clear();
gGroupmap = NULL;
gTree.clear();
+ Treenames.clear();
labels.clear(); lines.clear(); groups.clear();
allLines = 1;
}
if(gorder != NULL) { delete gorder; }
}
/*******************************************************/
+
+/*******************************************************/
+void GlobalData::parseTreeFile() {
+ //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;
+
+ //if you 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);
+ }
+ //if you 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;
+
+ //if there 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")) {
+cout << "there is a translate " << endl;
+ 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
+ }
+ }
+
+ }
+ 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);
+ }
+}
+/*******************************************************/
+
+/*******************************************************/
+void GlobalData::readTreeString(ifstream& filehandle) {
+ try {
+ int c;
+ string name; //k
+
+ while((c = filehandle.peek()) != ';') {
+ //if you 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);
+ }
+}
+
+/*******************************************************/
+
+/*******************************************************/
+
+
vector<string> Estimators, Groups; //holds estimators to be used
set<int> lines; //hold lines to be used
set<string> labels; //holds labels to be used
+ vector<string> Treenames;
string getPhylipFile();
string getColumnFile();
void clearAbund();
void parseGlobalData(string, string);
+
+ void parseTreeFile(); //parses through tree file to find names of nodes and number of them
+ //this is required in case user has sequences in the names file that are
+ //not included in the tree.
+ //only takes names from the first tree in the tree file and assumes that all trees use the same names.
+
private:
string phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, orderfile, fastafile, treefile, sharedfile, line, label, randomtree, groups;
GlobalData();
~GlobalData();
void reset(); //clears all non filename parameters
+ void readTreeString(ifstream&);
}else if (globaldata->helpRequest == "collect.single") {
cout << "The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. " << "\n";
cout << "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";
- cout << "The collect.single command parameters are label, line, freq, calc. No parameters are required, but you may not use " << "\n";
+ cout << "The collect.single command parameters are label, line, freq, calc and abund. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The collect.single command should be in the following format: " << "\n";
cout << "collect.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
- cout << "Example collect(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, calc=sobs-chao-ace-jack)." << "\n";
+ cout << "Example collect(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-chao-ace-jack)." << "\n";
cout << "The default values for freq is 100, and calc are sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson." << "\n";
cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
}else if (globaldata->helpRequest == "collect.shared") {
cout << "The collect.shared command can only be executed after a successful read.otu command." << "\n";
- cout << "The collect.shared command parameters are label, line, freq, jumble, calc. No parameters are required, but you may not use " << "\n";
+ cout << "The collect.shared command parameters are label, line, freq, jumble, calc and groups. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The collect.shared command should be in the following format: " << "\n";
- cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, jumble=yourJumble, calc=yourEstimators)." << "\n";
- cout << "Example collect.shared(label=unique-.01-.03, line=0,5,10, freq=10, jumble=1, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
+ cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
+ cout << "Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, jumble=1, groups=B-C, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
cout << "The default values for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100 and calc are sharedsobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
}else if (globaldata->helpRequest == "get.group") {
cout << "The get.group command can only be executed after a successful read.otu command of a group file." << "\n";
}else if (globaldata->helpRequest == "rarefaction.single") {
cout << "The rarefaction.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
cout << "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";
