}
/*******************************************************/
-/******************************************************/
-//This function parses through the option string of the command to remove its parameters
-void GlobalData::parseGlobalData(string commandString, string optionText){
- try {
- commandName = commandString; //save command name to be used by other classes
-
- //set all non filename paramters to default
- reset();
-
- //clears out data from previous read
- if((commandName == "read.dist") || (commandName == "read.otu") || (commandName == "read.tree")) {
- clear();
- gGroupmap = NULL;
- gListVector = NULL;
- gSparseMatrix = NULL;
- gTree.clear();
- Treenames.clear();
- labels.clear(); lines.clear(); Groups.clear();
- allLines = 1;
- }
-
- //saves help request
- if(commandName =="help") {
- helpRequest = optionText;
- }
-
- if(commandName == "libshuff") {
- iters = "10000";
- cutoff = "1.0";
- }
-
- //set default value for cutoff and phylip
- if (commandName == "dist.seqs") { cutoff = "1.0"; phylipfile = "F"; }
-
- string key, value;
- //reads in parameters and values
- if((optionText != "") && (commandName != "help")){
- while((optionText.find_first_of(',') != -1)) { //while there are parameters
- splitAtComma(value, optionText);
- splitAtEquals(key, value);
-
- if(key == "phylip") { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; }
- if(key == "column") { columnfile = value; inputFileName = value; fileroot = value; format = "column"; }
- if(key == "list") { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
- if(key == "rabund") { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
- if(key == "sabund") { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
- if(key == "fasta") { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
- if(key == "tree") { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
- if(key == "shared") { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; }
- if(key == "name") { namefile = value; }
- if(key == "order") { orderfile = value; }
- if(key == "group") { groupfile = value; }
- if(key == "cutoff") { cutoff = value; }
- if(key == "precision") { precision = value; }
- if(key == "iters") { iters = value; }
- if(key == "jumble") { jumble = value; }
- if(key == "freq") { freq = value; }
- if(key == "method") { method = value; }
- if(key == "fileroot") { fileroot = value; }
- if(key == "abund") { abund = value; }
- if(key == "random") { randomtree = value; }
- if(key == "calc") { calc = value; }
- if(key == "step") { step = value; }
- if(key == "form") { form = value; }
- if(key == "sorted") { sorted = value; }
- if(key == "vertical") { vertical = value; }
- if(key == "trump") { trump = value; }
- if(key == "hard") { hard = value; }
- if(key == "soft") { soft = value; }
- if(key == "scale") { scale = value; }
- if(key == "countends") { countends = value; }
- if(key == "processors") { processors = value; }
- if(key == "size") { size = value; }
- if(key == "candidate") { candidatefile = value; }
- if(key == "search") { search = value; }
- if(key == "ksize") { ksize = value; }
- if(key == "align") { align = value; }
- if(key == "match") { match = value; }
- if(key == "mismatch") { mismatch = value; }
- if(key == "gapopen") { gapopen = value; }
- if(key == "gapextend") { gapextend = value; }
- if(key == "start") { startPos = value; }
- if(key == "end") { endPos = value; }
- if(key == "maxambig") { maxAmbig = value; }
- if(key == "maxhomop") { maxHomoPolymer = value; }
- if(key == "minlength") { minLength = value; }
- if(key == "maxlength") { maxLength = value; }
- if(key == "flip" ) { flip = value; }
- if(key == "oligos" ) { oligoFile = value; }
-
- if(key == "line") {//stores lines to be used in a vector
- lines.clear();
- labels.clear();
- line = value;
- label = "";
- if(line != "all") { splitAtDash(value, lines); allLines = 0; }
- else { allLines = 1; }
- }
-
- if(key == "label") {//stores lines to be used in a vector
- labels.clear();
- lines.clear();
- label = value;
- line = "";
- if(label != "all") { splitAtDash(value, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- if(key == "groups") {//stores groups to be used in a vector
- Groups.clear();
- groups = value;
- splitAtDash(value, Groups);
- }
-
- }
-
- //saves the last parameter ==> this seems silly...
