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A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */,
A7E9B85812D37EC400DA6239 /* summarycommand.h */,
A7E9B85712D37EC400DA6239 /* summarycommand.cpp */,
+ A754149514840CF7005850D1 /* summaryqualcommand.h */,
+ A754149614840CF7005850D1 /* summaryqualcommand.cpp */,
A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */,
A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */,
A7FFB556142CA02C004884F2 /* summarytaxcommand.h */,
A774101414695AF60098E6AC /* shhhseqscommand.cpp in Sources */,
A774104814696F320098E6AC /* myseqdist.cpp in Sources */,
A77410F614697C300098E6AC /* seqnoise.cpp in Sources */,
+ A754149714840CF7005850D1 /* summaryqualcommand.cpp in Sources */,
);
runOnlyForDeploymentPostprocessing = 0;
};
#include "summarytaxcommand.h"
#include "chimeraperseuscommand.h"
#include "shhhseqscommand.h"
+#include "summaryqualcommand.h"
/*******************************************************/
commands["sens.spec"] = "sens.spec";
commands["seq.error"] = "seq.error";
commands["summary.tax"] = "summary.tax";
+ commands["summary.qual"] = "summary.qual";
commands["shhh.seqs"] = "shhh.seqs";
-
commands["quit"] = "MPIEnabled";
}
else if(commandName == "count.groups") { command = new CountGroupsCommand(optionString); }
else if(commandName == "clear.memory") { command = new ClearMemoryCommand(optionString); }
else if(commandName == "summary.tax") { command = new SummaryTaxCommand(optionString); }
+ else if(commandName == "summary.qual") { command = new SummaryQualCommand(optionString); }
else if(commandName == "chimera.perseus") { command = new ChimeraPerseusCommand(optionString); }
else if(commandName == "shhh.seqs") { command = new ShhhSeqsCommand(optionString); }
else { command = new NoCommand(optionString); }
else if(commandName == "count.groups") { pipecommand = new CountGroupsCommand(optionString); }
else if(commandName == "clear.memory") { pipecommand = new ClearMemoryCommand(optionString); }
else if(commandName == "summary.tax") { pipecommand = new SummaryTaxCommand(optionString); }
+ else if(commandName == "summary.qual") { pipecommand = new SummaryQualCommand(optionString); }
else if(commandName == "chimera.perseus") { pipecommand = new ChimeraPerseusCommand(optionString); }
else if(commandName == "shhh.seqs") { pipecommand = new ShhhSeqsCommand(optionString); }
else { pipecommand = new NoCommand(optionString); }
else if(commandName == "count.groups") { shellcommand = new CountGroupsCommand(); }
else if(commandName == "clear.memory") { shellcommand = new ClearMemoryCommand(); }
else if(commandName == "summary.tax") { shellcommand = new SummaryTaxCommand(); }
+ else if(commandName == "summary.qual") { shellcommand = new SummaryQualCommand(); }
else if(commandName == "chimera.perseus") { shellcommand = new ChimeraPerseusCommand(); }
else if(commandName == "shhh.seqs") { shellcommand = new ShhhSeqsCommand(); }
else { shellcommand = new NoCommand(); }
//custom data structure for threads to use.
// This is passed by void pointer so it can be any data type
// that can be passed using a single void pointer (LPVOID).
