put back no command and worked on libshuff

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 9a0846214bb97a9f4cce7fa42540b0e4a642dda0..cb2dce42fbf4f40e4c5e2a5107a6e1d33c1b89c7 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -44,7 +44,10 @@ void ErrorCheck::refresh() {
 
 /******************************************************/
 
-ErrorCheck::~ErrorCheck() {}
+ErrorCheck::~ErrorCheck() {
+       delete validCommand;
+       delete validParameter;
+}
 
 /*******************************************************/
 
@@ -80,7 +83,7 @@ bool ErrorCheck::checkInput(string input) {
                                splitAtComma(value, optionText);
                                splitAtEquals(parameter, value);
                                
-                               //is it a valid parameter
+                               //is it a valid parameter for the command
                                if (validParameter->isValidParameter(parameter, commandName) != true) { return false; }
                                
                                if (parameter == "phylip" )             { phylipfile = value; }
@@ -111,7 +114,8 @@ bool ErrorCheck::checkInput(string input) {
                        if (errorFree)  { //gets the last parameter and value
                                value = optionText;
                                splitAtEquals(parameter, value);
-                               //is it a valid parameter
+                               
+                               //is it a valid parameter for the command
                                if (validParameter->isValidParameter(parameter, commandName) != true) { return false; }
                                
                                if (parameter == "phylip" )             { phylipfile = value; }
@@ -142,6 +146,7 @@ bool ErrorCheck::checkInput(string input) {
                //make sure the user does not use both the line and label parameters
                if ((line != "") && (label != "")) { cout << "You may use either the line or label parameters, but not both." << endl; return false; }
                
+               //check for valid files 
                if (commandName == "read.dist") { 
                        validateReadFiles();
                        validateReadDist();
@@ -149,12 +154,15 @@ bool ErrorCheck::checkInput(string input) {
                        //you want to do shared commands
                        if ((listfile != "") && (groupfile != ""))      {
                                validateParseFiles(); //checks the listfile and groupfile parameters
-                       }else if (listfile != "") { //you want to do single commands
+                       //you want to do single commands
+                       }else if ((listfile != "") || (rabundfile != "") || (sabundfile != "")){ 
                                validateReadFiles();
                                validateReadPhil();
-                       }else if ((listfile == "") && (sharedfile == "")) {
-                               cout << "You must enter either a listfile or a sharedfile with the read.otu command. " << endl; return false; 
-                       }else{//you are reading a shared file
+                       //you have not given a file
+                       }else if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "")) {
+                               cout << "You must enter either a listfile, rabundfile, sabundfile or a sharedfile with the read.otu command. " << endl; return false; 
+                       //you want to do shared commands with a shared file
+                       }else if (sharedfile != "") {//you are reading a shared file
                                validateReadFiles();
                        }
                }else if (commandName == "read.tree") { 
@@ -172,7 +180,7 @@ bool ErrorCheck::checkInput(string input) {
                } 
                
                if ((commandName == "libshuff") && ((globaldata->gMatrix == NULL) || (globaldata->gGroupmap == NULL))) {
-                        cout << "You must read in a matrix and groupfile before you use the libshuff command. " << endl; return false; 
+                        cout << "You must read in a matrix and groupfile using the read.dist command, before you use the libshuff command. " << endl; return false; 
                }
                
                if (commandName == "parsimony") {