- value = optionText;
- splitAtEquals(key, value);
- if(key == "phylip") { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; }
- if(key == "column") { columnfile = value; inputFileName = value; fileroot = value; format = "column"; }
- if(key == "list") { listfile = value; inputFileName = value; fileroot = value; format = "list"; }
- if(key == "rabund") { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; }
- if(key == "sabund") { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; }
- if(key == "fasta") { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; }
- if(key == "tree") { treefile = value; inputFileName = value; fileroot = value; format = "tree"; }
- if(key == "shared") { sharedfile = value; inputFileName = value; fileroot = value; format = "sharedfile"; }
- if(key == "name") { namefile = value; }
- if(key == "order") { orderfile = value; }
- if(key == "group") { groupfile = value; }
- if(key == "cutoff") { cutoff = value; }
- if(key == "precision") { precision = value; }
- if(key == "iters") { iters = value; }
- if(key == "jumble") { jumble = value; }
- if(key == "freq") { freq = value; }
- if(key == "method") { method = value; }
- if(key == "fileroot") { fileroot = value; }
- if(key == "abund") { abund = value; }
- if(key == "random") { randomtree = value; }
- if(key == "calc") { calc = value; }
- if(key == "step") { step = value; }
- if(key == "form") { form = value; }
- if(key == "sorted") { sorted = value; }
- if(key == "vertical") { vertical = value; }
- if(key == "trump") { trump = value; }
- if(key == "hard") { hard = value; }
- if(key == "soft") { soft = value; }
- if(key == "scale") { scale = value; }
- if(key == "countends") { countends = value; }
- if(key == "processors") { processors = value; }
- if(key == "size") { size = value; }
- if(key == "candidate") { candidatefile = value; }
- if(key == "search") { search = value; }
- if(key == "ksize") { ksize = value; }
- if(key == "align") { align = value; }
- if(key == "match") { match = value; }
- if(key == "mismatch") { mismatch = value; }
- if(key == "gapopen") { gapopen = value; }
- if(key == "gapextend") { gapextend = value; }
- if(key == "start") { startPos = value; }
- if(key == "end") { endPos = value; }
- if(key == "maxambig") { maxAmbig = value; }
- if(key == "maxhomop") { maxHomoPolymer = value; }
- if(key == "minlength") { minLength = value; }
- if(key == "maxlength") { maxLength = value; }
- if(key == "flip" ) { flip = value; }
- if(key == "oligos" ) { oligoFile = value; }
-
-
- if(key == "line") {//stores lines to be used in a vector
- lines.clear();
- labels.clear();
- line = value;
- label = "";
- if(line != "all") { splitAtDash(value, lines); allLines = 0; }
- else { allLines = 1; }
- }
-
- if(key == "label") {//stores lines to be used in a vector
- labels.clear();
- lines.clear();
- label = value;
- line = "";
- if(label != "all") { splitAtDash(value, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- if(key == "groups") {//stores groups to be used in a vector
- Groups.clear();
- groups = value;
- splitAtDash(value, Groups);
- }
- }
-
- //set format for shared
- if ((listfile != "") && (groupfile != "")) { format = "shared"; }
- if ((phylipfile != "") && (groupfile != "")) { format = "matrix"; }
-
- //set default value for cutoff
- if (commandName == "dist.seqs") { format = "fasta"; inputFileName = fastafile; fileroot = fastafile; }
-
- //input defaults for calculators
- if(commandName == "collect.single") {
-
- if((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if(commandName == "rarefaction.single") {
- if((calc == "default") || (calc == "")) { calc = "sobs"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if(commandName == "collect.shared") {
- if((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if(commandName == "summary.single") {
- if((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if(commandName == "summary.shared") {
- if((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if(commandName == "rarefaction.shared") {
- if((calc == "default") || (calc == "")) { calc = "sharedobserved"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if(commandName == "dist.seqs") {
- if((calc == "default") || (calc == "")) { calc = "onegap"; }
- if(countends == "") { countends = "T"; }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if(commandName == "venn") {
- if((calc == "default") || (calc == "")) {
- if(format == "list") { calc = "sobs"; }
- else { calc = "sharedsobs"; }
- }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
- if((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared") || (commandName == "heatmap.sim")) {
- if((calc == "default") || (calc == "")) {
- calc = "jclass-thetayc";