-typedef struct seqSumData {
+struct seqSumData {
vector<int>* startPosition;
vector<int>* endPosition;
vector<int>* seqLength;
--- /dev/null
+/*
+ * summaryqualcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 11/28/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "summaryqualcommand.h"
+
+
+//**********************************************************************************************************************
+vector<string> SummaryQualCommand::setParameters(){
+ try {
+ CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqual);
+ CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string SummaryQualCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The summary.qual command reads a quality file and an optional name file, and summarizes the quality information.\n";
+ helpString += "The summary.tax command parameters are qfile, name and processors. qfile is required, unless you have a valid current quality file.\n";
+ helpString += "The name parameter allows you to enter a name file associated with your quality file. \n";
+ helpString += "The summary.qual command should be in the following format: \n";
+ helpString += "summary.qual(qfile=yourQualityFile) \n";
+ helpString += "Note: No spaces between parameter labels (i.e. qfile), '=' and parameters (i.e.yourQualityFile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+SummaryQualCommand::SummaryQualCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "SummaryQualCommand");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+
+SummaryQualCommand::SummaryQualCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ vector<string> myArray = setParameters();
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string,string>::iterator it;
+
+ //check to make sure all parameters are valid for command
+ for (it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //if the user changes the input directory command factory will send this info to us in the output parameter
+ string inputDir = validParameter.validFile(parameters, "inputdir", false);
+ if (inputDir == "not found"){ inputDir = ""; }
+ else {
+ string path;
+ it = parameters.find("qfile");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["qfile"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["name"] = inputDir + it->second; }
+ }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+
+ //check for required parameters
+ qualfile = validParameter.validFile(parameters, "qfile", true);
+ if (qualfile == "not open") { abort = true; }
+ else if (qualfile == "not found") {
+ qualfile = m->getQualFile();
+ if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current quality file and the qfile parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setQualFile(qualfile); }
+
+ namefile = validParameter.validFile(parameters, "name", true);
+ if (namefile == "not open") { namefile = ""; abort = true; }
+ else if (namefile == "not found") { namefile = ""; }
+ else { m->setNameFile(namefile); }
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(qualfile); //if user entered a file with a path then preserve it
+ }
+
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ convert(temp, processors);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "SummaryQualCommand");
+ exit(1);
+ }
+}
+//***************************************************************************************************************
+int SummaryQualCommand::execute(){
+ try{
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ int start = time(NULL);
+ int numSeqs = 0;
+
+ vector<int> position;
+ vector<int> averageQ;
+ vector< vector<int> > scores;
+
+ if (m->control_pressed) { return 0; }
+
+ if (namefile != "") { nameMap = m->readNames(namefile); }
+
+ vector<unsigned long long> positions;
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ positions = m->divideFile(qualfile, processors);
+ for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
+#else
+ if (processors == 1) {
+ lines.push_back(linePair(0, 1000));
+ }else {
+ positions = m->setFilePosFasta(qualfile, numSeqs);
+
+ //figure out how many sequences you have to process
+ int numSeqsPerProcessor = numSeqs / processors;
+ for (int i = 0; i < processors; i++) {
+ int startIndex = i * numSeqsPerProcessor;
+ if(i == (processors - 1)){ numSeqsPerProcessor = numSeqs - i * numSeqsPerProcessor; }
+ lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
+ }
+ }
+#endif
+
+
+ if(processors == 1){ numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[0]); }
+ else{ numSeqs = createProcessesCreateSummary(position, averageQ, scores, qualfile); }
+
+ if (m->control_pressed) { return 0; }
+
+ //print summary file
+ string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "qual.summary";
+ printQual(summaryFile, position, averageQ, scores);
+
+ if (m->control_pressed) { m->mothurRemove(summaryFile); return 0; }
+
+ //output results to screen
+ cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+ m->mothurOutEndLine();
