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 debugOut(string); //writes to cout and the logfile if debugging is on
  41                 void mothurOutEndLine(); //writes to cout and the logfile
  42                 void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile
  43                 void debugOut(string, ofstream&); //writes to the ofstream, cout and the logfile if debugging is on
  44                 void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile
  45         void mothurOutJustToScreen(string); //writes to cout
  46                 void mothurOutJustToLog(string);
  47                 void errorOut(exception&, string, string);
  48                 void closeLog();
  49                 string getDefaultPath() { return defaultPath; }
  50                 void setDefaultPath(string);
  51                 string getOutputDir() { return outputDir; }
  52                 void setOutputDir(string);
  53
  54                 string getReleaseDate() { return releaseDate; }
  55                 void setReleaseDate(string r) { releaseDate = r; }
  56                 string getVersion() { return version; }
  57                 void setVersion(string r) { version = r; }
  58
  59                 void addGroup(string g) { Groups.push_back(g); }
  60                 void setGroups(vector<string>& g) { sort(g.begin(), g.end()); Groups = g; }
  61                 void clearGroups() { Groups.clear(); }
  62             int getNumGroups() { return Groups.size(); }
  63                 vector<string> getGroups() { sort(Groups.begin(), Groups.end()); return Groups; }
  64                 void addAllGroup(string g) { namesOfGroups.push_back(g); }
  65                 void setAllGroups(vector<string>& g) { sort(g.begin(), g.end()); namesOfGroups = g; }
  66                 void clearAllGroups() { namesOfGroups.clear(); }
  67                 int getNumAllGroups() { return namesOfGroups.size(); }
  68
  69                 vector<string> getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; }
  70                 vector<string> Treenames;
  71                 vector<string> sharedBinLabelsInFile;
  72                 vector<string> currentSharedBinLabels;
  73         vector<string> listBinLabelsInFile;
  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 appendBinaryFiles(string, string);
  88         int appendFilesWithoutHeaders(string, string);
  89                 int renameFile(string, string); //oldname, newname
  90                 string getFullPathName(string);
  91         string findProgramPath(string programName);
  92                 string hasPath(string);
  93                 string getExtension(string);
  94                 string getPathName(string);
  95                 string getSimpleName(string);
  96                 string getRootName(string);
  97                 bool isBlank(string);
  98                 int openOutputFile(string, ofstream&);
  99         int openOutputFileBinary(string, ofstream&);
 100                 int openOutputFileAppend(string, ofstream&);
 101         int openOutputFileBinaryAppend(string, ofstream&);
 102                 int openInputFile(string, ifstream&);
 103         int openInputFileBinary(string, ifstream&);
 104         int openInputFileBinary(string, ifstream&, string);
 105                 int openInputFile(string, ifstream&, string); //no error given
 106
 107         bool checkLocations(string&, string);  //filename, inputDir. checks for file in ./, inputdir, default and mothur's exe location.  Returns false if cant be found. If found completes name with location
 108                 string getline(ifstream&);
 109                 string getline(istringstream&);
 110                 void gobble(istream&);
 111                 void gobble(istringstream&);
 112         vector<string> splitWhiteSpace(string& rest, char[], int);
 113         vector<string> splitWhiteSpace(string);
 114         set<string> readAccnos(string);
 115         int readAccnos(string, vector<string>&);
 116         map<string, int> readNames(string);
 117         map<string, int> readNames(string, unsigned long int&);
 118         int readTax(string, map<string, string>&);
 119         vector<consTax> readConsTax(string);
 120         int readConsTax(string, map<string, consTax2>&);
 121         int readNames(string, map<string, string>&, map<string, int>&);
 122                 int readNames(string, map<string, string>&);
 123         int readNames(string, map<string, string>&, bool);
 124         int readNames(string, map<string, string>&, int);
 125                 int readNames(string, map<string, vector<string> >&);
 126                 int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
 127                 int mothurRemove(string);
 128                 bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 129         bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 130                 bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 131                 bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this.
