting unevenness at line breaks
  82                 int divideFile(string, int&, vector<string>&);
  83                 vector<unsigned long long> setFilePosEachLine(string, int&);
  84                 vector<unsigned long long> setFilePosFasta(string, int&);
  85                 string sortFile(string, string);
  86                 int appendFiles(string, string);
  87         int appendFilesWithoutHeaders(string, string);
  88                 int renameFile(string, string); //oldname, newname
  89                 string getFullPathName(string);
  90         string findProgramPath(string programName);
  91                 string hasPath(string);
  92                 string getExtension(string);
  93                 string getPathName(string);
  94                 string getSimpleName(string);
  95                 string getRootName(string);
  96                 bool isBlank(string);
  97                 int openOutputFile(string, ofstream&);
  98         int openOutputFileBinary(string, ofstream&);
  99                 int openOutputFileAppend(string, ofstream&);
 100         int openOutputFileBinaryAppend(string, ofstream&);
 101                 int openInputFile(string, ifstream&);
 102                 int openInputFile(string, ifstream&, string); //no error given
 103                 string getline(ifstream&);
 104                 string getline(istringstream&);
 105                 void gobble(istream&);
 106                 void gobble(istringstream&);
 107         vector<string> splitWhiteSpace(string& rest, char[], int);
 108         vector<string> splitWhiteSpace(string);
 109         set<string> readAccnos(string);
 110         int readAccnos(string, vector<string>&);
 111         map<string, int> readNames(string);
 112         map<string, int> readNames(string, unsigned long int&);
 113         int readTax(string, map<string, string>&);
 114         vector<consTax> readConsTax(string);
 115         int readConsTax(string, map<string, consTax2>&);
 116         int readNames(string, map<string, string>&, map<string, int>&);
 117                 int readNames(string, map<string, string>&);
 118         int readNames(string, map<string, string>&, bool);
 119         int readNames(string, map<string, string>&, int);
 120                 int readNames(string, map<string, vector<string> >&);
 121                 int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
 122                 int mothurRemove(string);
 123                 bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 124         bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 125                 bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 126                 bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 127
 128
 129                 //searchs and checks
 130                 bool checkReleaseVersion(ifstream&, string);
 131                 bool anyLabelsToProcess(string, set<string>&, string);
 132                 bool inUsersGroups(vector<string>, vector<string>);
 133         bool inUsersGroups(vector<int>, vector< vector<int> >);
 134                 bool inUsersGroups(string, vector<string>);
 135         bool inUsersGroups(int, vector<int>);
 136                 void getNumSeqs(ifstream&, int&);
 137                 int getNumSeqs(ifstream&);
 138                 int getNumNames(string);
 139                 int getNumChar(string, char);
 140                 bool isTrue(string);
 141                 bool isContainingOnlyDigits(string);
 142                 bool isNumeric1(string);
 143         bool isLabelEquivalent(string, string);
 144         string getSimpleLabel(string);
 145         string findEdianness();
 146
 147
 148                 //string manipulation
 149                 void splitAtEquals(string&, string&);
 150                 void splitAtComma(string&, string&);
 151                 void splitAtComma(string&, vector<string>&);
 152                 void splitAtDash(string&, set<int>&);
 153                 void splitAtDash(string&, set<string>&);
 154                 void splitAtDash(string&, vector<string>&);
 155                 void splitAtChar(string&, vector<string>&, char);
 156         void splitAtChar(string&, string&, char);
 157         vector<string> splitWhiteSpaceWithQuotes(string);
 158                 int removeConfidences(string&);
 159         string removeQuotes(string);
 160         string makeList(vector<string>&);
 161         bool isSubset(vector<string>, vector<string>); //bigSet, subset
 162         int checkName(string&);
 163         map<string, vector<string> > parseClasses(string);
 164
 165                 //math operation
 166         double max(vector<double>&); //returns largest value in vector
 167         double min(vector<double>&); //returns smallest value in vector
 168                 int factorial(int num);
 169                 vector<vector<double> > binomial(int);
 170                 float ceilDist(float, int);
 171                 float roundDist(float, int);
 172                 unsigned int fromBase36(string);
 173         double median(vector<double>);
 174                 int getRandomIndex(int); //highest
 175         double getStandardDeviation(vector<int>&);
 176         vector<double> getStandardDeviation(vector< vector<double> >&);
 177         vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
 178         vector<double> getAverages(vector< vector<double> >&);
 179         double getAverage(vector<double>);
 180         vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&);
 181         vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&, vector< vector<seqDist> >&);
 182         vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&, string);
 183         vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&);
 184
 185                 int control_pressed;
 186                 bool executing, runParse, jumble, gui, mothurCalling, debug;
 187
 188                 //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.
