exit(1);\r
}\r
}\r
-#ifdef USE_MPI \r
-/**************************************************************************************************/\r
-int AlignmentDB::MPISend(int receiver) {\r
- try {\r
- \r
- //send numSeqs - int\r
- MPI_Send(&numSeqs, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD); \r
- \r
- //send longest - int\r
- MPI_Send(&longest, 1, MPI_INT, receiver, 2001, MPI_COMM_WORLD); \r
- \r
- //send templateSequences\r
- for (int i = 0; i < templateSequences.size(); i++) {\r
- templateSequences[i].MPISend(receiver);\r
- }\r
- \r
- //send Database\r
- search->MPISend(receiver);\r
- \r
- return 0;\r
- }\r
- catch(exception& e) {\r
- m->errorOut(e, "AlignmentDB", "MPISend");\r
- exit(1);\r
- }\r
-}\r
-/**************************************************************************************************/\r
-int AlignmentDB::MPIRecv(int sender) {\r
- try {\r
- MPI_Status status;\r
- //receive numSeqs - int\r
- MPI_Recv(&numSeqs, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);\r
- \r
- //receive longest - int\r
- MPI_Recv(&longest, 1, MPI_INT, sender, 2001, MPI_COMM_WORLD, &status);\r
-\r
- //receive templateSequences\r
- templateSequences.resize(numSeqs);\r
- for (int i = 0; i < templateSequences.size(); i++) {\r
- templateSequences[i].MPIRecv(sender);\r
- }\r
-\r
- //receive Database\r
- search->MPIRecv(sender);\r
- \r
- for (int i = 0; i < templateSequences.size(); i++) {\r
- search->addSequence(templateSequences[i]);\r
- }\r
- search->generateDB();\r
- search->setNumSeqs(numSeqs);\r
-\r
- return 0;\r
- }\r
- catch(exception& e) {\r
- m->errorOut(e, "AlignmentDB", "MPIRecv");\r
- exit(1);\r
- }\r
-}\r
-#endif\r
/**************************************************************************************************/\r
\r
\r
Sequence findClosestSequence(Sequence*);
float getSearchScore() { return search->getSearchScore(); }
int getLongestBase() { return longest; }
- int MPISend(int);
- int MPIRecv(int);
private:
int numSeqs, longest;
exit(1);
}
}
+/**************************************************************************************************/
+Bayesian::~Bayesian() {
+ try {
+ delete phyloTree;
+ if (database != NULL) { delete database; }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Bayesian", "~Bayesian");
+ exit(1);
+ }
+}
+
/**************************************************************************************************/
string Bayesian::getTaxonomy(Sequence* seq) {
try {
public:
Bayesian(string, string, string, int, int, int);
- ~Bayesian() {};
+ ~Bayesian();
string getTaxonomy(Sequence*);
}
m8FileHandle.close();
- string root = dbFileName;
- string temp = dbFileName + ".nsq";
- remove(temp.c_str());
- temp = dbFileName + ".nsi";
- remove(temp.c_str());
-
- temp = dbFileName + ".nsd";
- remove(temp.c_str());
-
- temp = dbFileName + ".nin";
- remove(temp.c_str());
-
- temp = dbFileName + ".nhr";
- remove(temp.c_str());
-
-
-
return topMatches;
}
catch(exception& e) {
unalignedFastaFile << '>' << count << endl; // sequences, which will be input to formatdb
unalignedFastaFile << seq.getUnaligned() << endl;
unalignedFastaFile.close();
-
+
count++;
}
catch(exception& e) {
public:
Classify();
-
- virtual ~Classify(){ delete phyloTree; if (database != NULL) { delete database; } };
+ virtual ~Classify(){};
virtual string getTaxonomy(Sequence*) = 0;
- //virtual map<string, int> getConfidenceScores() { return taxConfidenceScore; }
- //virtual vector<string> parseTax(string);
virtual string getSimpleTax() { return simpleTax; }
virtual void generateDatabaseAndNames(string, string, string, int, float, float, float, float);
-/*
- * clearcutcommand.cpp
- * Mothur
- *
- * Created by westcott on 5/11/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "clearcutcommand.h"
-#include "globaldata.hpp"
-
-/**************************************************************************************/
-ClearcutCommand::ClearcutCommand(string option) {
- try {
- abort = false;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; }
-
- else {
- //valid paramters for this command
- string Array[] = {"fasta","phylip","version","verbose","quiet","seed","norandom","shuffle","neighbor","expblen",
- "expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","stdin","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
-
- 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("fasta");
- //user has given a template file
- if(it != parameters.end()){
- path = hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["fasta"] = inputDir + it->second; }
- }
-
- it = parameters.find("phylip");
- //user has given a template file
- if(it != parameters.end()){
- path = hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["phylip"] = inputDir + it->second; }
- }
- }
-
- //check for required parameters
- fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not open") { fastafile = ""; abort = true; }
- else if (fastafile == "not found") { fastafile = ""; }
- else { inputFile = fastafile; }
-
- phylipfile = validParameter.validFile(parameters, "phylip", true);
- if (phylipfile == "not open") { phylipfile = ""; abort = true; }
- else if (phylipfile == "not found") { phylipfile = ""; }
- else { inputFile = phylipfile; }
-
- if ((phylipfile == "") && (fastafile == "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file."); m->mothurOutEndLine(); abort=true; }
- if ((phylipfile != "") && (fastafile != "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file, not BOTH."); m->mothurOutEndLine(); abort=true; }
-
-
- //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 = ""; }
-
- string temp;
- temp = validParameter.validFile(parameters, "version", false); if (temp == "not found"){ temp = "F"; }
- version = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "verbose", false); if (temp == "not found"){ temp = "F"; }
- verbose = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "quiet", false); if (temp == "not found"){ temp = "F"; }
- quiet = isTrue(temp);
-
- seed = validParameter.validFile(parameters, "seed", false); if (seed == "not found"){ seed = "*"; }
-
- temp = validParameter.validFile(parameters, "norandom", false); if (temp == "not found"){ temp = "F"; }
- norandom = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "shuffle", false); if (temp == "not found"){ temp = "F"; }
- shuffle = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "F"; }
- neighbor = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "stdin", false); if (temp == "not found"){ temp = "F"; }
- stdin = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "DNA", false); if (temp == "not found"){ temp = "F"; }
- DNA = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "protein", false); if (temp == "not found"){ temp = "F"; }