- }
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }
-
- if(commandName == "filter.seqs"){
- if(trump == "" && vertical == "" && hard == "" && soft == ""){
- trump = '.';
- }
-
- }
-
- //ifyou have done a read.otu with a groupfile but don't want to use it anymore because you want to do single commands
- if((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")) {
- if(listfile != "") { format = "list"; }
- else if(sabundfile != "") { format = "sabund"; }
- else if(rabundfile != "") { format = "rabund"; }
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function parseGlobalData. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
-/*******************************************************/
-
/******************************************************/
// These functions give you the option parameters of the commands
string GlobalData::getPhylipFile() { return phylipfile; }
string GlobalData::getTreeFile() { return treefile; }
string GlobalData::getSharedFile() { return sharedfile; }
string GlobalData::getFastaFile() { return fastafile; }
-string GlobalData::getCutOff() { return cutoff; }
string GlobalData::getFormat() { return format; }
-string GlobalData::getPrecision() { return precision; }
-string GlobalData::getMethod() { return method; }
-string GlobalData::getFileRoot() { return fileroot; }
-string GlobalData::getIters() { return iters; }
-string GlobalData::getJumble() { return jumble; }
-string GlobalData::getFreq() { return freq; }
-string GlobalData::getAbund() { return abund; }
-string GlobalData::getRandomTree() { return randomtree; }
-string GlobalData::getGroups() { return groups; }
-string GlobalData::getStep() { return step; }
-string GlobalData::getForm() { return form; }
-string GlobalData::getSorted() { return sorted; }
-string GlobalData::getVertical() { return vertical; }
-string GlobalData::getTrump() { return trump; }
-string GlobalData::getSoft() { return soft; }
-string GlobalData::getHard() { return hard; }
-string GlobalData::getScale() { return scale; }
-string GlobalData::getCountEnds() { return countends; }
-string GlobalData::getProcessors() { return processors; }
-string GlobalData::getSize() { return size; }
string GlobalData::getCandidateFile() { return candidatefile; }
-string GlobalData::getSearch() { return search; }
-string GlobalData::getKSize() { return ksize; }
-string GlobalData::getAlign() { return align; }
-string GlobalData::getMatch() { return match; }
-string GlobalData::getMismatch() { return mismatch; }
-string GlobalData::getGapopen() { return gapopen; }
-string GlobalData::getGapextend() { return gapextend; }
-string GlobalData::getStartPos() { return startPos; }
-string GlobalData::getEndPos() { return endPos; }
-string GlobalData::getMaxAmbig() { return maxAmbig; }
-string GlobalData::getMaxHomoPolymer() { return maxHomoPolymer; }
-string GlobalData::getMinLength() { return minLength; }
-string GlobalData::getMaxLength() { return maxLength; }
-string GlobalData::getFlip() { return flip; }
-string GlobalData::getOligosFile() { return oligoFile; }
void GlobalData::setListFile(string file) { listfile = file; inputFileName = file; }
+void GlobalData::setFastaFile(string file) { fastafile = file; inputFileName = file; }
+void GlobalData::setTreeFile(string file) { treefile = file; inputFileName = file; }
+void GlobalData::setCandidateFile(string file) { candidatefile = file; }
void GlobalData::setRabundFile(string file) { rabundfile = file; inputFileName = file; }
void GlobalData::setSabundFile(string file) { sabundfile = file; inputFileName = file; }
void GlobalData::setPhylipFile(string file) { phylipfile = file; inputFileName = file; }
void GlobalData::setColumnFile(string file) { columnfile = file; inputFileName = file; }
void GlobalData::setGroupFile(string file) { groupfile = file; }
-void GlobalData::setSharedFile(string file) { sharedfile = file; inputFileName = file; fileroot = file; }
+void GlobalData::setSharedFile(string file) { sharedfile = file; inputFileName = file; }
void GlobalData::setNameFile(string file) { namefile = file; }
+void GlobalData::setOrderFile(string file) { orderfile = file; }
void GlobalData::setFormat(string Format) { format = Format; }
-void GlobalData::setRandomTree(string Random) { randomtree = Random; }
-void GlobalData::setGroups(string g) { groups = g; }
-void GlobalData::setCalc(string Calc) { calc = Calc; }
-void GlobalData::setCountEnds(string e) { countends = e; }
-void GlobalData::setProcessors(string p) { processors = p; }
/*******************************************************/
/******************************************************/
GlobalData::GlobalData() {
//option definitions should go here...
