X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.h;h=3cf6fa4963672b5d69acb7de389eb266b957ba24;hp=e1c8222ae1938e8b63422cc9ee6567d309b668f5;hb=615301e57c25e241356a9c2380648d117709458d;hpb=57b3c96832667c1b70d4d526331f52e3d49e8237 diff --git a/mothurout.h b/mothurout.h index e1c8222..3cf6fa4 100644 --- a/mothurout.h +++ b/mothurout.h @@ -40,6 +40,7 @@ class MothurOut { void mothurOutEndLine(); //writes to cout and the logfile void mothurOut(string, ofstream&); //writes to the ofstream, cout and the logfile void mothurOutEndLine(ofstream&); //writes to the ofstream, cout and the logfile + void mothurOutJustToScreen(string); //writes to cout void mothurOutJustToLog(string); void errorOut(exception&, string, string); void closeLog(); @@ -65,22 +66,26 @@ class MothurOut { vector getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; } vector Treenames; - map names; + //map names; vector binLabelsInFile; vector currentBinLabels; - string saveNextLabel, argv, sharedHeaderMode; - bool printedHeaders, commandInputsConvertError; + string saveNextLabel, argv, sharedHeaderMode, groupMode; + bool printedHeaders, commandInputsConvertError, changedSeqNames, modifyNames; //functions from mothur.h //file operations - vector divideFile(string, int&); + bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable. + vector divideFile(string, int&); //divides splitting unevenness by sequence + vector divideFilePerLine(string, int&); //divides splitting unevenness at line breaks int divideFile(string, int&, vector&); vector setFilePosEachLine(string, int&); vector setFilePosFasta(string, int&); string sortFile(string, string); int appendFiles(string, string); + int appendFilesWithoutHeaders(string, string); int renameFile(string, string); //oldname, newname string getFullPathName(string); + string findProgramPath(string programName); string hasPath(string); string getExtension(string); string getPathName(string); @@ -88,19 +93,33 @@ class MothurOut { string getRootName(string); bool isBlank(string); int openOutputFile(string, ofstream&); + int openOutputFileBinary(string, ofstream&); int openOutputFileAppend(string, ofstream&); + int openOutputFileBinaryAppend(string, ofstream&); int openInputFile(string, ifstream&); int openInputFile(string, ifstream&, string); //no error given string getline(ifstream&); string getline(istringstream&); void gobble(istream&); void gobble(istringstream&); - map readNames(string); + vector splitWhiteSpace(string& rest, char[], int); + vector splitWhiteSpace(string); + set readAccnos(string); + int readAccnos(string, vector&); + map readNames(string); + map readNames(string, unsigned long int&); + int readTax(string, map&); + vector readConsTax(string); + int readConsTax(string, map&); + int readNames(string, map&, map&); int readNames(string, map&); + int readNames(string, map&, bool); + int readNames(string, map&, int); int readNames(string, map >&); int readNames(string, vector&, map&); int mothurRemove(string); bool mothurConvert(string, int&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this. + bool mothurConvert(string, intDist&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this. bool mothurConvert(string, float&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this. bool mothurConvert(string, double&); //use for converting user inputs. Sets commandInputsConvertError to true if error occurs. Engines check this. @@ -109,7 +128,9 @@ class MothurOut { bool checkReleaseVersion(ifstream&, string); bool anyLabelsToProcess(string, set&, string); bool inUsersGroups(vector, vector); + bool inUsersGroups(vector, vector< vector >); bool inUsersGroups(string, vector); + bool inUsersGroups(int, vector); void getNumSeqs(ifstream&, int&); int getNumSeqs(ifstream&); int getNumNames(string); @@ -127,7 +148,14 @@ class MothurOut { void splitAtDash(string&, set&); void splitAtDash(string&, vector&); void splitAtChar(string&, vector&, char); + void splitAtChar(string&, string&, char); + vector splitWhiteSpaceWithQuotes(string); int removeConfidences(string&); + string removeQuotes(string); + string makeList(vector&); + bool isSubset(vector, vector); //bigSet, subset + int checkName(string&); + map > parseClasses(string); //math operation int factorial(int num); @@ -136,11 +164,20 @@ class MothurOut { float roundDist(float, int); unsigned int fromBase36(string); int getRandomIndex(int); //highest + double getStandardDeviation(vector&); + vector getStandardDeviation(vector< vector >&); + vector getStandardDeviation(vector< vector >&, vector&); + vector getAverages(vector< vector >&); + double getAverage(vector); + vector< vector > getStandardDeviation(vector< vector< vector > >&); + vector< vector > getStandardDeviation(vector< vector< vector > >&, vector< vector >&); + vector< vector > getAverages(vector< vector< vector > >&, string); + vector< vector > getAverages(vector< vector< vector > >&); int control_pressed; - bool executing, runParse, jumble, gui, mothurCalling; + bool executing, runParse, jumble, gui, mothurCalling, debug; - //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles. + //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. string getPhylipFile() { return phylipfile; } string getColumnFile() { return columnfile; } string getListFile() { return listfile; } @@ -161,11 +198,14 @@ class MothurOut { string getAccnosFile() { return accnosfile; } string getTaxonomyFile() { return taxonomyfile; } string getFlowFile() { return flowfile; } + string getBiomFile() { return biomfile; } + string getCountTableFile() { return counttablefile; } + string getSummaryFile() { return summaryfile; } string getProcessors() { return processors; } void setListFile(string f) { listfile = getFullPathName(f); } void setTreeFile(string f) { treefile = getFullPathName(f); } - void setGroupFile(string f) { groupfile = getFullPathName(f); } + void setGroupFile(string f) { groupfile = getFullPathName(f); groupMode = "group"; } void setPhylipFile(string f) { phylipfile = getFullPathName(f); } void setColumnFile(string f) { columnfile = getFullPathName(f); } void setNameFile(string f) { namefile = getFullPathName(f); } @@ -183,11 +223,15 @@ class MothurOut { void setAccnosFile(string f) { accnosfile = getFullPathName(f); } void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); } void setFlowFile(string f) { flowfile = getFullPathName(f); } - void setProcessors(string p) { processors = p; } + void setBiomFile(string f) { biomfile = getFullPathName(f); } + void setSummaryFile(string f) { summaryfile = getFullPathName(f); } + void setCountTableFile(string f) { counttablefile = getFullPathName(f); groupMode = "count"; } + void setProcessors(string p) { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n"); } void printCurrentFiles(); bool hasCurrentFiles(); void clearCurrentFiles(); + set getCurrentTypes(); private: static MothurOut* _uniqueInstance; @@ -216,11 +260,18 @@ class MothurOut { taxonomyfile = ""; processors = "1"; flowfile = ""; + biomfile = ""; + counttablefile = ""; + summaryfile = ""; gui = false; printedHeaders = false; commandInputsConvertError = false; mothurCalling = false; + debug = false; sharedHeaderMode = ""; + groupMode = "group"; + changedSeqNames = false; + modifyNames = true; } ~MothurOut(); @@ -228,8 +279,8 @@ class MothurOut { string defaultPath, outputDir; string releaseDate, version; - string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile; - string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile; + string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile; + string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile; vector Groups; vector namesOfGroups;