- protein = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "jukes", false); if (temp == "not found"){ temp = "F"; }
- jukes = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "kimura", false); if (temp == "not found"){ temp = "F"; }
- kimura = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "stdout", false); if (temp == "not found"){ temp = "F"; }
- stdout = isTrue(temp);
-
- matrixout = validParameter.validFile(parameters, "matrixout", false); if (matrixout == "not found"){ matrixout = ""; }
-
- ntrees = validParameter.validFile(parameters, "ntrees", false); if (ntrees == "not found"){ ntrees = "1"; }
-
- temp = validParameter.validFile(parameters, "expblen", false); if (temp == "not found"){ temp = "F"; }
- expblen = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "expdist", false); if (temp == "not found"){ temp = "F"; }
- expdist = isTrue(temp);
-
- if ((fastafile != "") && ((!DNA) && (!protein))) { m->mothurOut("You must specify the type of sequences you are using: DNA or protein"); m->mothurOutEndLine(); abort=true; }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "ClearcutCommand", "ClearcutCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-void ClearcutCommand::help(){
- try {
- m->mothurOut("The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n");
- m->mothurOut("For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n");
- m->mothurOut("The clearcut executable must be in a folder called clearcut in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
- m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA, stdin. \n");
- m->mothurOut("The phylip parameter allows you to enter your phylip formatted distance matrix. \n");
- m->mothurOut("The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n");
-
- m->mothurOut("The version parameter prints out the version of clearcut you are using, default=F. \n");
- m->mothurOut("The verbose parameter prints out more output from clearcut, default=F. \n");
- m->mothurOut("The quiet parameter turns on silent operation mode, default=F. \n");
- m->mothurOut("The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n");
- m->mothurOut("The norandom parameter allows you to attempt joins deterministically, default=F. \n");
- m->mothurOut("The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n");
- m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=F. \n");
-
- m->mothurOut("The stdin parameter reads input from STDIN, default=F. \n");
- m->mothurOut("The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n");
- m->mothurOut("The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n");
-
- m->mothurOut("The stdout parameter outputs your tree to STDOUT, default=F. \n");
- m->mothurOut("The matrixout parameter allows you to specify a filename to output a distance matrix to. \n");
- m->mothurOut("The ntrees parameter allows you to specify the number of output trees, default=1. \n");
- m->mothurOut("The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n");
- m->mothurOut("The expdist parameter allows you to use exponential notation for distance outputs, default=F. \n");
-
- m->mothurOut("The clearcut command should be in the following format: \n");
- m->mothurOut("clearcut(phylip=yourDistanceFile) \n");
- m->mothurOut("Example: clearcut(phylip=abrecovery.phylip.dist) \n");
- }
- catch(exception& e) {
- m->errorOut(e, "ClearcutCommand", "help");
- exit(1);
- }
-}
-
-/**************************************************************************************/
-int ClearcutCommand::execute() {
- try {
-
- if (abort == true) { return 0; }
-
- //prepare filename
- string outputName = outputDir + getRootName(getSimpleName(inputFile)) + "tre";
-
- //get location of clearcut
- GlobalData* globaldata = GlobalData::getInstance();
- string path = globaldata->argv;
- path = path.substr(0, (path.find_last_of('m')));
-
- string clearcutCommand = path + "clearcut/clearcut ";
-
- //you gave us a distance matrix
- if (phylipfile != "") { clearcutCommand += "--distance "; }
-
- //you gave us a fastafile
- if (fastafile != "") { clearcutCommand += "--alignment "; }
-
- if (version) { clearcutCommand += "--version "; }
- if (verbose) { clearcutCommand += "--verbose "; }
- if (quiet) { clearcutCommand += "--quiet "; }
- if (seed != "*") { clearcutCommand += "--seed=" + seed + " "; }
- if (norandom) { clearcutCommand += "--norandom "; }
- if (shuffle) { clearcutCommand += "--shuffle "; }
- if (neighbor) { clearcutCommand += "--neighbor "; }
-
- if (stdin) { clearcutCommand += "--stdin "; }
- else { clearcutCommand += "--in=" + inputFile + " "; }
- if (stdout) { clearcutCommand += "--stdout "; }
- else { clearcutCommand += "--out=" + outputName + " "; }
-
- if (DNA) { clearcutCommand += "--DNA "; }
- if (protein) { clearcutCommand += "--protein "; }
- if (jukes) { clearcutCommand += "--jukes "; }
- if (kimura) { clearcutCommand += "--kimura "; }
- if (matrixout != "") { clearcutCommand += "--matrixout=" + matrixout + " "; }
- if (ntrees != "1") { clearcutCommand += "--ntrees=" + ntrees + " "; }
- if (expblen) { clearcutCommand += "--expblen "; }
- if (expdist) { clearcutCommand += "--expdist "; }
-
- //run clearcut
- system(clearcutCommand.c_str());
-
- if (!stdout) {
- m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputName); m->mothurOutEndLine();
- m->mothurOutEndLine();
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "ClearcutCommand", "execute");
- exit(1);
- }
-}
-/**************************************************************************************/
-
-
-
-
+/*\r
+ * clearcutcommand.cpp\r
+ * Mothur\r
+ *\r
+ * Created by westcott on 5/11/10.\r
+ * Copyright 2010 Schloss Lab. All rights reserved.\r
+ *\r
+ */\r
+\r
+#include "clearcutcommand.h"\r
+\r
+/**************************************************************************************/\r
+ClearcutCommand::ClearcutCommand(string option) { \r
+ try {\r
+ abort = false;\r
+ \r
+ //allow user to run help\r
+ if(option == "help") { help(); abort = true; }\r
+ \r
+ else {\r
+ //valid paramters for this command\r
+ string Array[] = {"fasta","phylip","version","verbose","quiet","seed","norandom","shuffle","neighbor","expblen",\r
+ "expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","stdin","outputdir","inputdir"};\r
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));\r
+ \r
+ OptionParser parser(option);\r
+ map<string,string> parameters = parser.getParameters();\r
+ \r
+ ValidParameters validParameter;\r
+ map<string, string>::iterator it;\r
+ \r
+ //check to make sure all parameters are valid for command\r
+ for (it = parameters.begin(); it != parameters.end(); it++) { \r