 132
 133
 134                 //searchs and checks
 135                 bool checkReleaseVersion(ifstream&, string);
 136                 bool anyLabelsToProcess(string, set<string>&, string);
 137                 bool inUsersGroups(vector<string>, vector<string>);
 138         bool inUsersGroups(vector<int>, vector< vector<int> >);
 139                 bool inUsersGroups(string, vector<string>);
 140         bool inUsersGroups(int, vector<int>);
 141                 void getNumSeqs(ifstream&, int&);
 142                 int getNumSeqs(ifstream&);
 143                 int getNumNames(string);
 144                 int getNumChar(string, char);
 145                 bool isTrue(string);
 146                 bool isContainingOnlyDigits(string);
 147                 bool isNumeric1(string);
 148         bool isLabelEquivalent(string, string);
 149         string getSimpleLabel(string);
 150         string findEdianness();
 151
 152
 153                 //string manipulation
 154                 void splitAtEquals(string&, string&);
 155                 void splitAtComma(string&, string&);
 156                 void splitAtComma(string&, vector<string>&);
 157                 void splitAtDash(string&, set<int>&);
 158                 void splitAtDash(string&, set<string>&);
 159                 void splitAtDash(string&, vector<string>&);
 160                 void splitAtChar(string&, vector<string>&, char);
 161         void splitAtChar(string&, string&, char);
 162         vector<string> splitWhiteSpaceWithQuotes(string);
 163                 int removeConfidences(string&);
 164         string removeQuotes(string);
 165         string makeList(vector<string>&);
 166         bool isSubset(vector<string>, vector<string>); //bigSet, subset
 167         int checkName(string&);
 168         map<string, vector<string> > parseClasses(string);
 169
 170                 //math operation
 171         double max(vector<double>&); //returns largest value in vector
 172         double min(vector<double>&); //returns smallest value in vector
 173                 int factorial(int num);
 174                 vector<vector<double> > binomial(int);
 175                 float ceilDist(float, int);
 176                 float roundDist(float, int);
 177                 unsigned int fromBase36(string);
 178         double median(vector<double>);
 179                 int getRandomIndex(int); //highest
 180         double getStandardDeviation(vector<int>&);
 181         vector<double> getStandardDeviation(vector< vector<double> >&);
 182         vector<double> getStandardDeviation(vector< vector<double> >&, vector<double>&);
 183         vector<double> getAverages(vector< vector<double> >&);
 184         double getAverage(vector<double>);
 185         vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&);
 186         vector< vector<seqDist> > getStandardDeviation(vector< vector< vector<seqDist> > >&, vector< vector<seqDist> >&);
 187         vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&, string);
 188         vector< vector<seqDist> > getAverages(vector< vector< vector<seqDist> > >&);
 189
 190                 int control_pressed;
 191                 bool executing, runParse, jumble, gui, mothurCalling, debug;
 192
 193                 //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.
 194                 string getPhylipFile()          { return phylipfile;            }
 195                 string getColumnFile()          { return columnfile;            }
 196                 string getListFile()            { return listfile;                      }
 197                 string getRabundFile()          { return rabundfile;            }
 198                 string getSabundFile()          { return sabundfile;            }
 199                 string getNameFile()            { return namefile;                      }
 200                 string getGroupFile()           { return groupfile;                     }
 201                 string getOrderFile()           { return orderfile;                     }
 202                 string getOrderGroupFile()      { return ordergroupfile;        }
 203                 string getTreeFile()            { return treefile;                      }
 204                 string getSharedFile()          { return sharedfile;            }
 205                 string getRelAbundFile()        { return relabundfile;          }
 206                 string getDesignFile()          { return designfile;            }
 207                 string getFastaFile()           { return fastafile;                     }
 208                 string getSFFFile()                     { return sfffile;                       }
 209                 string getQualFile()            { return qualfile;                      }
 210                 string getOligosFile()          { return oligosfile;            }
 211                 string getAccnosFile()          { return accnosfile;            }
 212                 string getTaxonomyFile()        { return taxonomyfile;          }
 213                 string getFlowFile()            { return flowfile;                      }
 214         string getBiomFile()            { return biomfile;                      }
 215         string getCountTableFile()      { return counttablefile;        }
 216         string getSummaryFile()     { return summaryfile;       }
 217                 string getProcessors()          { return processors;            }
 218
 219                 void setListFile(string f)                      { listfile = getFullPathName(f);                        }