- cout << "The rarefaction.single command parameters are label, line, iters, freq, calc. No parameters are required, but you may not use " << "\n";
+ cout << "The rarefaction.single command parameters are label, line, iters, freq, calc and abund. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The rarefaction.single command should be in the following format: " << "\n";
cout << "rarefaction.single(label=yourLabel, line=yourLines, iters=yourIters, freq=yourFreq, calc=yourEstimators)." << "\n";
- cout << "Example rarefaction.single(label=unique-.01-.03, line=0,5,10, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson)." << "\n";
+ cout << "Example rarefaction.single(label=unique-.01-.03, line=0-5-10, iters=10000, freq=10, calc=sobs-rchao-race-rjack-rbootstrap-rshannon-rnpshannon-rsimpson)." << "\n";
cout << "The default values for iters is 1000, freq is 100, and calc is rarefaction which calculates the rarefaction curve for the observed richness." << "\n";
cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
}else if (globaldata->helpRequest == "rarefaction.shared") {
cout << "The rarefaction.shared command can only be executed after a successful read.otu command." << "\n";
- cout << "The rarefaction.shared command parameters are label, line, iters, jumble and calc. No parameters are required, but you may not use " << "\n";
+ cout << "The rarefaction.shared command parameters are label, line, iters, jumble, groups and calc. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The rarefaction command should be in the following format: " << "\n";
- cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, jumble=yourJumble, calc=yourEstimators)." << "\n";
- cout << "Example rarefaction.shared(label=unique-.01-.03, line=0,5,10, iters=10000, jumble=1, calc=sharedobserved)." << "\n";
+ cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
+ cout << "Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, jumble=1, groups=B-C, calc=sharedobserved)." << "\n";
cout << "The default values for iters is 1000, jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble), freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness." << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
}else if (globaldata->helpRequest == "summary.single") {
cout << "The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
cout << "The summary.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n";
- cout << "The summary.single command parameters are label, line, calc. No parameters are required, but you may not use " << "\n";
+ cout << "The summary.single command parameters are label, line, calc, abund. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The summary.single command should be in the following format: " << "\n";
cout << "summary.single(label=yourLabel, line=yourLines, calc=yourEstimators)." << "\n";
cout << "Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson)." << "\n";
cout << "The summary.shared command can only be executed after a successful read.otu command." << "\n";
cout << "The summary.shared command parameters are label, line, jumble and calc. No parameters are required, but you may not use " << "\n";
cout << "both the line and label parameters at the same time. The summary.shared command should be in the following format: " << "\n";
- cout << "summary.shared(label=yourLabel, line=yourLines, jumble=yourJumble, calc=yourEstimators)." << "\n";
- cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, jumble=1, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
+ cout << "summary.shared(label=yourLabel, line=yourLines, jumble=yourJumble, calc=yourEstimators, groups=yourGroups)." << "\n";
+ cout << "Example summary.shared(label=unique-.01-.03, line=0,5,10, jumble=1, groups=B-C, calc=sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN)." << "\n";
cout << "The default value for jumble is 1 (meaning jumble, if it’s set to 0 then it will not jumble) and calc is sharedsobs-sharedChao-sharedAce-sharedJabund-sharedSorensonAbund-sharedJclass-sharedSorClass-sharedJest-sharedSorEst-SharedThetaYC-SharedThetaN" << "\n";
+ cout << "The default value for groups is all the groups in your groupfile." << "\n";
cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
+ cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
}else if (globaldata->helpRequest == "parsimony") {
cout << "The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter." << "\n";
if (numGroups == 0) {
//get score for all users groups
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- groups.push_back(tmap->namesOfGroups[i]);
+ if (tmap->namesOfGroups[i] != "xxx") {