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }\r
+ }\r
+ \r
+ //if the user changes the input directory command factory will send this info to us in the output parameter \r
+ string inputDir = validParameter.validFile(parameters, "inputdir", false); \r
+ if (inputDir == "not found"){ inputDir = ""; }\r
+ else {\r
+ string path;\r
+ it = parameters.find("fasta");\r
+ //user has given a template file\r
+ if(it != parameters.end()){ \r
+ path = hasPath(it->second);\r
+ //if the user has not given a path then, add inputdir. else leave path alone.\r
+ if (path == "") { parameters["fasta"] = inputDir + it->second; }\r
+ }\r
+ \r
+ it = parameters.find("phylip");\r
+ //user has given a template file\r
+ if(it != parameters.end()){ \r
+ path = hasPath(it->second);\r
+ //if the user has not given a path then, add inputdir. else leave path alone.\r
+ if (path == "") { parameters["phylip"] = inputDir + it->second; }\r
+ }\r
+ }\r
+\r
+ //check for required parameters\r
+ fastafile = validParameter.validFile(parameters, "fasta", true);\r
+ if (fastafile == "not open") { fastafile = ""; abort = true; }\r
+ else if (fastafile == "not found") { fastafile = ""; } \r
+ else { inputFile = fastafile; }\r
+ \r
+ phylipfile = validParameter.validFile(parameters, "phylip", true);\r
+ if (phylipfile == "not open") { phylipfile = ""; abort = true; }\r
+ else if (phylipfile == "not found") { phylipfile = ""; }\r
+ else { inputFile = phylipfile; }\r
+ \r
+ if ((phylipfile == "") && (fastafile == "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file."); m->mothurOutEndLine(); abort=true; }\r
+ if ((phylipfile != "") && (fastafile != "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file, not BOTH."); m->mothurOutEndLine(); abort=true; }\r
+\r
+ \r
+ //if the user changes the output directory command factory will send this info to us in the output parameter \r
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }\r
+ \r
+ string temp;\r
+ temp = validParameter.validFile(parameters, "version", false); if (temp == "not found"){ temp = "F"; }\r
+ version = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "verbose", false); if (temp == "not found"){ temp = "F"; }\r
+ verbose = isTrue(temp); \r
+ \r
+ temp = validParameter.validFile(parameters, "quiet", false); if (temp == "not found"){ temp = "F"; }\r
+ quiet = isTrue(temp); \r
+ \r
+ seed = validParameter.validFile(parameters, "seed", false); if (seed == "not found"){ seed = "*"; }\r
+ \r
+ temp = validParameter.validFile(parameters, "norandom", false); if (temp == "not found"){ temp = "F"; }\r
+ norandom = isTrue(temp); \r
+ \r
+ temp = validParameter.validFile(parameters, "shuffle", false); if (temp == "not found"){ temp = "F"; }\r
+ shuffle = isTrue(temp); \r
+ \r
+ temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "F"; }\r
+ neighbor = isTrue(temp); \r
+ \r
+ temp = validParameter.validFile(parameters, "stdin", false); if (temp == "not found"){ temp = "F"; }\r
+ stdinWanted = isTrue(temp); \r
+ \r
+ temp = validParameter.validFile(parameters, "DNA", false); if (temp == "not found"){ temp = "F"; }\r
+ DNA = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "protein", false); if (temp == "not found"){ temp = "F"; }\r
+ protein = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "jukes", false); if (temp == "not found"){ temp = "F"; }\r
+ jukes = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "kimura", false); if (temp == "not found"){ temp = "F"; }\r
+ kimura = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "stdout", false); if (temp == "not found"){ temp = "F"; }\r
+ stdoutWanted = isTrue(temp); \r
+ \r
+ matrixout = validParameter.validFile(parameters, "matrixout", false); if (matrixout == "not found"){ matrixout = ""; }\r
+ \r
+ ntrees = validParameter.validFile(parameters, "ntrees", false); if (ntrees == "not found"){ ntrees = "1"; }\r
+ \r
+ temp = validParameter.validFile(parameters, "expblen", false); if (temp == "not found"){ temp = "F"; }\r
+ expblen = isTrue(temp);\r
+ \r
+ temp = validParameter.validFile(parameters, "expdist", false); if (temp == "not found"){ temp = "F"; }\r
+ expdist = isTrue(temp);\r
+ \r
+ if ((fastafile != "") && ((!DNA) && (!protein))) { m->mothurOut("You must specify the type of sequences you are using: DNA or protein"); m->mothurOutEndLine(); abort=true; }\r
+ }\r
+\r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "ClearcutCommand", "ClearcutCommand");\r
+ exit(1);\r
+ }\r
+}\r
+//**********************************************************************************************************************\r
+\r
+void ClearcutCommand::help(){\r
+ try {\r
+ m->mothurOut("The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n");\r
+ m->mothurOut("For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n");\r
+ m->mothurOut("The clearcut executable must be in a folder called clearcut in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");\r
+ m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdoutWanted, kimura, jukes, protein, DNA, stdinWanted. \n");\r
+ m->mothurOut("The phylip parameter allows you to enter your phylip formatted distance matrix. \n");\r
+ m->mothurOut("The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n");\r
+ \r
+ m->mothurOut("The version parameter prints out the version of clearcut you are using, default=F. \n");\r
+ m->mothurOut("The verbose parameter prints out more output from clearcut, default=F. \n");\r
+ m->mothurOut("The quiet parameter turns on silent operation mode, default=F. \n");\r
+ m->mothurOut("The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n");\r
+ m->mothurOut("The norandom parameter allows you to attempt joins deterministically, default=F. \n");\r
+ m->mothurOut("The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n");\r
+ m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=F. \n");\r
+ \r
+ m->mothurOut("The stdinWanted parameter reads input from STDIN, default=F. \n");\r
+ m->mothurOut("The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n");\r
+ m->mothurOut("The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n");\r
+ \r
+ m->mothurOut("The stdoutWanted parameter outputs your tree to STDOUT, default=F. \n");\r
+ m->mothurOut("The matrixout parameter allows you to specify a filename to output a distance matrix to. \n");\r
+ m->mothurOut("The ntrees parameter allows you to specify the number of output trees, default=1. \n");\r
+ m->mothurOut("The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n");\r
+ m->mothurOut("The expdist parameter allows you to use exponential notation for distance outputs, default=F. \n");\r
+\r
+ m->mothurOut("The clearcut command should be in the following format: \n");\r