 220                 void setTreeFile(string f)                      { treefile = getFullPathName(f);                        }
 221                 void setGroupFile(string f)                     { groupfile = getFullPathName(f);       groupMode = "group";            }
 222                 void setPhylipFile(string f)            { phylipfile = getFullPathName(f);                      }
 223                 void setColumnFile(string f)            { columnfile = getFullPathName(f);                      }
 224                 void setNameFile(string f)                      { namefile = getFullPathName(f);                        }
 225                 void setRabundFile(string f)            { rabundfile = getFullPathName(f);                      }
 226                 void setSabundFile(string f)            { sabundfile = getFullPathName(f);                      }
 227                 void setSharedFile(string f)            { sharedfile = getFullPathName(f);                      }
 228                 void setRelAbundFile(string f)          { relabundfile = getFullPathName(f);            }
 229                 void setOrderFile(string f)                     { orderfile = getFullPathName(f);                       }
 230                 void setOrderGroupFile(string f)        { ordergroupfile = getFullPathName(f);          }
 231                 void setDesignFile(string f)            { designfile = getFullPathName(f);                      }
 232                 void setFastaFile(string f)                     { fastafile = getFullPathName(f);                       }
 233                 void setSFFFile(string f)                       { sfffile = getFullPathName(f);                         }
 234                 void setQualFile(string f)                      { qualfile = getFullPathName(f);                        }
 235                 void setOligosFile(string f)            { oligosfile = getFullPathName(f);                      }
 236                 void setAccnosFile(string f)            { accnosfile = getFullPathName(f);                      }
 237                 void setTaxonomyFile(string f)          { taxonomyfile = getFullPathName(f);            }
 238                 void setFlowFile(string f)                      { flowfile = getFullPathName(f);                        }
 239         void setBiomFile(string f)                      { biomfile = getFullPathName(f);                        }
 240         void setSummaryFile(string f)           { summaryfile = getFullPathName(f);                     }
 241         void setCountTableFile(string f)        { counttablefile = getFullPathName(f);  groupMode = "count";    }
 242         void setProcessors(string p)            { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n");       }
 243
 244                 void printCurrentFiles();
 245                 bool hasCurrentFiles();
 246                 void clearCurrentFiles();
 247         set<string> getCurrentTypes();
 248
 249         private:
 250                 static MothurOut* _uniqueInstance;
 251                 MothurOut( const MothurOut& ); // Disable copy constructor
 252                 void operator=( const MothurOut& ); // Disable assignment operator
 253                 MothurOut() {
 254                         control_pressed = false; defaultPath="";
 255                         phylipfile = "";
 256                         columnfile = "";
 257                         listfile = "";
 258                         rabundfile = "";
 259                         sabundfile = "";
 260                         namefile = "";
 261                         groupfile = "";
 262                         designfile = "";
 263                         orderfile = "";
 264                         treefile = "";
 265                         sharedfile = "";
 266                         ordergroupfile = "";
 267                         relabundfile = "";
 268                         fastafile = "";
 269                         qualfile = "";
 270                         sfffile = "";
 271                         oligosfile = "";
 272                         accnosfile = "";
 273                         taxonomyfile = "";
 274                         processors = "1";
 275                         flowfile = "";
 276             biomfile = "";
 277             counttablefile = "";
 278             summaryfile = "";
 279                         gui = false;
 280                         printedSharedHeaders = false;
 281             printedListHeaders = false;
 282                         commandInputsConvertError = false;
 283             mothurCalling = false;
 284             debug = false;
 285                         sharedHeaderMode = "";
 286             groupMode = "group";
 287             changedSeqNames = false;
 288             modifyNames = true;
 289                 }
 290                 ~MothurOut();
 291
 292                 string logFileName;
 293                 string defaultPath, outputDir;
 294                 string releaseDate, version;
 295
 296                 string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile;
 297                 string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile;
 298
 299                 vector<string> Groups;
 300                 vector<string> namesOfGroups;
 301                 ofstream out;
 302
 303                 int mem_usage(double&, double&);
 304
 305 };
 306 /***********************************************/
 307
 308 #endif
 309