+ m->mothurOut("Position\tNumSeqs\tAverageQ"); m->mothurOutEndLine();
+ for (int i = 0; i < position.size(); i+=100) {
+ float average = averageQ[i] / (float) position[i];
+ cout << i << '\t' << position[i] << '\t' << average;
+ m->mothurOutJustToLog(toString(i) + "\t" + toString(position[i]) + "\t" + toString(average)); m->mothurOutEndLine();
+ }
+
+ m->mothurOutEndLine();
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to create the summary file for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(summaryFile); m->mothurOutEndLine(); outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
+ m->mothurOutEndLine();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "execute");
+ exit(1);
+ }
+}
+/**************************************************************************************/
+int SummaryQualCommand::driverCreateSummary(vector<int>& position, vector<int>& averageQ, vector< vector<int> >& scores, string filename, linePair filePos) {
+ try {
+ ifstream in;
+ m->openInputFile(filename, in);
+
+ in.seekg(filePos.start);
+
+ bool done = false;
+ int count = 0;
+
+ while (!done) {
+
+ if (m->control_pressed) { in.close(); return 1; }
+
+ QualityScores current(in); m->gobble(in);
+
+ if (current.getName() != "") {
+
+ int num = 1;
+ if (namefile != "") {
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = nameMap.find(current.getName());
+
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ vector<int> thisScores = current.getQualityScores();
+
+ //resize to num of positions setting number of seqs with that size to 1
+ if (position.size() < thisScores.size()) { position.resize(thisScores.size(), 0); }
+ if (averageQ.size() < thisScores.size()) { averageQ.resize(thisScores.size(), 0); }
+ if (scores.size() < thisScores.size()) {
+ scores.resize(thisScores.size());
+ for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
+ }
+
+ //increase counts of number of seqs with this position
+ //average is really the total, we will average in execute
+ for (int i = 0; i < thisScores.size(); i++) {
+ position[i] += num;
+ averageQ[i] += (thisScores[i] * num); //weighting for namesfile
+ if (thisScores[i] > 40) { m->mothurOut("[ERROR]: " + current.getName() + " has a quality scores of " + toString(thisScores[i]) + ", expecting values to be less than 40."); m->mothurOutEndLine(); m->control_pressed = true; }
+ else { scores[i][thisScores[i]] += num; }
+ }
+
+ count += num;
+ }
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ unsigned long long pos = in.tellg();
+ if ((pos == -1) || (pos >= filePos.end)) { break; }
+#else
+ if (in.eof()) { break; }
+#endif
+ }
+
+ in.close();
+
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "driverCreateSummary");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vector<int>& averageQ, vector< vector<int> >& scores, string filename) {
+ try {
+ int process = 1;
+ int numSeqs = 0;
+ processIDS.clear();
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[process]);
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = qualfile + toString(getpid()) + ".num.temp";
+ m->openOutputFile(tempFile, out);
+
+ out << numSeqs << endl;
+ out << position.size() << endl;
+ for (int k = 0; k < position.size(); k++) { out << position[k] << '\t'; } out << endl;
+ for (int k = 0; k < averageQ.size(); k++) { out << averageQ[k] << '\t'; } out << endl;
+ for (int k = 0; k < scores.size(); k++) {
+ for (int j = 0; j < 41; j++) {
+ out << scores[k][j] << '\t';
+ }
+ out << endl;
+ }
+ out << endl;
+
+ out.close();
+
+ exit(0);
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
+ }
+
+ //do your part
+ numSeqs = driverCreateSummary(position, averageQ, scores, qualfile, lines[0]);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //parent reads in and combine Filter info
+ for (int i = 0; i < processIDS.size(); i++) {
+ string tempFilename = qualfile + toString(processIDS[i]) + ".num.temp";
+ ifstream in;
+ m->openInputFile(tempFilename, in);
+
+ int temp, tempNum;
+ in >> tempNum; m->gobble(in); numSeqs += tempNum;
+ in >> tempNum; m->gobble(in);
+
+ if (position.size() < tempNum) { position.resize(tempNum, 0); }
+ if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }
+ if (scores.size() < tempNum) {
+ scores.resize(tempNum);
+ for (int i = 0; i < scores.size(); i++) { scores[i].resize(41, 0); }
+ }
+
+ for (int k = 0; k < tempNum; k++) { in >> temp; position[k] += temp; } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) { in >> temp; averageQ[k] += temp; } m->gobble(in);
+ for (int k = 0; k < tempNum; k++) {
+ for (int j = 0; j < 41; j++) {
+ in >> temp; scores[k][j] += temp;
+ m->gobble(in);
+ }
+ }
+
+ in.close();
+ m->mothurRemove(tempFilename);
+ }
+
+#else
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+ //Windows version shared memory, so be careful when passing variables through the seqSumQualData struct.
+ //Above fork() will clone, so memory is separate, but that's not the case with windows,
+ //Taking advantage of shared memory to allow both threads to add info to vectors.