+ m->mothurOut("clearcut(phylip=yourDistanceFile) \n");\r
+ m->mothurOut("Example: clearcut(phylip=abrecovery.phylip.dist) \n"); \r
+ \r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "ClearcutCommand", "help");\r
+ exit(1);\r
+ }\r
+}\r
+\r
+/**************************************************************************************/\r
+int ClearcutCommand::execute() { \r
+ try {\r
+ \r
+ if (abort == true) { return 0; }\r
+ \r
+ //prepare filename\r
+ string outputName = outputDir + getRootName(getSimpleName(inputFile)) + "tre";\r
+ \r
+ //get location of clearcut\r
+ GlobalData* globaldata = GlobalData::getInstance();\r
+ string path = globaldata->argv;\r
+ path = path.substr(0, (path.find_last_of('m')));\r
+ \r
+ string clearcutCommand = "";\r
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
+ clearcutCommand = path + "clearcut/clearcut ";\r
+ #else\r
+ clearcutCommand = path + "clearcut\\clearcut ";\r
+ #endif\r
+ \r
+ //you gave us a distance matrix\r
+ if (phylipfile != "") { clearcutCommand += "--distance "; }\r
+ \r
+ //you gave us a fastafile\r
+ if (fastafile != "") { clearcutCommand += "--alignment "; }\r
+ \r
+ if (version) { clearcutCommand += "--version "; }\r
+ if (verbose) { clearcutCommand += "--verbose "; }\r
+ if (quiet) { clearcutCommand += "--quiet "; }\r
+ if (seed != "*") { clearcutCommand += "--seed=" + seed + " "; }\r
+ if (norandom) { clearcutCommand += "--norandom "; }\r
+ if (shuffle) { clearcutCommand += "--shuffle "; }\r
+ if (neighbor) { clearcutCommand += "--neighbor "; }\r
+ \r
+ if (stdinWanted) { clearcutCommand += "--stdin "; }\r
+ else{ \r
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
+ clearcutCommand += "--in=" + inputFile + " "; }\r
+ #else\r
+ clearcutCommand += "--in=\"" + inputFile + "\" "; }\r
+ #endif\r
+ if (stdoutWanted) { clearcutCommand += "--stdout "; }\r
+ else{ \r
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
+ clearcutCommand += "--out=" + outputName + " "; }\r
+ #else\r
+ clearcutCommand += "--out=\"" + outputName + "\" "; }\r
+ #endif\r
+ \r
+ if (DNA) { clearcutCommand += "--DNA "; }\r
+ if (protein) { clearcutCommand += "--protein "; }\r
+ if (jukes) { clearcutCommand += "--jukes "; }\r
+ if (kimura) { clearcutCommand += "--kimura "; }\r
+ if (matrixout != "") { clearcutCommand += "--matrixout=" + matrixout + " "; }\r
+ if (ntrees != "1") { clearcutCommand += "--ntrees=" + ntrees + " "; }\r
+ if (expblen) { clearcutCommand += "--expblen "; }\r
+ if (expdist) { clearcutCommand += "--expdist "; }\r
+ \r
+ //run clearcut\r
+ system(clearcutCommand.c_str());\r
+ \r
+ if (!stdoutWanted) { \r
+ m->mothurOutEndLine();\r
+ m->mothurOut("Output File Names: "); m->mothurOutEndLine();\r
+ m->mothurOut(outputName); m->mothurOutEndLine(); \r
+ m->mothurOutEndLine();\r
+ }\r
+\r
+ return 0;\r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "ClearcutCommand", "execute");\r
+ exit(1);\r
+ }\r
+}\r
+/**************************************************************************************/\r
+\r
+\r
+\r
+\r
*/
#include "command.hpp"
-
+#include "globaldata.hpp"
/*
Evans, J., L. Sheneman, and J.A. Foster (2006) Relaxed Neighbor-Joining:
private:
string outputDir, phylipfile, fastafile, matrixout, inputFile, seed, ntrees;
- bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdout, kimura, jukes, protein, DNA, stdin;
+ bool version, verbose, quiet, norandom, shuffle, neighbor, expblen, expdist, stdoutWanted, kimura, jukes, protein, DNA, stdinWanted;
bool abort;
};
}
//convert freq percentage to number
- int increment = numSeqs * percentFreq;
+ int increment = 1;
+ if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
+ else { increment = percentFreq; }
for(int i=0;i<numSeqs;i++){
}
//convert freq percentage to number
- int increment = numSeqs * percentFreq;
+ int increment = 1;
+ if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
+ else { increment = percentFreq; }
//sample all the members
for(int i=0;i<numSeqs;i++){
splitAtDash(calc, Estimators);
string temp;
- temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "0.10"; }
+ temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
convert(temp, freq);
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
m->mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
m->mothurOut("The collect.single command parameters are label, freq, calc and abund. No parameters are required. \n");
m->mothurOut("The collect.single command should be in the following format: \n");
- m->mothurOut("The freq parameter is used indicate when to output your data. It is a percentage of the number of sequences. By default it is set to 0.10, meaning 10%. \n");
+ m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
m->mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
m->mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
m->mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
globaldata->Groups = Groups;
string temp;
- temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "0.10"; }
+ temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
convert(temp, freq);
temp = validParameter.validFile(parameters, "all", false); if (temp == "not found") { temp = "false"; }
m->mothurOut("Example collect.shared(label=unique-.01-.03, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
m->mothurOut("The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n");
m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
- m->mothurOut("The freq parameter is used indicate when to output your data. It is a percentage of the number of sequences. By default it is set to 0.10, meaning 10%. \n");
+ m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
validCalculator->printCalc("shared", cout);
m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
m->mothurOut("The all parameter is used to specify if you want the estimate of all your groups together. This estimate can only be made for sharedsobs and sharedchao calculators. The default is false.\n");
public:
DistanceDB();
- ~DistanceDB() {}
+ ~DistanceDB() { delete distCalculator; }
void generateDB() {} //doesn't generate a search db
void addSequence(Sequence);
}
}
/**************************************************************************************************/
+Knn::~Knn() {
+ try {
+ delete phyloTree;
+ if (database != NULL) { delete database; }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Knn", "~Knn");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
string Knn::getTaxonomy(Sequence* seq) {
try {
string tax;
public:
Knn(string, string, string, int, float, float, float, float, int);
- ~Knn() {};
+ ~Knn();
string getTaxonomy(Sequence*);
-/*
- * interface.cpp
- *
- *
- * Created by Pat Schloss on 8/14/08.
- * Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "engine.hpp"
-#include "globaldata.hpp"
-#include "mothurout.h"
-
-
-/**************************************************************************************************/
-
-GlobalData* GlobalData::_uniqueInstance = 0;
-CommandFactory* CommandFactory::_uniqueInstance = 0;
-MothurOut* MothurOut::_uniqueInstance = 0;
-
-/***********************************************************************/
-volatile int ctrlc_pressed = 0;
-void ctrlc_handler ( int sig ) {
- MothurOut* m = MothurOut::getInstance();
- ctrlc_pressed = 1;
- m->control_pressed = ctrlc_pressed;
-
- if (m->executing) { //if mid command quit execution, else quit mothur
- m->mothurOutEndLine(); m->mothurOut("quitting command..."); m->mothurOutEndLine();
- }else{
- m->mothurOut("quitting mothur"); m->mothurOutEndLine();
- exit(1);
- }
-}
-/***********************************************************************/
-int main(int argc, char *argv[]){
- MothurOut* m = MothurOut::getInstance();
- try {
-
- signal(SIGINT, ctrlc_handler );
-
- time_t ltime = time(NULL); /* calendar time */
- string logFileName = "mothur." + toString(ltime) + ".logfile";
-
- #ifdef USE_MPI
- MPI_Init(&argc, &argv);
- #endif
-
- m->setFileName(logFileName);
-
-
- //version
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- system("clear");
- #if defined (__APPLE__) || (__MACH__)
- m->mothurOutJustToLog("Mac version");
- m->mothurOutEndLine(); m->mothurOutEndLine();
- #else
- m->mothurOutJustToLog("Linux version");
- m->mothurOutEndLine(); m->mothurOutEndLine();
- #endif
-
- #else
- system("CLS");
- m->mothurOutJustToLog("Windows version");
- m->mothurOutEndLine(); m->mothurOutEndLine();
- #endif
-
- #ifdef USE_READLINE
- m->mothurOutJustToLog("Using ReadLine");
- m->mothurOutEndLine(); m->mothurOutEndLine();
- #endif
-
- //header
- m->mothurOut("mothur v.1.9");
- m->mothurOutEndLine();
- m->mothurOut("Last updated: 4/16/2010");
- m->mothurOutEndLine();
- m->mothurOutEndLine();
- m->mothurOut("by");
- m->mothurOutEndLine();
- m->mothurOut("Patrick D. Schloss");
- m->mothurOutEndLine();
- m->mothurOutEndLine();
- m->mothurOut("Department of Microbiology & Immunology");
- m->mothurOutEndLine();
- m->mothurOut("University of Michigan");
- m->mothurOutEndLine();
- m->mothurOut("pschloss@umich.edu");
- m->mothurOutEndLine();
- m->mothurOut("http://www.mothur.org");
- m->mothurOutEndLine();
- m->mothurOutEndLine();
- m->mothurOut("When using, please cite:");
- m->mothurOutEndLine();
- m->mothurOut("Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.");
- m->mothurOutEndLine();
- m->mothurOutEndLine();
- m->mothurOut("Distributed under the GNU General Public License");
- m->mothurOutEndLine();
- m->mothurOutEndLine();
- m->mothurOut("Type 'help()' for information on the commands that are available");
- m->mothurOutEndLine();
- m->mothurOutEndLine();
- m->mothurOut("Type 'quit()' to exit program");
- m->mothurOutEndLine();
-
- #ifdef USE_MPI
- m->mothurOutJustToLog("Using MPI\tversion ");
- int version, subversion;
- MPI_Get_version(&version, &subversion);
- m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");
- #endif
-
- //srand(54321);
- srand( (unsigned)time( NULL ) );
-
- Engine* mothur;
- bool bail = 0;
- string input;
-
- if(argc>1){
- input = argv[1];
-
- if (input[0] == '#') {
- m->mothurOutJustToLog("Script Mode");
- m->mothurOutEndLine(); m->mothurOutEndLine();
-
- mothur = new ScriptEngine(argv[0], argv[1]);
- }else{
- m->mothurOutJustToLog("Batch Mode");
- m->mothurOutEndLine(); m->mothurOutEndLine();
-
- mothur = new BatchEngine(argv[0], argv[1]);
- }
- }
- else{
- m->mothurOutJustToLog("Interactive Mode");
- m->mothurOutEndLine(); m->mothurOutEndLine();
-
- mothur = new InteractEngine(argv[0]);
- }
-
- while(bail == 0) { bail = mothur->getInput(); }
-
- //closes logfile so we can rename
- m->closeLog();
-
- string outputDir = mothur->getOutputDir();
- string tempLog = mothur->getLogFileName();
- bool append = mothur->getAppend();
-
- string newlogFileName;
- if (tempLog != "") {
- newlogFileName = outputDir + tempLog;
-
- if (!append) {
- //need this because m->mothurOut makes the logfile, but doesn't know where to put it
- rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
-
- }else {
- ofstream outNewLog;
- openOutputFileAppend(newlogFileName, outNewLog);
- outNewLog << endl << endl << "*********************************************************************************" << endl << endl;
- outNewLog.close();
-
- appendFiles(logFileName, newlogFileName);
- remove(logFileName.c_str());
- }
- }else{
- newlogFileName = outputDir + logFileName;
- //need this because m->mothurOut makes the logfile, but doesn't know where to put it
- rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp
- }
-
-
- delete mothur;
-
- #ifdef USE_MPI
- MPI_Finalize();
- #endif
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "mothur", "main");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
+/*\r
+ * interface.cpp\r
+ * \r
+ *\r
+ * Created by Pat Schloss on 8/14/08.\r
+ * Copyright 2008 Patrick D. Schloss. All rights reserved.\r
+ *\r
+ */\r
+ \r
+#include "mothur.h"\r
+#include "engine.hpp"\r
+#include "globaldata.hpp"\r
+#include "mothurout.h"\r
+\r
+\r
+/**************************************************************************************************/\r
+\r
+GlobalData* GlobalData::_uniqueInstance = 0;\r
+CommandFactory* CommandFactory::_uniqueInstance = 0;\r
+MothurOut* MothurOut::_uniqueInstance = 0;\r
+\r
+/***********************************************************************/\r
+volatile int ctrlc_pressed = 0;\r
+void ctrlc_handler ( int sig ) {\r
+ MothurOut* m = MothurOut::getInstance();\r
+ ctrlc_pressed = 1;\r
+ m->control_pressed = ctrlc_pressed;\r
+ \r
+ if (m->executing) { //if mid command quit execution, else quit mothur\r
+ m->mothurOutEndLine(); m->mothurOut("quitting command..."); m->mothurOutEndLine();\r
+ }else{\r
+ m->mothurOut("quitting mothur"); m->mothurOutEndLine();\r
+ exit(1);\r
+ }\r
+}\r
+/***********************************************************************/\r
+int main(int argc, char *argv[]){\r
+ MothurOut* m = MothurOut::getInstance();\r
+ try {\r
+ \r
+ signal(SIGINT, ctrlc_handler );\r
+ \r
+ time_t ltime = time(NULL); /* calendar time */ \r
+ string logFileName = "mothur." + toString(ltime) + ".logfile";\r
+ \r
+ #ifdef USE_MPI\r
+ MPI_Init(&argc, &argv); \r
+ #endif\r
+\r
+ m->setFileName(logFileName);\r
+ \r
+ \r
+ //version\r
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)\r
+ system("clear");\r
+ #if defined (__APPLE__) || (__MACH__)\r
+ m->mothurOutJustToLog("Mac version");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ #else\r
+ m->mothurOutJustToLog("Linux version");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ #endif\r
+\r
+ #else\r
+ system("CLS");\r
+ m->mothurOutJustToLog("Windows version");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ #endif \r
+ \r
+ #ifdef USE_READLINE\r
+ m->mothurOutJustToLog("Using ReadLine");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ #endif\r
+ \r
+ //header\r
+ m->mothurOut("mothur v.1.10.0");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Last updated: 5/14/2010");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("by");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Patrick D. Schloss");\r
+ m->mothurOutEndLine();\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Department of Microbiology & Immunology");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("University of Michigan");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("pschloss@umich.edu");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("http://www.mothur.org");\r
+ m->mothurOutEndLine();\r
+ m->mothurOutEndLine();\r
+ m->mothurOut("When using, please cite:");\r
+ m->mothurOutEndLine();\r
+ m->mothurOut("Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.");\r
+ m->mothurOutEndLine(); \r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Distributed under the GNU General Public License");\r
+ m->mothurOutEndLine();\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Type 'help()' for information on the commands that are available");\r
+ m->mothurOutEndLine();\r
+ m->mothurOutEndLine(); \r
+ m->mothurOut("Type 'quit()' to exit program");\r
+ m->mothurOutEndLine(); \r
+ \r
+ #ifdef USE_MPI\r
+ m->mothurOutJustToLog("Using MPI\tversion ");\r
+ int version, subversion;\r
+ MPI_Get_version(&version, &subversion);\r