+ groups.push_back(tmap->namesOfGroups[i]);
+ }
}
}else {
for (int i = 0; i < globaldata->Groups.size(); i++) {
if (globaldata->Groups.size() == 0) {
cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i] + "-";
+ if (tmap->namesOfGroups[i] != "xxx") {
+ allGroups += tmap->namesOfGroups[i] + "-";
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ }
}
allGroups = allGroups.substr(0, allGroups.length()-1);
}else {
}else{//user has enter "all" and wants the default groups
globaldata->Groups.clear();
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i] + "-";
+ if (tmap->namesOfGroups[i] != "xxx") {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ allGroups += tmap->namesOfGroups[i] + "-";
+ }
}
allGroups = allGroups.substr(0, allGroups.length()-1);
globaldata->setGroups("");
}
}else {
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- allGroups += tmap->namesOfGroups[i] + "-";
+ if (tmap->namesOfGroups[i] != "xxx") {
+ allGroups += tmap->namesOfGroups[i] + "-";
+ }
}
allGroups = allGroups.substr(0, allGroups.length()-1);
numGroups = 1;
}
}
-
/***********************************************************************/
/***********************************************************************/
-
//Child Classes Below
/***********************************************************************/
int ReadNewickTree::read() {
try {
+ holder = "";
int c, error;
int comment = 0;
//if you are not a nexus file
if ((c = filehandle.peek()) != '#') {
while((c = filehandle.peek()) != EOF) {
+ while ((c = filehandle.peek()) != EOF) {
+ // get past comments
+ if(c == '[') {
+ comment = 1;
+ }
+ if(c == ']'){
+ comment = 0;
+ }
+ if((c == '(') && (comment != 1)){ break; }
+ filehandle.get();
+ }
+
//make new tree
T = new Tree();
numNodes = T->getNumNodes();
globaldata->gTree.push_back(T);
}
}
+
+ if (error != 0) { readOk = error; }
return readOk;
}
catch(exception& e) {
n = numLeaves; //number of leaves / sequences, we want node 1 to start where the leaves left off
lc = readNewickInt(filehandle, n, T);
- if (lc == -1) { return -1; } //reports an error in reading
+ if (lc == -1) { cout << "error with lc" << endl; return -1; } //reports an error in reading
if(filehandle.peek()==','){
readSpecialChar(filehandle,',',"comma");
}
if(rooted != 1){
rc = readNewickInt(filehandle, n, T);
- if (rc == -1) { return -1; } //reports an error in reading
+ if (rc == -1) { cout << "error with rc" << endl; return -1; } //reports an error in reading
if(filehandle.peek() == ')'){
readSpecialChar(filehandle,')',"right parenthesis");
}
}
int blen = 0;
- if(d == ':') { blen = 1; }
+ if(d == ':') { blen = 1; }
f.putback(d);
int n1 = T->getIndex(name);
//adds sequence names that are not in group file to the "xxx" group
- if(n1 == -1) {
- cerr << "Name: " << name << " not found in your groupfile. \n"; readOk = -1; return n1;
+ if(group == "not found") {
+ cout << "Name: " << name << " is not in your groupfile, and will be disregarded. \n"; //readOk = -1; return n1;
- //globaldata->gTreemap->namesOfSeqs.push_back(name);
- //globaldata->gTreemap->treemap[name].groupname = "xxx";
- //globaldata->gTreemap->treemap[name].vectorIndex = (globaldata->gTreemap->namesOfSeqs.size() - 1);
+ globaldata->gTreemap->namesOfSeqs.push_back(name);
+ globaldata->gTreemap->treemap[name].groupname = "xxx";
- //map<string, int>::iterator it;
- //it = globaldata->gTreemap->seqsPerGroup.find("xxx");
- //if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
- // globaldata->gTreemap->namesOfGroups.push_back("xxx");
- // globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
- //}else {
- // globaldata->gTreemap->seqsPerGroup["xxx"]++;
- //}
+ map<string, int>::iterator it;
+ it = globaldata->gTreemap->seqsPerGroup.find("xxx");
+ if (it == globaldata->gTreemap->seqsPerGroup.end()) { //its a new group
+ globaldata->gTreemap->namesOfGroups.push_back("xxx");
+ globaldata->gTreemap->seqsPerGroup["xxx"] = 1;
+ }else {
+ globaldata->gTreemap->seqsPerGroup["xxx"]++;
+ }
- //find index in tree of name
- //n1 = T->getIndex(name);
- //group = "xxx";
- //numLeaves++;
- //numNodes = 2*numLeaves - 1;
+ group = "xxx";
}
T->tree[n1].setGroup(group);
//memory leak prevention
//if (globaldata->gTreemap != NULL) { delete globaldata->gTreemap; }
globaldata->gTreemap = treeMap;
+
+ //get names in tree
+ globaldata->parseTreeFile();
read = new ReadNewickTree(filename);
T[i]->assembleTree();
}
+ //output any names that are in names file but not in tree
+ if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
+ for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
+ //is that name in the tree?