- helpRequest = "";
clear();
gListVector = NULL;
gSparseMatrix = NULL;
treefile = "";
sharedfile = "";
candidatefile = "";
- cutoff = "10.00";
- format = "";
- precision = "100";
- iters = "1000";
- line = "";
- label = "";
- groups = "";
- jumble = "1"; //0 means don't jumble, 1 means jumble.
- randomtree = ""; //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
- freq = "100";
- method = "furthest";
- fileroot = "";
- abund = "10";
- step = "0.01";
- form = "integral";
- sorted = "T"; //F means don't sort, T means sort.
- vertical = "F";
- trump = "";
- hard = "";
- soft = "";
- scale = "log10";
- countends = "T"; //yes
- processors = "1";
- size = "0";
- search = "kmer";
- ksize = "8";
- align = "needleman";
- match = "1.0";
- mismatch = "-1.0";
- gapopen = "-1.0";
- gapextend = "-2.0";
- startPos = "-1";
- endPos = "-1";
- maxAmbig = "-1";
- maxHomoPolymer = "-1";
- minLength = "-1";
- maxLength = "-1";
- flip = "0";
- oligoFile = "";
-}
-
-//*******************************************************/
-
-/******************************************************/
-void GlobalData::reset() {
- label = "";
- line = "";
- cutoff = "10.00";
- precision = "100";
- iters = "1000";
- groups = "";
- jumble = "1"; //0 means don't jumble, 1 means jumble.
- sorted = "T"; //F means don't sort, T means sort.
- randomtree = ""; //"" means user will enter some user trees, "outputfile" means they just want the random tree distribution to be outputted to outputfile.
- freq = "100";
- method = "furthest";
- calc = "";
- abund = "10";
- step = "0.01";
- form = "integral";
- countends = "T";
- processors = "1";
- size = "0";
- search = "kmer";
- ksize = "8";
- align = "needleman";
- match = "1.0";
- mismatch = "-1.0";
- gapopen = "-1.0";
- gapextend = "-2.0";
- vertical = "";
- trump = "";
- hard = "";
- soft = "";
- startPos = "-1";
- endPos = "-1";
- maxAmbig = "-1";
- maxHomoPolymer = "-1";
- minLength = "-1";
- maxLength = "-1";
- flip = "0";
- oligoFile = "";
-
}
/*******************************************************/
/******************************************************/
-GlobalData::~GlobalData() {
- _uniqueInstance = 0;
- if(gListVector != NULL) { delete gListVector; }
- if(gSparseMatrix != NULL) { delete gSparseMatrix; }
- if(gorder != NULL) { delete gorder; }
-}
-/*******************************************************/
-
-/*******************************************************/
-void GlobalData::parseTreeFile() {
- //Why is THIS in GlobalData??? - PDS
-
- //only takes names from the first tree and assumes that all trees use the same names.