+ m->mothurOutJustToLog(toString(version) + "." + toString(subversion) + "\n");\r
+ #endif\r
+ \r
+ //srand(54321);\r
+ srand( (unsigned)time( NULL ) );\r
+ \r
+ Engine* mothur;\r
+ bool bail = 0;\r
+ string input;\r
+\r
+ if(argc>1){\r
+ input = argv[1];\r
+\r
+ if (input[0] == '#') {\r
+ m->mothurOutJustToLog("Script Mode");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+\r
+ mothur = new ScriptEngine(argv[0], argv[1]);\r
+ }else{\r
+ m->mothurOutJustToLog("Batch Mode");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ \r
+ mothur = new BatchEngine(argv[0], argv[1]);\r
+ }\r
+ }\r
+ else{\r
+ m->mothurOutJustToLog("Interactive Mode");\r
+ m->mothurOutEndLine(); m->mothurOutEndLine();\r
+ \r
+ mothur = new InteractEngine(argv[0]); \r
+ }\r
+ \r
+ while(bail == 0) { bail = mothur->getInput(); }\r
+ \r
+ //closes logfile so we can rename\r
+ m->closeLog();\r
+ \r
+ string outputDir = mothur->getOutputDir();\r
+ string tempLog = mothur->getLogFileName();\r
+ bool append = mothur->getAppend();\r
+ \r
+ string newlogFileName;\r
+ if (tempLog != "") {\r
+ newlogFileName = outputDir + tempLog;\r
+ \r
+ if (!append) { \r
+ //need this because m->mothurOut makes the logfile, but doesn't know where to put it\r
+ rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp\r
+\r
+ }else {\r
+ ofstream outNewLog;\r
+ openOutputFileAppend(newlogFileName, outNewLog);\r
+ outNewLog << endl << endl << "*********************************************************************************" << endl << endl;\r
+ outNewLog.close();\r
+ \r
+ appendFiles(logFileName, newlogFileName);\r
+ remove(logFileName.c_str());\r
+ }\r
+ }else{ \r
+ newlogFileName = outputDir + logFileName;\r
+ //need this because m->mothurOut makes the logfile, but doesn't know where to put it\r
+ rename(logFileName.c_str(), newlogFileName.c_str()); //logfile with timestamp\r
+ }\r
+ \r
+ \r
+ delete mothur;\r
+ \r
+ #ifdef USE_MPI\r
+ MPI_Finalize();\r
+ #endif\r
+ \r
+ return 0;\r
+ }\r
+ catch(exception& e) {\r
+ m->errorOut(e, "mothur", "main");\r
+ exit(1);\r
+ }\r
+}\r
+\r
+/**************************************************************************************************/\r
+\r
}
#else
if (path.find("~") != -1) { //go to home directory
- string homeDir = getenv ("HOME");
+ string homeDir = getenv ("HOMEPATH");
newFileName = homeDir + fileName.substr(fileName.find("~")+1);
return newFileName;
}else { //find path
m->mothurOut("You must execute the read.tree command, before you may execute the phylo.diversity command."); m->mothurOutEndLine(); abort = true; }
string temp;
- temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "0.10"; }
+ temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
convert(temp, freq);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
m->mothurOut("The phylo.diversity command parameters are groups, iters, freq and rarefy. No parameters are required.\n");
m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. The group names are separated by dashes. By default all groups are used.\n");
m->mothurOut("The iters parameter allows you to specify the number of randomizations to preform, by default iters=1000, if you set rarefy to true.\n");
- m->mothurOut("The freq parameter is used indicate when to output your data. It is a percentage of the number of sequences. By default it is set to 0.10, meaning 10%. \n");
+ m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
m->mothurOut("The rarefy parameter allows you to create a rarefaction curve. The default is false.\n");
m->mothurOut("The phylo.diversity command should be in the following format: phylo.diversity(groups=yourGroups, rarefy=yourRarefy, iters=yourIters).\n");
m->mothurOut("Example phylo.diversity(groups=A-B-C, rarefy=T, iters=500).\n");
numLeafNodes = randomLeaf.size(); //reset the number of leaf nodes you are using
//convert freq percentage to number
- int increment = numLeafNodes * freq;
+ int increment = 100;
+ if (freq < 1.0) { increment = numLeafNodes * freq; }
+ else { increment = freq; }
//each group, each sampling, if no rarefy iters = 1;
vector< vector<float> > diversity;
}
//convert freq percentage to number
- int increment = numSeqs * percentFreq;
-
+ int increment = 1;
+ if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
+ else { increment = percentFreq; }
+
for(int iter=0;iter<nIters;iter++){
for(int i=0;i<displays.size();i++){
if (globaldata->jumble == false) { nIters = 1; }
//convert freq percentage to number
- int increment = numSeqs * percentFreq;
+ int increment = 1;
+ if (percentFreq < 1.0) { increment = numSeqs * percentFreq; }
+ else { increment = percentFreq; }
for(int iter=0;iter<nIters;iter++){
splitAtDash(calc, Estimators);
string temp;
- temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "0.10"; }
+ temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
convert(temp, freq);
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
m->mothurOut("The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
m->mothurOut("The rarefaction.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
m->mothurOut("The rarefaction.single command parameters are label, iters, freq, calc and abund. No parameters are required. \n");
- m->mothurOut("The freq parameter is used indicate when to output your data. It is a percentage of the number of sequences. By default it is set to 0.10, meaning 10%. \n");
+ m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
m->mothurOut("The rarefaction.single command should be in the following format: \n");
m->mothurOut("rarefaction.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
m->mothurOut("Example rarefaction.single(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson).\n");
globaldata->Groups = Groups;
string temp;
- temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "0.10"; }
+ temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
convert(temp, freq);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
m->mothurOut("The rarefaction.shared command parameters are label, iters, groups, jumble and calc. No parameters are required.\n");
m->mothurOut("The rarefaction command should be in the following format: \n");
m->mothurOut("rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n");
- m->mothurOut("The freq parameter is used indicate when to output your data. It is a percentage of the number of sequences. By default it is set to 0.10, meaning 10%. \n");
+ m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
m->mothurOut("Example rarefaction.shared(label=unique-0.01-0.03, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n");
m->mothurOut("The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n");
m->mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n");
if (m->control_pressed) { return 0; }
#else
ifstream inFASTA;
- openInputFile(fastafileNames[s], inFASTA);
+ openInputFile(fastafile, inFASTA);
numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
inFASTA.close();
if (m->control_pressed) { return 0; }
#else
ifstream inFASTA;
- openInputFile(fastafileNames[s], inFASTA);
- numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ openInputFile(fastaFile, inFASTA);
+ int numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
inFASTA.close();
lines.push_back(new linePair(0, numSeqs));
- driverCreateSummary(fastafile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
+ driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, groupFile, fastaFileNames, lines[0], lines[0]);
if (m->control_pressed) { return 0; }
#endif
if (oligoFile != "") {
openOutputFile(groupFile, outGroups);
for (int i = 0; i < fastaNames.size(); i++) {
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
+ #else
+ fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));
+ #endif
}
}
}
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
-// cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,alnLength) << " raw aligned = " << temp << endl;
- cout << seq.getName() << endl;
- cout << temp << endl;
- cout << oligo << endl;
- cout << alnLength << endl;
- cout << endl;
+//
int newStart=0;
int numDiff = countDiffs(oligo, temp);
}
oligo = oligo.substr(0,alnLength);
temp = temp.substr(0,alnLength);
-// cout << "barcode = " << oligo << " raw = " << rawSequence.substr(0,alnLength) << " raw aligned = " << temp << endl;
- cout << seq.getName() << endl;
- cout << temp << endl;
- cout << oligo << endl;
- cout << alnLength << endl;
- cout << endl;
-
+//
int newStart=0;
int numDiff = countDiffs(oligo, temp);