 189                 string getPhylipFile()          { return phylipfile;            }
 190                 string getColumnFile()          { return columnfile;            }
 191                 string getListFile()            { return listfile;                      }
 192                 string getRabundFile()          { return rabundfile;            }
 193                 string getSabundFile()          { return sabundfile;            }
 194                 string getNameFile()            { return namefile;                      }
 195                 string getGroupFile()           { return groupfile;                     }
 196                 string getOrderFile()           { return orderfile;                     }
 197                 string getOrderGroupFile()      { return ordergroupfile;        }
 198                 string getTreeFile()            { return treefile;                      }
 199                 string getSharedFile()          { return sharedfile;            }
 200                 string getRelAbundFile()        { return relabundfile;          }
 201                 string getDesignFile()          { return designfile;            }
 202                 string getFastaFile()           { return fastafile;                     }
 203                 string getSFFFile()                     { return sfffile;                       }
 204                 string getQualFile()            { return qualfile;                      }
 205                 string getOligosFile()          { return oligosfile;            }
 206                 string getAccnosFile()          { return accnosfile;            }
 207                 string getTaxonomyFile()        { return taxonomyfile;          }
 208                 string getFlowFile()            { return flowfile;                      }
 209         string getBiomFile()            { return biomfile;                      }
 210         string getCountTableFile()      { return counttablefile;        }
 211         string getSummaryFile()     { return summaryfile;       }
 212                 string getProcessors()          { return processors;            }
 213
 214                 void setListFile(string f)                      { listfile = getFullPathName(f);                        }
 215                 void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
 216                 void setGroupFile(string f)                     { groupfile = getFullPathName(f);       groupMode = "group";            }
 217                 void setPhylipFile(string f)            { phylipfile = getFullPathName(f);                      }
 218                 void setColumnFile(string f)            { columnfile = getFullPathName(f);                      }
 219                 void setNameFile(string f)                      { namefile = getFullPathName(f);                        }
 220                 void setRabundFile(string f)            { rabundfile = getFullPathName(f);                      }
 221                 void setSabundFile(string f)            { sabundfile = getFullPathName(f);                      }
 222                 void setSharedFile(string f)            { sharedfile = getFullPathName(f);                      }
 223                 void setRelAbundFile(string f)          { relabundfile = getFullPathName(f);            }
 224                 void setOrderFile(string f)                     { orderfile = getFullPathName(f);                       }
 225                 void setOrderGroupFile(string f)        { ordergroupfile = getFullPathName(f);          }
 226                 void setDesignFile(string f)            { designfile = getFullPathName(f);                      }
 227                 void setFastaFile(string f)                     { fastafile = getFullPathName(f);                       }
 228                 void setSFFFile(string f)                       { sfffile = getFullPathName(f);                         }
 229                 void setQualFile(string f)                      { qualfile = getFullPathName(f);                        }
 230                 void setOligosFile(string f)            { oligosfile = getFullPathName(f);                      }
 231                 void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
 232                 void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
 233                 void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
 234         void setBiomFile(string f)                      { biomfile = getFullPathName(f);                        }
 235         void setSummaryFile(string f)           { summaryfile = getFullPathName(f);                     }
 236         void setCountTableFile(string f)        { counttablefile = getFullPathName(f);  groupMode = "count";    }
 237         void setProcessors(string p)            { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");       }
 238
 239                 void printCurrentFiles();
 240                 bool hasCurrentFiles();
 241                 void clearCurrentFiles();
 242         set<string> getCurrentTypes();
 243
 244         private:
 245                 static MothurOut* _uniqueInstance;
 246                 MothurOut( const MothurOut& ); // Disable copy constructor
 247                 void operator=( const MothurOut& ); // Disable assignment operator
 248                 MothurOut() {
 249                         control_pressed = false; defaultPath="";
 250                         phylipfile = "";
 251                         columnfile = "";
 252                         listfile = "";
 253                         rabundfile = "";
 254                         sabundfile = "";
 255                         namefile = "";
 256                         groupfile = "";
 257                         designfile = "";
 258                         orderfile = "";
 259                         treefile = "";
 260                         sharedfile = "";
 261                         ordergroupfile = "";
 262                         relabundfile = "";
 263                         fastafile = "";
 264                         qualfile = "";
 265                         sfffile = "";
 266                         oligosfile = "";
 267                         accnosfile = "";
 268                         taxonomyfile = "";
 269                         processors = "1";
 270                         flowfile = "";
 271             biomfile = "";
 272             counttablefile = "";
 273             summaryfile = "";
 274                         gui = false;
 275                         printedSharedHeaders = false;
 276             printedListHeaders = false;
 277                         commandInputsConvertError = false;
 278             mothurCalling = false;
 279             debug = false;
 280                         sharedHeaderMode = "";
 281             groupMode = "group";
 282             changedSeqNames = false;
 283             modifyNames = true;
 284                 }
 285                 ~MothurOut();
 286
 287                 string logFileName;
 288                 string defaultPath, outputDir;
 289                 string releaseDate, version;
 290
 291                 string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
 292                 string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile;
 293
 294                 vector<string> Groups;
 295                 vector<string> namesOfGroups;
 296                 ofstream out;
 297
 298                 int mem_usage(double&, double&);
 299
 300 };
 301 /***********************************************/
 302
 303 #endif
 304