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