added read.shared, broke up globaldata a bit

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 067d246d4c50f1427840c3879be04bac2ff7cdf8..8556c27266ab0c2fa56bd4c9ddeb644e1d81e0b8 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -17,7 +17,6 @@ ErrorCheck::ErrorCheck() {
        globaldata = GlobalData::getInstance();
        validCommand = new ValidCommands();
        validParameter = new ValidParameters();
-       validCalculator = new ValidCalculators();
 }
 /*******************************************************/
 
@@ -38,6 +37,7 @@ void ErrorCheck::refresh() {
        format = globaldata->getFormat();
        method = globaldata->getMethod();
        randomtree = globaldata->getRandomTree();
+       sharedfile = globaldata->getSharedFile();
 }
 
 /*******************************************************/
@@ -76,8 +76,8 @@ bool ErrorCheck::checkInput(string input) {
                //reads in parameters and values
                if((optionText != "") && (commandName != "help")){
                        while((optionText.find_first_of(',') != -1) && (errorFree)) {  //while there are parameters
-                               globaldata->splitAtComma(value, optionText);
-                               globaldata->splitAtEquals(parameter, value);
+                               splitAtComma(value, optionText);
+                               splitAtEquals(parameter, value);
                                
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter) != true) { return false; }
@@ -92,6 +92,7 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "fasta" )              { fastafile = value; }
                                if (parameter == "tree" )               { treefile = value; }
                                if (parameter == "group" )              { groupfile = value; }
+                               if (parameter == "shared" )             { sharedfile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
                                if (parameter == "precision" )          { precision = value; }
                                if (parameter == "iters" )                      { iters = value; }
@@ -103,52 +104,12 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "label" )                      { label = value; }
                                if (parameter == "randomtree" )         { randomtree = value;   }
 
-                               if (parameter == "single") {//stores estimators in a vector
-                                       singleEsimators.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, singleEsimators);
-                                       for (int i = 0; i < singleEsimators.size(); i++) { //loop through estimators
-                                               //is it a valid calculator
-                                               if (validCalculator->isValidCalculator(parameter, singleEsimators[i]) != true) { return false; }
-                                       }
-                               }
-                               if (parameter == "rarefaction") {//stores estimators in a vector
-                                       rareEstimators.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, rareEstimators);
-                                       for (int i = 0; i < rareEstimators.size(); i++) { //loop through estimators
-                                               //is it a valid calculator
-                                               if (validCalculator->isValidCalculator(parameter, rareEstimators[i]) != true) { return false; }
-                                       }
-                               }
-                               if (parameter == "shared") {//stores estimators in a vector
-                                       sharedEstimators.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, sharedEstimators);
-                                       for (int i = 0; i < sharedEstimators.size(); i++) { //loop through estimators
-                                               //is it a valid calculator
-                                               if (validCalculator->isValidCalculator(parameter, sharedEstimators[i]) != true) { return false; }
-                                       }
-                               }
-                               if (parameter == "summary") { //stores summaries to be used in a vector
-                                       summaryEstimators.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, summaryEstimators);
-                                       for (int i = 0; i < summaryEstimators.size(); i++) { //loop through estimators
-                                               //is it a valid calculator
-                                               if (validCalculator->isValidCalculator(parameter, summaryEstimators[i]) != true) { return false; }
-                                       }
-                               }
-                               if (parameter == "sharedrarefaction") { //stores summaries to be used in a vector
-                                       sharedRareEstimators.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, sharedRareEstimators);
-                                       for (int i = 0; i < sharedRareEstimators.size(); i++) { //loop through estimators
-                                               //is it a valid calculator
-                                               if (validCalculator->isValidCalculator(parameter, sharedRareEstimators[i]) != true) { return false; }
-                                       }
-                               }
                        }
                        
                        //gets the last parameter and value
                        if (errorFree)  { //gets the last parameter and value
                                value = optionText;
-                               globaldata->splitAtEquals(parameter, value);
+                               splitAtEquals(parameter, value);
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter) != true) { return false; }
                                
