X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=mothurout.h;h=1747b1480c732ae42f361940ff57dcbe151bbc7b;hp=84f9be31f82ebc2c27aa19563fb5366519e1cba8;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=20071b183e619c122bf9f63b4bb42722507c4e4a diff --git a/mothurout.h b/mothurout.h index 84f9be3..1747b14 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(); @@ -65,21 +66,24 @@ class MothurOut { vector getAllGroups() { sort(namesOfGroups.begin(), namesOfGroups.end()); return namesOfGroups; } vector Treenames; - //map names; - vector binLabelsInFile; - vector currentBinLabels; + vector sharedBinLabelsInFile; + vector currentSharedBinLabels; + vector listBinLabelsInFile; string saveNextLabel, argv, sharedHeaderMode, groupMode; - bool printedHeaders, commandInputsConvertError; + bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames; //functions from mothur.h //file operations bool dirCheck(string&); //completes path, appends appropriate / or \, makes sure dir is writable. - vector divideFile(string, int&); + 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 appendBinaryFiles(string, string); + int appendFilesWithoutHeaders(string, string); int renameFile(string, string); //oldname, newname string getFullPathName(string); string findProgramPath(string programName); @@ -90,9 +94,15 @@ 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 + int openInputFileBinary(string, ifstream&); + int openInputFileBinary(string, ifstream&, string); + int openInputFile(string, ifstream&, string); //no error given + + 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 string getline(ifstream&); string getline(istringstream&); void gobble(istream&); @@ -102,7 +112,10 @@ class MothurOut { 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); @@ -130,6 +143,9 @@ class MothurOut { bool isTrue(string); bool isContainingOnlyDigits(string); bool isNumeric1(string); + bool isLabelEquivalent(string, string); + string getSimpleLabel(string); + string findEdianness(); //string manipulation @@ -146,23 +162,33 @@ class MothurOut { string removeQuotes(string); string makeList(vector&); bool isSubset(vector, vector); //bigSet, subset + int checkName(string&); + map > parseClasses(string); //math operation + double max(vector&); //returns largest value in vector + double min(vector&); //returns smallest value in vector int factorial(int num); vector > binomial(int); float ceilDist(float, int); float roundDist(float, int); unsigned int fromBase36(string); + double median(vector); 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, debug; - //current files - if you add a new type you must edit optionParser->getParameters, get.current command and mothurOut->printCurrentFiles/clearCurrentFiles/getCurrentTypes. + //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; } @@ -185,6 +211,7 @@ class MothurOut { 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); } @@ -208,6 +235,7 @@ class MothurOut { void setTaxonomyFile(string f) { taxonomyfile = getFullPathName(f); } void setFlowFile(string f) { flowfile = getFullPathName(f); } 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"); } @@ -245,13 +273,17 @@ class MothurOut { flowfile = ""; biomfile = ""; counttablefile = ""; + summaryfile = ""; gui = false; - printedHeaders = false; + printedSharedHeaders = false; + printedListHeaders = false; commandInputsConvertError = false; mothurCalling = false; debug = false; sharedHeaderMode = ""; groupMode = "group"; + changedSeqNames = false; + modifyNames = true; } ~MothurOut(); @@ -260,7 +292,7 @@ class MothurOut { string releaseDate, version; 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; + string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile; vector Groups; vector namesOfGroups;