fixed xp user bug with rarefact commands and cluster error checking

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index da1d1bbb614ffd78f03484c3ca956e3f5aba21ac..728d4d27303a3c3b9d9ad602693ba4b309a36202 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -23,21 +23,21 @@ ErrorCheck::ErrorCheck() {
 /******************************************************/
 
 void ErrorCheck::refresh() {
-       columnfile = globaldata->getColumnFile();
-       phylipfile = globaldata->getPhylipFile();
-       listfile = globaldata->getListFile();
-       rabundfile = globaldata->getRabundFile();
-       sabundfile = globaldata->getSabundFile();
-       namefile = globaldata->getNameFile();
-       groupfile = globaldata->getGroupFile();
-       orderfile = globaldata->getOrderFile();
-       fastafile = globaldata->getFastaFile();
-       treefile = globaldata->getTreeFile();
-       cutoff = globaldata->getCutOff();
-       format = globaldata->getFormat();
-       method = globaldata->getMethod();
-       randomtree = globaldata->getRandomTree();
-       sharedfile = globaldata->getSharedFile();
+       //columnfile = globaldata->getColumnFile();
+       //phylipfile = globaldata->getPhylipFile();
+       //listfile = globaldata->getListFile();
+       //rabundfile = globaldata->getRabundFile();
+       //sabundfile = globaldata->getSabundFile();
+       //namefile = globaldata->getNameFile();
+       //groupfile = globaldata->getGroupFile();
+       //orderfile = globaldata->getOrderFile();
+       //fastafile = globaldata->getFastaFile();
+       //treefile = globaldata->getTreeFile();
+       //cutoff = globaldata->getCutOff();
+       //format = globaldata->getFormat();
+       //method = globaldata->getMethod();
+       //randomtree = globaldata->getRandomTree();
+       //sharedfile = globaldata->getSharedFile();
 }
 
 /*******************************************************/
@@ -85,8 +85,6 @@ bool ErrorCheck::checkInput(string input) {
                                
                                //is it a valid parameter
                                if (validParameter->isValidParameter(parameter, commandName, value) != true) { return false; }
-
-
                                
                                if (parameter == "phylip" )             { phylipfile = value; }
                                if (parameter == "column" )             { columnfile = value; }
@@ -111,6 +109,8 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "abund" )          { abund = value; }
                                if (parameter == "random" )                     { randomtree = value;   }
                                if (parameter == "sorted" )                     { sorted = value;       }
+                               if (parameter == "scale" )                      { scale = value;        }
+                               
                        }
                        
                        //gets the last parameter and value
@@ -144,6 +144,7 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "random" )                     { randomtree = value;   }
                                if (parameter == "abund" )          { abund = value; }
                                if (parameter == "sorted" )                     { sorted = value;       }
+                               if (parameter == "scale" )                      { scale = value;        }
                        }
                }
                
@@ -176,7 +177,7 @@ bool ErrorCheck::checkInput(string input) {
                        validateReadFiles();
                }
                
-               //are you trying to cluster before you have read something                      
+               //are you trying to cluster before you have read something      
                if (((commandName == "cluster") && (globaldata->gSparseMatrix == NULL)) ||
                        ((commandName == "cluster") && (globaldata->gListVector == NULL))) {
                                cout << "Before you use the cluster command, you first need to read in a distance matrix." << endl; 
@@ -195,9 +196,9 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }
                
-               if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted")) {
+               if ((commandName == "unifrac.weighted") || (commandName == "unifrac.unweighted") || (commandName == "concensus")) {
                        if (globaldata->gTree.size() == 0) {//no trees were read
-                               cout << "You must execute the read.tree command, before you may execute the unifrac.weighted or unifrac.unweighted command." << endl; return false;  }
+                               cout << "You must execute the read.tree command, before you may execute the unifrac.weighted, unifrac.unweighted or concensus command." << endl; return false;  }
                }
                
                //check for valid method
@@ -216,10 +217,10 @@ bool ErrorCheck::checkInput(string input) {
                        if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the collect.single, rarefaction.single or summary.single commands." << endl; return false; }
                }
                
-               if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){ 
+               if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.shared") || (commandName == "bootstrap.shared")){ 
                        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; }
+                               if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared, rarefaction.shared, summary.shared, tree.shared or bootstrap.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, summary.shared, tree.shared or bootstrap.shared commands." << endl; return false; }
                        }
                }
                
@@ -233,6 +234,16 @@ bool ErrorCheck::checkInput(string input) {
                        if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs command." << endl; return false; }
                        validateBinFiles();
                }
+               
+               if ((commandName == "get.oturep")) { 
+                       if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
+                               cout << "Before you use the get.oturep command, you first need to read in a distance matrix." << endl; 
+                               errorFree = false;
+                       }
+                       if (listfile == "") { cout << "list is a required parameter for the get.oturep command." << endl; errorFree = false; }
+                       validateBinFiles();
+               } 
+
 
                return errorFree;
 }
@@ -484,13 +495,19 @@ void ErrorCheck::validateBinFiles() {
                int ableToOpen;
                
                if (fastafile == "") {
-                               cout << "fasta is a required parameter for bin.seqs." << endl; errorFree = false; 
+                               cout << "fasta is a required parameter for bin.seqs and get.oturep commands." << endl; errorFree = false; 
                }else if (fastafile != "") {
                        //is it a valid filename'
                        ableToOpen = openInputFile(fastafile, filehandle);
                        filehandle.close();
                        //unable to open
                        if (ableToOpen == 1) {  errorFree = false; }
+               }else if (listfile != "") {
+                       //is it a valid filename'
+                       ableToOpen = openInputFile(listfile, filehandle);
+                       filehandle.close();
+                       //unable to open
+                       if (ableToOpen == 1) {  errorFree = false; }
                }else if (globaldata->getNameFile() != "") {
                        //is it a valid filename'
                        ifstream filehandle;