+ //////////////////////////////////////////////////////////////////////////////////////////////////////
+
+ vector<seqSumQualData*> pDataArray;
+ DWORD dwThreadIdArray[processors];
+ HANDLE hThreadArray[processors];
+
+ //Create processor worker threads.
+ for( int i=0; i<processors; i++ ){
+
+ // Allocate memory for thread data.
+ seqSumQualData* tempSum = new seqSumQualData(&position, &averageQ, &scores, filename, m, lines[i].start, lines[i].end, namefile, nameMap);
+ pDataArray.push_back(tempSum);
+ processIDS.push_back(i);
+
+ //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
+ //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
+ hThreadArray[i] = CreateThread(NULL, 0, MySeqSumQualThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
+ }
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ numSeqs += pDataArray[i]->count;
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
+#endif
+ return numSeqs;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "createProcessesCreateSummary");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+int SummaryQualCommand::printQual(string sumFile, vector<int>& position, vector<int>& averageQ, vector< vector<int> >& scores) {
+ try {
+ ofstream out;
+ m->openOutputFile(sumFile, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ outputNames.push_back(sumFile); outputTypes["summary"].push_back(sumFile);
+
+ //print headings
+ out << "Position\tnumSeqs\tAverageQ\t";
+ for (int i = 0; i < 41; i++) { out << "q" << i << '\t'; }
+ out << endl;
+
+ for (int i = 0; i < position.size(); i++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ float average = averageQ[i] / (float) position[i];
+ out << i << '\t' << position[i] << '\t' << average << '\t';
+
+ for (int j = 0; j < 41; j++) {
+ out << scores[i][j] << '\t';
+ }
+ out << endl;
+ }
+
+ out.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryQualCommand", "printQual");
+ exit(1);
+ }
+}
+
+/**************************************************************************************/
+
+
--- /dev/null
+#ifndef SUMMARYQUALCOMMAND_H
+#define SUMMARYQUALCOMMAND_H
+
+/*
+ * summaryqualcommand.h
+ * Mothur
+ *
+ * Created by westcott on 11/28/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "qualityscores.h"
+
+/**************************************************************************************************/
+
+class SummaryQualCommand : public Command {
+public:
+ SummaryQualCommand(string);
+ SummaryQualCommand();
+ ~SummaryQualCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "summary.qual"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
+ string getDescription() { return "summarize the quality of a set of sequences"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+ bool abort;
+ string qualfile, outputDir, namefile;
+ vector<string> outputNames;
+ map<string, int> nameMap;
+ int processors;
+
+ struct linePair {
+ unsigned long long start;
+ unsigned long long end;
+ linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+ };
+
+ vector<linePair> lines;
+ vector<int> processIDS;
+
+ int createProcessesCreateSummary(vector<int>&, vector<int>&, vector< vector<int> >&, string);
+ int driverCreateSummary(vector<int>&, vector<int>&, vector< vector<int> >&, string, linePair);
+ int printQual(string, vector<int>&, vector<int>&, vector< vector<int> >&);
+};
+
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+struct seqSumQualData {
+ vector<int>* position;
+ vector<int>* averageQ;
+ vector< vector<int> >* scores;
+ string filename, namefile;
+ unsigned long long start;
+ unsigned long long end;
+ int count;
+ MothurOut* m;
+ map<string, int> nameMap;
+
+ ~seqSumQualData(){}
+ seqSumQualData(vector<int>* p, vector<int>* a, vector< vector<int> >* s, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
+ position = p;
+ averageQ = a;
+ scores = s;
+ filename = f;
+ m = mout;
+ start = st;
+ end = en;
+ namefile = n;
+ nameMap = nam;
+ count = 0;
+ }
+};
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
+ seqSumQualData* pDataArray;
+ pDataArray = (seqSumQualData*)lpParam;
+
+ try {
+ ifstream in;
+ pDataArray->m->openInputFile(pDataArray->filename, in);
+
+ //print header if you are process 0
+ if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+ in.seekg(0);
+ }else { //this accounts for the difference in line endings.
