added bootstrap.shared command and fixed some bugs with heatmap

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index a057e5d1b396d69af85142d3695d326176b8fd0c..4eef3b041aaf724e87efb980c6115c9cc78036ce 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -111,6 +111,8 @@ 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 +146,7 @@ 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;        }
                        }
                }
                
@@ -216,18 +219,33 @@ 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; }
                        }
                }
                
-               if (commandName == "heatmap"){ 
+               if ((commandName == "heatmap") || (commandName == "venn")) { 
                        if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
-                                cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap command." << endl; return false; 
+                                cout << "You must read a list, or a list and a group, or a shared before you can use the heatmap or venn commands." << endl; return false; 
                        }
                }
+               
+               if ((commandName == "bin.seqs")) { 
+                       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;
 }
@@ -470,6 +488,58 @@ void ErrorCheck::validateReadPhil() {
 }
 /*******************************************************/
 
+/******************************************************/
+//This function checks to make sure the user entered appropriate
+// format parameters on a bin.seq command
+void ErrorCheck::validateBinFiles() {
+       try {
+               ifstream filehandle;
+               int ableToOpen;
+               
+               if (fastafile == "") {
+                               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;
+                       int ableToOpen = openInputFile(globaldata->getNameFile(), filehandle);
+                       filehandle.close();
+                       //unable to open
+                       if (ableToOpen == 1) {  errorFree = false; }
+               }else if (namefile != "") {
+                       //is it a valid filename'
+                       ifstream filehandle;
+                       int ableToOpen = openInputFile(namefile, filehandle);
+                       filehandle.close();
+                       //unable to open
+                       if (ableToOpen == 1) {  errorFree = false; }
+               }
+
+
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ErrorCheck class function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
+
+/*******************************************************/
+
 /******************************************************/
 
 void ErrorCheck::clear() {