if(numDiff < minDiff){
string itersArray[] = {">=","10", "<","NA", "between"};
parameterRanges["iters"] = addParameters(itersArray, rangeSize);
- string freqArray[] = {">=","1", "<","NA", "between"};
- parameterRanges["freq"] = addParameters(freqArray, rangeSize);
-
- //string lineArray[] = {">=","1", "<","NA", "between"};
- //parameterRanges["line"] = addParameters(lineArray, rangeSize);
-
string abundArray[] = {">=","5", "<","NA", "between"};
parameterRanges["abund"] = addParameters(abundArray, rangeSize);
vector<double> data = vCalcs[i]->getValues(sabund);
+ int width = 1500;
+ int height = 1500;
+
//svg image
- outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\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(height) + " \" >\n";
outsvg << "<g>\n";
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
- outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\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 << "<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";
if (data.size() == 3) {
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
+ 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 << "</g>\n</svg>\n";
vector<SharedRAbundVector*> subset;
vector<string> outputNames;
+ int width = 1500;
+ int height = 1500;
+
/******************* 1 Group **************************/
if (lookup.size() == 1) {
vector<double> data = singleCalc->getValues(sabund);
//svg image
- outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\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(height) + " \">\n";
outsvg << "<g>\n";
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
- outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"165\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\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 << "<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";
if (data.size() == 3) {
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
+ 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 << "</g>\n</svg>\n";
vector<double> numB = singleCalc->getValues(sabundB);
//image window
- outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\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(height) + " \" >\n";
outsvg << "<g>\n";
//draw circles
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
- outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"250\" cy=\"200\" r=\"150\"/>";
- outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"435\" cy=\"200\" r=\"150\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]).length() / 2)) + "\" y=\"195\">" + toString(numA[0] - shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(numB[0]).length() / 2)) + "\" y=\"195\">" + toString(numB[0] - shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(shared[0]).length() / 2)) + "\" y=\"195\">" + toString(shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"460\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
+ 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 << "<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]);
if (numA.size() == 3) {
outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
}else { outsvg << "</text>\n"; }
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"480\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
+ 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]);
if (numB.size() == 3) {
outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
}else { outsvg << "</text>\n"; }
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"500\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"520\">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\" x=\"175\" y=\"540\">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=\"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]) + "</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=\"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";
//close file
outsvg << "</g>\n</svg>\n";
/******************* 3 Groups **************************/
}else if (lookup.size() == 3) {
+
+ height = 1600;
+
//get sabund vector pointers so you can use the single calculators
//one for each group
SAbundVector sA, sB, sC;
}
//image window
- outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 800 800\" >\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(height) + " \" >\n";
outsvg << "<g>\n";
//draw circles
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"800\" height=\"800\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
- outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>";
- outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>";
- outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>";
+ 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 << "<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\" x=\"" + toString(200 - ((int)toString(numA[0]-sharedAwithBC[0]).length() / 2)) + "\" y=\"170\">" + toString(numA[0]-sharedAwithBC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\" y=\"170\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)toString(numB[0]-sharedBwithAC[0]).length() / 2)) + "\" y=\"170\">" + toString(numB[0]-sharedBwithAC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(numC[0]-sharedCwithAB[0]).length() / 2)) + "\" y=\"430\">" + toString(numC[0]-sharedCwithAB[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"410\">" + lookup[2]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedABC).length() / 2)) + "\" y=\"280\">" + toString(sharedABC) + "</text>\n";
+ 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\" x=\"175\" y=\"660\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"720\">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\" x=\"175\" y=\"740\">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\" x=\"175\" y=\"760\">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\" x=\"175\" y=\"580\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
+ 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]) + "</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]) + "</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]) + "</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]);
if (numA.size() == 3) {
outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
}else { outsvg << "</text>\n"; }
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"600\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
+ 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]);
if (numB.size() == 3) {
outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
}else { outsvg << "</text>\n"; }
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"620\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
+ 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]);
if (numC.size() == 3) {
outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
}else { outsvg << "</text>\n"; }
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"640\">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\" x=\"175\" y=\"780\">The total shared richness is " + toString(sharedABC) + "</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) + "</text>\n";
delete singleCalc;
vector<double> sharedabc = vCalcs[i]->getValues(subset);
//image window
- outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 800 800\" >\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(height) + " \" >\n";
outsvg << "<g>\n";
//draw circles
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"800\" height=\"800\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
- outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>";
- outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>";
- outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>";
+ 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 << "<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\" x=\"" + toString(200 - ((int)toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]).length() / 2)) + "\" y=\"170\">" + toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedab[0] - sharedabc[0]).length() / 2)) + "\" y=\"170\">" + toString(sharedab[0] - sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\" y=\"170\">" + toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedac[0] - sharedabc[0]).length() / 2)) + "\" y=\"305\">" + toString(sharedac[0] - sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\" y=\"430\">" + toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"410\">" + lookup[2]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedbc[0] - sharedabc[0]).length() / 2)) + "\" y=\"305\">" + toString(sharedbc[0] - sharedabc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedabc[0]).length() / 2)) + "\" y=\"280\">" + toString(sharedabc[0]) + "</text>\n";