+ in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+ }
+
+ int count = 0;
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
+
+ QualityScores current(in); pDataArray->m->gobble(in);
+
+ if (current.getName() != "") {
+
+ int num = 1;
+ if (pDataArray->namefile != "") {
+ //make sure this sequence is in the namefile, else error
+ map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
+
+ if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+ else { num = it->second; }
+ }
+
+ vector<int> thisScores = current.getQualityScores();
+
+ //resize to num of positions setting number of seqs with that size to 1
+ if (pDataArray->position->size() < thisScores.size()) { pDataArray->position->resize(thisScores.size(), 0); }
+ if (pDataArray->averageQ->size() < thisScores.size()) { pDataArray->averageQ->resize(thisScores.size(), 0); }
+ if (pDataArray->scores->size() < thisScores.size()) {
+ pDataArray->scores->resize(thisScores.size());
+ for (int i = 0; i < pDataArray->scores->size(); i++) { pDataArray->scores->at(i).resize(41, 0); }
+ }
+
+ //increase counts of number of seqs with this position
+ //average is really the total, we will average in execute
+ for (int i = 0; i < thisScores.size(); i++) {
+ pDataArray->position->at(i) += num;
+ pDataArray->averageQ->at(i) += (thisScores[i] * num); //weighting for namesfile
+ if (thisScores[i] > 40) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " has a quality scores of " + toString(thisScores[i]) + ", expecting values to be less than 40."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+ else { pDataArray->scores->at(i)[thisScores[i]] += num; }
+ }
+
+ count += num;
+ }
+ }
+
+ pDataArray->count = count;
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "SummaryQualCommand", "MySeqSumQualThreadFunction");
+ exit(1);
+ }
+}
+#endif
+
+
+/**************************************************************************************************/
+
+
+#endif
+
//**********************************************************************************************************************
-Venn::Venn(string o, bool n, string f) : outputDir(o), nseqs(n), inputfile(f) {
+Venn::Venn(string o, bool n, string f, int fs) : outputDir(o), nseqs(n), inputfile(f), fontSize(fs) {
try {
m = MothurOut::getInstance();
}
outsvg << "<g>\n";
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"" + toString(int(0.50 * width)) + "\" cy=\"" + toString(int(0.29 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString((width / 2) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(data[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString((width / 2) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(data[0]) + "</text>\n";
if (data.size() == 3) {
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.60 * height)) + "\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.645 * height)) + "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.60 * height)) + "\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.645 * height)) + "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
}
if (nseqs) {
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.70 * height)) + "\">The number of sequences represented is " + toString(sabund->getNumSeqs()) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.70 * height)) + "\">The number of sequences represented is " + toString(sabund->getNumSeqs()) + "</text>\n";
}
outsvg << "</g>\n</svg>\n";
outsvg << "<g>\n";
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"" + toString(int(0.50 * width)) + "\" cy=\"" + toString(int(0.29 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.50 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.24 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.50 * width) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(data[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.50 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.24 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.50 * width) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(data[0]) + "</text>\n";
if (data.size() == 3) {
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.60 * height)) + "\" >The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.645 * height)) + "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.60 * height)) + "\" >The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.645 * height)) + "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
}
if (nseqs) {
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.70 * height)) + "\">The number of sequences represented is " + toString(sabund->getNumSeqs()) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.35 * width)) + "\" y=\"" + toString(int(0.70 * height)) + "\">The number of sequences represented is " + toString(sabund->getNumSeqs()) + "</text>\n";
}
outsvg << "</g>\n</svg>\n";
//draw circles
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.36 * width)) + "\" cy=\"" + toString(int(0.29 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.62 * width)) + "\" cy=\"" + toString(int(0.29 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numA[0] - shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numB[0] - shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.25 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.25 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(shared[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.66 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numA[0] - shared[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(numB[0] - shared[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.25 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.25 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(shared[0]).length() / 2)) + "\" y=\"" + toString(int(0.28 * height)) + "\">" + toString(shared[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.66 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
if (numA.size() == 3) {
outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]);
}
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA) + "; " + toString(uniqSeqsToA) + " sequences are not shared"; }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.69 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.69 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
if (numB.size() == 3) {
outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]);
}
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB) + "; " + toString(uniqSeqsToB) + " sequences are not shared"; }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.72 * height)) + "\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.72 * height)) + "\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedVal) + "; " + toString((sharedVal / (float)(numSeqsA + numSeqsB))*100) + "% of these sequences are shared"; }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))*100) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))*100) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.78 * height)) + "\">The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0]))+ "</text>\n";;
