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