+ int count = 0;
+ for (int j = 0; j < globaldata->Treenames.size(); j++) {
+ if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
+ count++;
+ }
+
+ //then you did not find it so report it
+ if (count == globaldata->Treenames.size()) {
+ cout << treeMap->namesOfSeqs[i] << " is in your namefile and not in your tree. It will be disregarded." << endl;
+ }
+ }
+ }
+
return 0;
}
catch(exception& e) {
/*****************************************************************/
Tree::Tree() {
try {
-
globaldata = GlobalData::getInstance();
- numLeaves = globaldata->gTreemap->getNumSeqs();
+
+ numLeaves = globaldata->Treenames.size();
numNodes = 2*numLeaves - 1;
tree.resize(numNodes);
for (int i = 0; i < numNodes; i++) {
//initialize leaf nodes
if (i <= (numLeaves-1)) {
- tree[i].setName(globaldata->gTreemap->namesOfSeqs[i]);
- tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i]));
+ tree[i].setName(globaldata->Treenames[i]);
+ tree[i].setGroup(globaldata->gTreemap->getGroup(globaldata->Treenames[i]));
//set pcount and pGroup for groupname to 1.
- tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
- tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->gTreemap->namesOfSeqs[i])] = 1;
+ tree[i].pcount[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
+ tree[i].pGroups[globaldata->gTreemap->getGroup(globaldata->Treenames[i])] = 1;
//Treemap knows name, group and index to speed up search
- globaldata->gTreemap->setIndex(globaldata->gTreemap->namesOfSeqs[i], i);
+ globaldata->gTreemap->setIndex(globaldata->Treenames[i], i);
//intialize non leaf nodes
}else if (i > (numLeaves-1)) {
try {
for (int i = 0; i < numNodes; i++) {
//you found the root
- if (tree[i].getParent() == -1) { return i; }
+ if (tree[i].getParent() == -1) { return i; }
}
return -1;
}
}
/************************************************************/
void TreeMap::setIndex(string seq, int index) {
- treemap[seq].vectorIndex = index;
+ it = treemap.find(seq);
+ if (it != treemap.end()) { //sequence name was in group file
+ treemap[seq].vectorIndex = index;
+ }else {
+ treemap[seq].vectorIndex = index;
+ treemap[seq].groupname = "not found";
+ }
}
/************************************************************/
int TreeMap::getIndex(string seq) {
if (globaldata->Groups.size() == 0) {
cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i] + "-";
+ if (tmap->namesOfGroups[i] != "xxx") {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ allGroups += tmap->namesOfGroups[i] + "-";
+ }
}
allGroups = allGroups.substr(0, allGroups.length()-1);
}else {
}else{//user has enter "all" and wants the default groups
globaldata->Groups.clear();
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
- numGroups++;
- allGroups += tmap->namesOfGroups[i] + "-";
+ if (tmap->namesOfGroups[i] != "xxx") {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ allGroups += tmap->namesOfGroups[i] + "-";
+ }
}
allGroups = allGroups.substr(0, allGroups.length()-1);
globaldata->setGroups("");
}
}else {
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- allGroups += tmap->namesOfGroups[i] + "-";
+ if (tmap->namesOfGroups[i] != "xxx") {
+ allGroups += tmap->namesOfGroups[i] + "-";
+ }
}
allGroups = allGroups.substr(0, allGroups.length()-1);
numGroups = 1;
/***********************************************************/
void UnifracWeightedCommand::setGroups() {
try {
+ numGroups = 0;
//if the user has not entered specific groups to analyze then do them all
if (globaldata->Groups.size() == 0) {
- numGroups = tmap->getNumGroups();
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ for (int i=0; i < tmap->getNumGroups(); i++) {
+ if (tmap->namesOfGroups[i] != "xxx") {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ }
}
}else {
if (globaldata->getGroups() != "all") {
//if the user only entered invalid groups
if (globaldata->Groups.size() == 0) {
- numGroups = tmap->getNumGroups();
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ for (int i=0; i < tmap->getNumGroups(); i++) {
+ if (tmap->namesOfGroups[i] != "xxx") {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ }
}
cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
}else if (globaldata->Groups.size() == 1) {
cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
- numGroups = tmap->getNumGroups();
globaldata->Groups.clear();
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ for (int i=0; i < tmap->getNumGroups(); i++) {