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.78 * height)) + "\">The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0]))+ "</text>\n";;
//close file
//draw circles
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.44 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.44 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.33 * width)) + "\" cy=\"" + toString(int(0.25 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.65 * width)) + "\" cy=\"" + toString(int(0.25 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.5 * width)) + "\" cy=\"" + toString(int(0.5 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
//place labels within overlaps
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.33 * width) - ((int)toString(numA[0]-sharedAwithBC[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numA[0]-sharedAwithBC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.33 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]-sharedBwithAC[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numB[0]-sharedBwithAC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedCwithAB[0]).length() / 2)) + "\" y=\"" + toString(int(0.54 * height)) + "\">" + toString(numC[0]-sharedCwithAB[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.52 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.58 * width) - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.34 * height)) + "\">" + toString(sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.33 * width) - ((int)toString(numA[0]-sharedAwithBC[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numA[0]-sharedAwithBC[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.33 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]-sharedBwithAC[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numB[0]-sharedBwithAC[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedCwithAB[0]).length() / 2)) + "\" y=\"" + toString(int(0.54 * height)) + "\">" + toString(numC[0]-sharedCwithAB[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.52 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.58 * width) - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.34 * height)) + "\">" + toString(sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedABVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedACVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedBCVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and combined groups " + lookup[1]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedAwithBC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.925 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedBwithAC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.95 * height)) + "\">The number of species shared between groups " + lookup[2]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[1]->getGroup() + " is " + toString(sharedCwithAB[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and combined groups " + lookup[1]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedAwithBC[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.925 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedBwithAC[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.95 * height)) + "\">The number of species shared between groups " + lookup[2]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[1]->getGroup() + " is " + toString(sharedCwithAB[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
if (numA.size() == 3) {
outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]);
}
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA) + "; " + toString(uniqSeqsToA) + " sequences are not shared"; }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
if (numB.size() == 3) {
outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]);
}
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB) + "; " + toString(uniqSeqsToB) + " sequences are not shared"; }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
if (numC.size() == 3) {
outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]);
}
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsC) + "; " + toString(uniqSeqsToC) + " sequences are not shared"; }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.80 * height)) + "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.975 * height)) + "\">The total shared richness is " + toString(sharedABC);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.80 * height)) + "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.975 * height)) + "\">The total shared richness is " + toString(sharedABC);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedVal); }
outsvg << "</text>\n";
//draw circles
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(height) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.33 * width)) + "\" cy=\"" + toString(int(0.25 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.65 * width)) + "\" cy=\"" + toString(int(0.25 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"" + toString(int(0.5 * width)) + "\" cy=\"" + toString(int(0.5 * height)) + "\" r=\"" + toString(int(0.22 * width)) + "\"/>";
//place labels within overlaps
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedab[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(sharedab[0] - sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.68 * width) - ((int)toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.68 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedac[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedac[0] - sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.54 * height)) + "\">" + toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.51 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.59 * width) - ((int)toString(sharedbc[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedbc[0] - sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.35 * height)) + "\">" + toString(sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedab[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(sharedab[0] - sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.68 * width) - ((int)toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.22 * height)) + "\">" + toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.68 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.19 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedac[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedac[0] - sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.54 * height)) + "\">" + toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.51 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.59 * width) - ((int)toString(sharedbc[0] - sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.38 * height)) + "\">" + toString(sharedbc[0] - sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedabc[0]).length() / 2)) + "\" y=\"" + toString(int(0.35 * height)) + "\">" + toString(sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedABVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedACVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedBCVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
