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();
+ labels.clear(); lines.clear(); Groups.clear();
allLines = 1;
}
cutoff = "1.0";
}
+ //set default value for cutoff
+ if (commandName == "dist.seqs") { cutoff = "1.0"; }
+
string key, value;
//reads in parameters and values
if((optionText != "") && (commandName != "help")){
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 == "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 == "step") { step = value; }
if (key == "form") { form = value; }
if (key == "sorted") { sorted = value; }
- if (key == "scaler") { scaler = 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 == "line") {//stores lines to be used in a set
+ if (key == "line") {//stores lines to be used in a vector
lines.clear();
labels.clear();
line = value;
label = "";
- splitAtDash(value, lines);
- allLines = 0;
+ if (line != "all") { splitAtDash(value, lines); allLines = 0; }
+ else { allLines = 1; }
}
- if (key == "label") {//stores labels to be used in a set
+
+ if (key == "label") {//stores lines to be used in a vector
labels.clear();
lines.clear();
label = value;
line = "";
- splitAtDash(value, labels);
- allLines = 0;
+ if (label != "all") { splitAtDash(value, labels); allLines = 0; }
+ else { allLines = 1; }
}
if (key == "groups") {//stores groups to be used in a vector
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 == "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 == "step") { step = value; }
if (key == "form") { form = value; }
if (key == "sorted") { sorted = value; }
- if (key == "scaler") { scaler = 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 == "line") {//stores lines to be used in a vector
lines.clear();
//input defaults for calculators
if (commandName == "collect.single") {
- if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson-geom-qstat-logsd-bergerparker-bstick"; }
+
+ if ((calc == "default") || (calc == "")) { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
splitAtDash(calc, Estimators);
}
if (commandName == "collect.shared") {
- if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+ 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-bootstrap-shannon-npshannon-simpson-geom-logsd-qstat-bergerparker-bstick"; }
+ 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-sharedjabund-sharedsorensonabund-sharedjclass-sharedsorclass-sharedjest-sharedsorest-sharedthetayc-sharedthetan-sharedkstest-sharedbdiversity"; }
+ if ((calc == "default") || (calc == "")) { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
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"; }
Estimators.clear();
splitAtDash(calc, Estimators);
}
- if (commandName == "tree.groups") {
- if (calc != "") {
- Estimators.clear();
- splitAtDash(calc, Estimators);
- }else { cout << "You have not specified any calculators." << endl; }
+ if ((commandName == "tree.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.shared")) {
+ if ((calc == "default") || (calc == "")) {
+ calc = "jclass-thetayc";
+ }
+ Estimators.clear();
+ splitAtDash(calc, Estimators);
}
+
+ if(commandName == "filter.seqs"){
+ if(trump == "" && vertical == "" && hard == "" && soft == ""){
+ trump = '.';
+ }
+ }
//if you 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")) {
string GlobalData::getStep() { return step; }
string GlobalData::getForm() { return form; }
string GlobalData::getSorted() { return sorted; }
-string GlobalData::getScaler() { return scaler; }
-void GlobalData::setListFile(string file) { listfile = file; inputFileName = 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;}
+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; }
+
+
+void GlobalData::setListFile(string file) { listfile = file; inputFileName = 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::setNameFile(string file) { namefile = 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; }
+
/*******************************************************/
//option definitions should go here...
helpRequest = "";
clear();
+ gListVector = NULL;
+ gSparseMatrix = NULL;
}
/*******************************************************/
fastafile = "";
treefile = "";
sharedfile = "";
+ candidatefile = "";
cutoff = "10.00";
format = "";
precision = "100";
abund = "10";
step = "0.01";
form = "integral";
- sorted = "1"; //0 means don't sort, 1 means sort.
- scaler = "log10";
+ 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";
+
}
//*******************************************************/
/******************************************************/
void GlobalData::reset() {
+ label = "";
+ line = "";
cutoff = "10.00";
precision = "100";
iters = "1000";
groups = "";
jumble = "1"; //0 means don't jumble, 1 means jumble.
- sorted = "1"; //0 means don't sort, 1 means sort.
+ 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";
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";
+
}
/*******************************************************/
/*******************************************************/
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;
//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 != ";")) {
projects / mothur.git / blobdiff