working on readtree

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index cc6cbf9d8d96ac90a55dc68d16d2ffa157079cb1..b76542aec7907c0cc3ef80b896c5308985c1c73d 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -8,7 +8,6 @@
  */
 
 #include "errorchecking.h"
-#include <math.h>
 
 /*******************************************************/
 
@@ -37,9 +36,12 @@ void ErrorCheck::refresh() {
        cutoff = globaldata->getCutOff();
        format = globaldata->getFormat();
        method = globaldata->getMethod();
+       randomtree = globaldata->getRandomTree();
+       sharedfile = globaldata->getSharedFile();
+
 
        
-       string p[] = {
+/*     string p[] = {
                "phylip",              //0
                "column",             //1
                "list",               //2
@@ -65,7 +67,7 @@ void ErrorCheck::refresh() {
                "summary",            //22
                "sharedrarefaction",  //23
                "sharedsummary",      //24
-               "comparegroups",      //25
+               "groups",                         //25
                "abund",              //26
                };
        
@@ -156,10 +158,8 @@ void ErrorCheck::refresh() {
        intParams[p[13]] = ipv2;
        intParams[p[14]] = ipv3;
        intParams[p[17]] = ipv4;
-       intParams[p[26]] = ipv5;
+       intParams[p[26]] = ipv5;   */
        
-       randomtree = globaldata->getRandomTree();
-       sharedfile = globaldata->getSharedFile();
 }
 
 /*******************************************************/
@@ -204,15 +204,15 @@ bool ErrorCheck::checkInput(string input) {
                                
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter) != true) { return false; }
-                               if(!validCommandParameter(parameter,commandName)) { 
-                                       cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
-                                       return false; 
-                               }
-                               if(!validParameterValue(value, parameter)) {
-                                       if(parameter.compare("precision") == 0)
-                                               cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
-                                       else {
-                                       vector<double> bounds = intParams[parameter];
+                               //if(!validCommandParameter(parameter,commandName)) { 
+                               //      cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
+                               //      return false; 
+                               //}
+                               //if(!validParameterValue(value, parameter)) {
+                               //      if(parameter.compare("precision") == 0)
+                               //              cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
+                               //      else {
+                               /*      vector<double> bounds = intParams[parameter];
                                        double a = bounds.at(0);
                                        double b = bounds.at(1);
                                        double c = bounds.at(2);
@@ -244,7 +244,7 @@ bool ErrorCheck::checkInput(string input) {
                                        }
                                        }
                                        return false;
-                               }
+                               } */
 
                                if (parameter == "phylip" )             { phylipfile = value; }
                                if (parameter == "column" )             { columnfile = value; }
@@ -268,12 +268,6 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "label" )                      { label = value; }
                                if (parameter == "abund" )          { abund = value; }
                                if (parameter == "random" )                     { randomtree = value;   }
-
-                               if (parameter == "comparegroups") { //stores groups to be compared
-                                       sharedGroups.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, sharedGroups);
-                               }
-
                        }
                        
                        //gets the last parameter and value
@@ -282,11 +276,11 @@ bool ErrorCheck::checkInput(string input) {
                                splitAtEquals(parameter, value);
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter) != true) { return false; }
-                               if(!validCommandParameter(parameter,commandName)) { 
-                                       cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
-                                       return false; 
-                               }
-                               if(!validParameterValue(value, parameter)) {
+                       //      if(!validCommandParameter(parameter,commandName)) { 
+                       //              cout << "'" << parameter << "' is not a valid parameter for the " << commandName << " command.\n";
+                       //              return false; 
+                       //      }
+                       /*      if(!validParameterValue(value, parameter)) {
                                        if(parameter.compare("precision") == 0)
                                                cout << "The precision parameter can only take powers of 10 as a value (e.g. 10,1000,1000, etc.)\n";
                                        else {
@@ -322,7 +316,7 @@ bool ErrorCheck::checkInput(string input) {
                                        }
                                        }
                                        return false;
-                               }
+                               }*/
                                if (parameter == "phylip" )             { phylipfile = value; }
                                if (parameter == "column" )             { columnfile = value; }                         
                                if (parameter == "list" )               { listfile = value; }
@@ -345,11 +339,6 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "label" )                      { label = value; }
                                if (parameter == "random" )                     { randomtree = value;   }
                                if (parameter == "abund" )          { abund = value; }
-
-                               if (parameter == "comparegroups") { //stores groups to be compared
-                                       sharedGroups.clear(); //clears out old values
-                                       globaldata->splitAtDash(value, sharedGroups);
-                               }
                        }
                }
                
@@ -378,8 +367,8 @@ bool ErrorCheck::checkInput(string input) {
                }
                
                //are you trying to cluster before you have read something                      
-               if ((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL) ||
-                       (commandName == "cluster") && (globaldata->getListVector() == NULL)) {
+               if (((commandName == "cluster") && (globaldata->getSparseMatrix() == NULL)) ||
+                       ((commandName == "cluster") && (globaldata->getListVector() == NULL))) {
                                cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; 
                                errorFree = false;
                } 
@@ -420,8 +409,6 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }
 
-               globaldata->clearAbund();
-
                return errorFree;
 }
 
@@ -499,7 +486,7 @@ void ErrorCheck::validateReadFiles() {
 }
 /*******************************************************/
 
-/******************************************************/
+/******************************************************
 //This function checks to see if the given paramter
 //is a valid paramter for the given command.
 bool ErrorCheck::validCommandParameter(string parameter, string commandName) {
@@ -521,7 +508,7 @@ bool ErrorCheck::validCommandParameter(string parameter, string commandName) {
 }
 /*******************************************************/
 
-/******************************************************/
+/******************************************************
 //This function checks to see if the given paramter value
 //is convertable into an int if that parameter requires it.
 bool ErrorCheck::validParameterValue(string value, string parameter) {