if (numA.size() == 3) {
outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]);
}
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
if (numB.size() == 3) {
outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]);
}
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
if (numC.size() == 3) {
outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]);
}
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsC); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.8 * height)) + "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedab[0] - sharedac[0] - sharedbc[0] + sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The total shared richness is " + toString(sharedabc[0]);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.8 * height)) + "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedab[0] - sharedac[0] - sharedbc[0] + sharedabc[0]) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The total shared richness is " + toString(sharedabc[0]);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedVal); }
outsvg << "</text>\n";
outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(width) + " " + toString(windowSize) + " \" >\n";
outsvg << "<g>\n";
outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(width) + "\" height=\"" + toString(windowSize) + "\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\" >Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.40 * width)) + "\" y=\"" + toString(int(0.05 * height)) + "\" >Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.625 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.625 * height)) + "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA);
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsA); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.65 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.65 * height)) + "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB);
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsB); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.675 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.675 * height)) + "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC);
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsC); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.7 * height)) + "\">The number of species in group " + lookup[3]->getGroup() + " is " + toString(numD);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.7 * height)) + "\">The number of species in group " + lookup[3]->getGroup() + " is " + toString(numD);
if (nseqs) { outsvg << ", and the number of squences is " + toString(numSeqsD); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.725 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedABVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.75 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedACVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.775 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedADVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.8 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.8 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedBCVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.825 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedBDVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.85 * height)) + "\">The number of species shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedCDVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.875 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedABCVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.9 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedABDVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.925 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.925 * height)) + "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedACDVal); }
outsvg << "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.95 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD);
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.95 * height)) + "\">The number of species shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD);
if (nseqs) { outsvg << ", and the number of squences is " + toString(sharedBCDVal); }
outsvg << "</text>\n";
//A = red, B = green, C = blue, D = yellow
//place labels within overlaps
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.66 * width) - ((int)toString(numA).length() / 2)) + "\" y=\"" + toString(int(0.14 * height)) + "\">" + toString(numA) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.66 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.11 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB).length() / 2)) + "\" y=\"" + toString(int(0.2 * height)) + "\">" + toString(sharedAB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.36 * width) - ((int)toString(numB).length() / 2)) + "\" y=\"" + toString(int(0.14 * height)) + "\">" + toString(numB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.36 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.11 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(sharedAC).length() / 2)) + "\" y=\"" + toString(int(0.24 * height)) + "\">" + toString(sharedAC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.785 * width) - ((int)toString(numC).length() / 2)) + "\" y=\"" + toString(int(0.29 * height)) + "\">" + toString(numC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.785 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.26 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.31 * width) - ((int)toString(sharedBD).length() / 2)) + "\" y=\"" + toString(int(0.24 * height)) + "\">" + toString(sharedBD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.22 * width) - ((int)toString(numD).length() / 2)) + "\" y=\"" + toString(int(0.29 * height)) + "\">" + toString(numD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.22 * width) - ((int)lookup[3]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.26 * height)) + "\">" + lookup[3]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.34 * width) - ((int)toString(sharedAD).length() / 