+ if (tmap->namesOfGroups[i] != "xxx") {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ }
}
}else { numGroups = globaldata->Groups.size(); }
}else { //users wants all groups
- numGroups = tmap->getNumGroups();
globaldata->Groups.clear();
globaldata->setGroups("");
- for (int i=0; i < numGroups; i++) {
- globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ for (int i=0; i < tmap->getNumGroups(); i++) {
+ if (tmap->namesOfGroups[i] != "xxx") {
+ globaldata->Groups.push_back(tmap->namesOfGroups[i]);
+ numGroups++;
+ }
}
}
}
if (numGroups == 0) {
//get score for all users groups
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- groups.push_back(tmap->namesOfGroups[i]);
+ if (tmap->namesOfGroups[i] != "xxx") {
+ groups.push_back(tmap->namesOfGroups[i]);
+ }
}
}else {
for (int i = 0; i < globaldata->Groups.size(); i++) {
if (numGroups == 0) {
//get score for all users groups
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
- groups.push_back(tmap->namesOfGroups[i]);
+ if (tmap->namesOfGroups[i] != "xxx") {
+ groups.push_back(tmap->namesOfGroups[i]);
+ }
}
}else {
for (int i = 0; i < globaldata->Groups.size(); i++) {
try {
//{"parameter1","parameter2",...,"last parameter"};
- string readdistArray[] = {"phylip","column", "name","cutoff","precision"};
+ string readdistArray[] = {"phylip","column","name","cutoff","precision","group"};
commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
- string readotuArray[] = {"list","order","shared", "line", "label","group","shared", "sabund", "rabund"};
+ string readotuArray[] = {"list","order","shared", "line", "label","group","sabund", "rabund"};
commandParameters["read.otu"] = addParameters(readotuArray, sizeof(readotuArray)/sizeof(string));
string readtreeArray[] = {"tree","group"};
string deconvoluteArray[] = {"fasta"};
commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
- string collectsingleArray[] = {"freq","line","label","calc","precision","abund"};
+ string collectsingleArray[] = {"freq","line","label","calc","abund"};
commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
string collectsharedArray[] = {"jumble","freq","line","label","calc","groups"};
string rarefactionsingleArray[] = {"iters","freq","line","label","calc","abund"};
commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
- string rarefactionsharedArray[] = {"iters","jumble","line","label","calc"};
+ string rarefactionsharedArray[] = {"iters","jumble","line","label","calc","groups"};
commandParameters["rarefaction.shared"] = addParameters(rarefactionsharedArray, sizeof(rarefactionsharedArray)/sizeof(string));
string libshuffArray[] = {"iters","groups","step","form","cutoff"};
string summarysingleArray[] = {"line","label","calc","abund"};
commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
- string summarysharedArray[] = {"jumble","line","label","calc"};
+ string summarysharedArray[] = {"jumble","line","label","calc","groups"};
commandParameters["summary.shared"] = addParameters(summarysharedArray, sizeof(summarysharedArray)/sizeof(string));
- string parsimonyArray[] = {"random","group","iters"};
+ string parsimonyArray[] = {"random","groups","iters"};
commandParameters["parsimony"] = addParameters(parsimonyArray, sizeof(parsimonyArray)/sizeof(string));
- string unifracWeightedArray[] = {"group","iters"};
+ string unifracWeightedArray[] = {"groups","iters"};
commandParameters["unifrac.weighted"] = addParameters(unifracWeightedArray, sizeof(unifracWeightedArray)/sizeof(string));
- string unifracUnweightedArray[] = {"group","iters"};
+ string unifracUnweightedArray[] = {"groups","iters"};
commandParameters["unifrac.unweighted"] = addParameters(unifracUnweightedArray, sizeof(unifracUnweightedArray)/sizeof(string));
- string heatmapArray[] = {"group","line","label","sorted"};
+ string heatmapArray[] = {"groups","line","label","sorted"};
commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
string vennArray[] = {"groups","line","label","calc"};
string freqArray[] = {">","1", "<","NA", "between"};
parameterRanges["freq"] = addParameters(freqArray, rangeSize);
- string lineArray[] = {">=","1", "<","NA", "between"};
- parameterRanges["line"] = addParameters(lineArray, rangeSize);
+ //string lineArray[] = {">=","1", "<","NA", "between"};
+ //parameterRanges["line"] = addParameters(lineArray, rangeSize);
string abundArray[] = {">=","5", "<","NA", "between"};
parameterRanges["abund"] = addParameters(abundArray, rangeSize);
projects / mothur.git / commitdiff