- try {
- string filename = treefile;
- ifstream filehandle;
- openInputFile(filename, filehandle);
- int c, comment;
- comment = 0;
-
- //ifyou are not a nexus file
- if((c = filehandle.peek()) != '#') {
- while((c = filehandle.peek()) != ';') {
- while ((c = filehandle.peek()) != ';') {
- // get past comments
- if(c == '[') {
- comment = 1;
- }
- if(c == ']'){
- comment = 0;
- }
- if((c == '(') && (comment != 1)){ break; }
- filehandle.get();
- }
-
- readTreeString(filehandle);
- }
- //ifyou are a nexus file
- }else if((c = filehandle.peek()) == '#') {
- string holder = "";
-
- // get past comments
- while(holder != "translate" && holder != "Translate"){
- if(holder == "[" || holder == "[!"){
- comment = 1;
- }
- if(holder == "]"){
- comment = 0;
- }
- filehandle >> holder;
-
- //ifthere is no translate then you must read tree string otherwise use translate to get names
- if(holder == "tree" && comment != 1){
- //pass over the "tree rep.6878900 = "
- while (((c = filehandle.get()) != '(') && ((c = filehandle.peek()) != EOF)) {;}
-
- if(c == EOF) { break; }
- filehandle.putback(c); //put back first ( of tree.
- readTreeString(filehandle);
- break;
- }
- }
-
- //use nexus translation rather than parsing tree to save time
- if((holder == "translate") || (holder == "Translate")) {
-
- string number, name, h;
- h = ""; // so it enters the loop the first time
- while((h != ";") && (number != ";")) {
- filehandle >> number;
- filehandle >> name;
-
- //c = , until done with translation then c = ;
- h = name.substr(name.length()-1, name.length());
- name.erase(name.end()-1); //erase the comma
- Treenames.push_back(number);
- }
- if(number == ";") { Treenames.pop_back(); } //in case ';' from translation is on next line instead of next to last name
- }
- }
-
+void GlobalData::newRead() {
+ try{
+ clear();
+ gGroupmap = NULL;
+ gListVector = NULL;
+ gSparseMatrix = NULL;
+ gTree.clear();
+ Treenames.clear();
+ labels.clear(); lines.clear(); Groups.clear();
+ allLines = 1;
+ runParse = true;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function newRead. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
}
catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ cout << "An unknown error has occurred in the GlobalData class function newRead. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
exit(1);
- }
+ }
}
-/*******************************************************/
-
-/*******************************************************/
-void GlobalData::readTreeString(ifstream& filehandle) {
- try {
- int c;
- string name; //k
-
- while((c = filehandle.peek()) != ';') {
- //ifyou are a name
- if((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != '\t') && (c != 32)) { //32 is space
- name = "";
- c = filehandle.get();
- // k = c;
-//cout << k << endl;
- while ((c != '(') && (c != ')') && (c != ',') && (c != ':') && (c != '\n') && (c != 32) && (c != '\t')) {
- name += c;
- c = filehandle.get();
- // k = c;
-//cout << " in name while " << k << endl;
- }
-
-//cout << "name = " << name << endl;
- Treenames.push_back(name);
- filehandle.putback(c);
-//k = c;
-//cout << " after putback" << k << endl;
- }
-
- if(c == ':') { //read until you reach the end of the branch length
- while ((c != '(') && (c != ')') && (c != ',') && (c != ';') && (c != '\n') && (c != '\t') && (c != 32)) {
- c = filehandle.get();
- // k = c;
- //cout << " in branch while " << k << endl;
- }
- filehandle.putback(c);
- }
- c = filehandle.get();
- if(c == ';') { break; }
- // k = c;
-//cout << k << endl;
- }
- }
- catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GlobalData class Function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the GlobalData class function parseTreeFile. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
+//******************************************************/
+/******************************************************/
+GlobalData::~GlobalData() {
+ _uniqueInstance = 0;
+ if(gListVector != NULL) { delete gListVector; }
+ if(gSparseMatrix != NULL) { delete gSparseMatrix; }
+ if(gorder != NULL) { delete gorder; }
+}
/*******************************************************/
/*******************************************************/
projects / mothur.git / blobdiff