2)) + "\" y=\"" + toString(int(0.41 * height)) + "\">" + toString(sharedAD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.675 * width) - ((int)toString(sharedBC).length() / 2)) + "\" y=\"" + toString(int(0.41 * height)) + "\">" + toString(sharedBC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedCD).length() / 2)) + "\" y=\"" + toString(int(0.54 * height)) + "\">" + toString(sharedCD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.39 * width) - ((int)toString(sharedABD).length() / 2)) + "\" y=\"" + toString(int(0.3 * height)) + "\">" + toString(sharedABD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.57 * width) - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"" + toString(int(0.45 * height)) + "\">" + toString(sharedBCD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.435 * width) - ((int)toString(sharedACD).length() / 2)) + "\" y=\"" + toString(int(0.45 * height)) + "\">" + toString(sharedACD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.63 * width) - ((int)toString(sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.3 * height)) + "\">" + toString(sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABCD).length() / 2)) + "\" y=\"" + toString(int(0.4 * height)) + "\">" + toString(sharedABCD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.66 * width) - ((int)toString(numA).length() / 2)) + "\" y=\"" + toString(int(0.14 * height)) + "\">" + toString(numA) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.66 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.11 * height)) + "\">" + lookup[0]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB).length() / 2)) + "\" y=\"" + toString(int(0.2 * height)) + "\">" + toString(sharedAB) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.36 * width) - ((int)toString(numB).length() / 2)) + "\" y=\"" + toString(int(0.14 * height)) + "\">" + toString(numB) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.36 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.11 * height)) + "\">" + lookup[1]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)toString(sharedAC).length() / 2)) + "\" y=\"" + toString(int(0.24 * height)) + "\">" + toString(sharedAC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.785 * width) - ((int)toString(numC).length() / 2)) + "\" y=\"" + toString(int(0.29 * height)) + "\">" + toString(numC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.785 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.26 * height)) + "\">" + lookup[2]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.31 * width) - ((int)toString(sharedBD).length() / 2)) + "\" y=\"" + toString(int(0.24 * height)) + "\">" + toString(sharedBD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.22 * width) - ((int)toString(numD).length() / 2)) + "\" y=\"" + toString(int(0.29 * height)) + "\">" + toString(numD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.22 * width) - ((int)lookup[3]->getGroup().length() / 2)) + "\" y=\"" + toString(int(0.26 * height)) + "\">" + lookup[3]->getGroup() + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.34 * width) - ((int)toString(sharedAD).length() / 2)) + "\" y=\"" + toString(int(0.41 * height)) + "\">" + toString(sharedAD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.675 * width) - ((int)toString(sharedBC).length() / 2)) + "\" y=\"" + toString(int(0.41 * height)) + "\">" + toString(sharedBC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedCD).length() / 2)) + "\" y=\"" + toString(int(0.54 * height)) + "\">" + toString(sharedCD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.39 * width) - ((int)toString(sharedABD).length() / 2)) + "\" y=\"" + toString(int(0.3 * height)) + "\">" + toString(sharedABD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.57 * width) - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"" + toString(int(0.45 * height)) + "\">" + toString(sharedBCD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.435 * width) - ((int)toString(sharedACD).length() / 2)) + "\" y=\"" + toString(int(0.45 * height)) + "\">" + toString(sharedACD) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.63 * width) - ((int)toString(sharedABC).length() / 2)) + "\" y=\"" + toString(int(0.3 * height)) + "\">" + toString(sharedABC) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABCD).length() / 2)) + "\" y=\"" + toString(int(0.4 * height)) + "\">" + toString(sharedABCD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.975 * height)) + "\">The total richness of all the groups is " + toString((float)(numA + numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD));
+ outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.25 * width)) + "\" y=\"" + toString(int(0.975 * height)) + "\">The total richness of all the groups is " + toString((float)(numA + numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD));
if (nseqs) { outsvg << ", and the number of squences in the otus shared by all groups is " + toString(sharedVal); }
outsvg << "</text>\n";
class Venn {
public:
- Venn(string, bool, string);
+ Venn(string, bool, string, int);
~Venn(){};
vector<string> getPic(SAbundVector*, vector<Calculator*>);
ofstream outsvg;
MothurOut* m;
bool nseqs;
+ int fontSize;
};
/***********************************************************************/
CommandParameter pcalc("calc", "String", "", "", "", "", "",false,false); parameters.push_back(pcalc);
CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnseqs);
+ CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppermute);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
string VennCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
+ helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n";
helpString += "The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n";
+ helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
helpString += "The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n";
temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found"){ temp = "f"; }
nseqs = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; }
+ temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; }
perm = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
+ convert(temp, fontsize);
}
//if the users entered no valid calculators don't execute command
if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0; }
- venn = new Venn(outputDir, nseqs, inputfile);
+ venn = new Venn(outputDir, nseqs, inputfile, fontsize);
input = new InputData(inputfile, format);
string lastLabel;
vector<SharedRAbundVector*> lookup;
set< set<int> > combosOfFour;
SAbundVector* sabund;
- int abund;
+ int abund, fontsize;
bool abort, allLines, nseqs, perm;
set<string> labels; //holds labels to be used
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