@@ -160,6 +121,7 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "name" )               { namefile = value; }
                                if (parameter == "order" )              { orderfile = value; }
                                if (parameter == "group" )              { groupfile = value; }
+                               if (parameter == "shared" )             { sharedfile = value; }
                                if (parameter == "fasta" )              { fastafile = value; }
                                if (parameter == "tree" )               { treefile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
@@ -173,47 +135,6 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "label" )                      { label = value; }
                                if (parameter == "randomtree" )         { randomtree = value;   }
 
-                               if (parameter == "single") {//stores estimators in a vector
-                                       singleEsimators.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, singleEsimators);
-                                       for (int i = 0; i < singleEsimators.size(); i++) { //loop through estimators
-                                               //is it a valid calculator
-                                               if (validCalculator->isValidCalculator(parameter, singleEsimators[i]) != true) { return false; }
-                                       }
-                               }
-                               if (parameter == "rarefaction") {//stores estimators in a vector
-                                       rareEstimators.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, rareEstimators);
-                                       for (int i = 0; i < rareEstimators.size(); i++) { //loop through estimators
-                                               //is it a valid calculator
-                                               if (validCalculator->isValidCalculator(parameter, rareEstimators[i]) != true) { return false; }
-                                       }
-                               }
-                               if (parameter == "shared") {//stores estimators in a vector
-                                       sharedEstimators.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, sharedEstimators);
-                                       for (int i = 0; i < sharedEstimators.size(); i++) { //loop through estimators
-                                               //is it a valid calculator
-                                               if (validCalculator->isValidCalculator(parameter, sharedEstimators[i]) != true) { return false; }
-                                       }
-                               }
-                               if (parameter == "summary") { //stores summaries to be used in a vector
-                                       summaryEstimators.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, summaryEstimators);
-                                       for (int i = 0; i < summaryEstimators.size(); i++) { //loop through estimators
-                                               //is it a valid calculator
-                                               if (validCalculator->isValidCalculator(parameter, summaryEstimators[i]) != true) { return false; }
-                                       }
-                               }
-                               if (parameter == "sharedrarefaction") { //stores summaries to be used in a vector
-                                       sharedRareEstimators.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, sharedRareEstimators);
-                                       for (int i = 0; i < sharedRareEstimators.size(); i++) { //loop through estimators
-                                               //is it a valid calculator
-                                               if (validCalculator->isValidCalculator(parameter, sharedRareEstimators[i]) != true) { return false; }
-                                       }
-                               }
-
                        }
                }
                
@@ -232,6 +153,9 @@ bool ErrorCheck::checkInput(string input) {
                                validateReadFiles();
                                validateReadPhil();
                        }
+               }else if (commandName == "read.shared") { 
+                       //you want to do shared commands with just the shared file
+                       validateReadFiles();
                }else if (commandName == "read.tree") { 
                        validateTreeFiles(); //checks the treefile and groupfile parameters
                }else if (commandName == "deconvolute") {
@@ -270,11 +194,12 @@ bool ErrorCheck::checkInput(string input) {
                }
                
                if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){ 
-                       if (globaldata->getListFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
-                       else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+                       if (globaldata->getSharedFile() == "") {
+                               if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+                               else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
+                       }
                }
  
-               
                return errorFree;
 }
 
@@ -330,6 +255,12 @@ void ErrorCheck::validateReadFiles() {
                        //unable to open
                        if (ableToOpen == 1) {  errorFree = false; }
                        else { globaldata->inputFileName = fastafile; }
+               }else if (sharedfile != "") {
+                       ableToOpen = openInputFile(sharedfile, filehandle);
+                       filehandle.close();
+                       //unable to open
+                       if (ableToOpen == 1) {  errorFree = false; }
+                       else { globaldata->inputFileName = sharedfile; }
                }else{ //no file given
                        errorFree = false;
                }
@@ -515,6 +446,7 @@ void ErrorCheck::clear() {
        namefile                =       "";
        groupfile               =       ""; 
        orderfile               =       "";
+       sharedfile              =       "";
        line                    =       "";
        label                   =       "";
        method                  =   "furthest";