+ 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\" x=\"175\" y=\"660\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"580\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
+ 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]) + "</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]) + "</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]) + "</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]);
if (numA.size() == 3) {
outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
}else { outsvg << "</text>\n"; }
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"600\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
+ 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]);
if (numB.size() == 3) {
outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
}else { outsvg << "</text>\n"; }
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"620\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
+ 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]);
if (numC.size() == 3) {
outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
}else { outsvg << "</text>\n"; }
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"640\">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\" x=\"175\" y=\"720\">The total shared richness is " + toString(sharedabc[0]) + "</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]) + "</text>\n";
}
/******************* 4 Groups **************************/
}else if (lookup.size() == 4) {
+
+ height = 1600;
+
//calc the shared otu
float sharedABCD = 0;
float numA = 0; float numB = 0; float numC = 0; float numD = 0;
//image window
- outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 800\" >\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(height) + " \" >\n";
outsvg << "<g>\n";
- outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"800\"/>";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\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\" x=\"175\" y=\"490\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"510\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"530\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"550\">The number of species in group " + lookup[3]->getGroup() + " is " + toString(numD) + "</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) + "</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) + "</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) + "</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) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"570\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"590\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"610\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"630\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"650\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"670\">The number of species shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD) + "</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) + "</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) + "</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) + "</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) + "</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) + "</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) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"690\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"710\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"730\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"750\">The number of species shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD) + "</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) + "</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) + "</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) + "</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) + "</text>\n";
//make adjustments
sharedABC = sharedABC - sharedABCD;
//cout << "num d = " << numD << endl;
//draw circles
- outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
- outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
- outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 440 315) \" cx=\"440\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
- outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 270 315) \" cx=\"270\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
+ outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 " + toString(int(0.51 * width)) + " " + toString(int(0.27 * height)) + ") \" cx=\"" + toString(int(0.51 * width)) + "\" cy=\"" + toString(int(0.27 * height)) + "\" rx=\"" + toString(int(0.29 * width)) + "\" ry=\"" + toString(int(0.14 * height)) + "\"/>\n ";
+ outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 " + toString(int(0.51 * width)) + " " + toString(int(0.27 * height)) + ") \" cx=\"" + toString(int(0.51 * width)) + "\" cy=\"" + toString(int(0.27 * height)) + "\" rx=\"" + toString(int(0.29 * width)) + "\" ry=\"" + toString(int(0.14 * height)) + "\"/>\n ";
+ outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 " + toString(int(0.63 * width)) + " " + toString(int(0.36 * height)) + ") \" cx=\"" + toString(int(0.63 * width)) + "\" cy=\"" + toString(int(0.36 * height)) + "\" rx=\"" + toString(int(0.29 * width)) + "\" ry=\"" + toString(int(0.14 * height)) + "\"/>\n ";
+ outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 " + toString(int(0.36 * width)) + " " + toString(int(0.36 * height)) + ") \" cx=\"" + toString(int(0.36 * width)) + "\" cy=\"" + toString(int(0.36 * height)) + "\" rx=\"" + toString(int(0.29 * width)) + "\" ry=\"" + toString(int(0.14 * height)) + "\"/>\n ";
//A = red, B = green, C = blue, D = yellow
//place labels within overlaps
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)toString(numA).length() / 2)) + "\" y=\"110\">" + toString(numA) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"90\">" + lookup[0]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedAB).length() / 2)) + "\" y=\"160\">" + toString(sharedAB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)toString(numB).length() / 2)) + "\" y=\"110\">" + toString(numB) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"90\">" + lookup[1]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(sharedAC).length() / 2)) + "\" y=\"190\">" + toString(sharedAC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(550 - ((int)toString(numC).length() / 2)) + "\" y=\"230\">" + toString(numC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(550 - ((int)lookup[2]->getGroup().length() / 2)) + "\" y=\"210\">" + lookup[2]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(215 - ((int)toString(sharedBD).length() / 2)) + "\" y=\"190\">" + toString(sharedBD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(150 - ((int)toString(numD).length() / 2)) + "\" y=\"230\">" + toString(numD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(150 - ((int)lookup[3]->getGroup().length() / 2)) + "\" y=\"210\">" + lookup[3]->getGroup() + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(240 - ((int)toString(sharedAD).length() / 2)) + "\" y=\"325\">" + toString(sharedAD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(470 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedBC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedCD).length() / 2)) + "\" y=\"430\">" + toString(sharedCD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(275 - ((int)toString(sharedABD).length() / 2)) + "\" y=\"240\">" + toString(sharedABD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(400 - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"360\">" + toString(sharedBCD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(305 - ((int)toString(sharedACD).length() / 2)) + "\" y=\"360\">" + toString(sharedACD) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(440 - ((int)toString(sharedABC).length() / 2)) + "\" y=\"240\">" + toString(sharedABC) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedABCD).length() / 2)) + "\" y=\"320\">" + toString(sharedABCD) + "</text>\n";
+ 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\" x=\"175\" y=\"770\">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)) + "</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)) + "</text>\n";
outsvg << "</g>\n</svg>\n";
projects / mothur.git / commitdiff