fixed some bugs

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 39fb17e47a4e2f72692f5d5be15f19866fca2bef..caf7f73dc31cf02bd48ac7352f339e41b4f6cb96 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -205,8 +205,8 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }else if (commandName == "read.tree") { 
                        validateTreeFiles(); //checks the treefile and groupfile parameters
-               }else if (commandName == "deconvolute") {
-                       if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
+               }else if (commandName == "unique.seqs") {
+                       if (fastafile == "") { cout << "You must enter a fastafile with the unique.seqs() command." << endl; return false; }
                        validateReadFiles();
                }
                
@@ -246,10 +246,18 @@ bool ErrorCheck::checkInput(string input) {
                        else {cout << "Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average." << endl; return false; }
                }
                
-               if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single") ){ 
+               if ((commandName == "collect.single") || (commandName == "rarefaction.single") || (commandName == "summary.single")){ 
                        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 == "get.rabund") {
+                       if (globaldata->getListFile() == "") { cout << "You must read a listfile before you can use the get.rabund command." << endl; return false; }
+               }
+               
+               if (commandName == "get.sabund") {
+                       if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << endl; return false; }
+               }
+               
                if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "bootstrap.shared") || (commandName == "dist.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, summary.shared, tree.shared, bootstrap.shared or dist.shared commands." << endl; return false; }
@@ -273,8 +281,8 @@ bool ErrorCheck::checkInput(string input) {
                }
                
                if ((commandName == "filter.seqs") || (commandName == "dist.seqs")) { 
-                       if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) {
-                                cout << "You must enter either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs or dist.seqs command." << endl; return false; 
+                       if (fastafile == "") {
+                                cout << "You must enter either a fasta file before you can use the filter.seqs or dist.seqs command." << endl; return false; 
                        }
                        validateSeqsFiles();
                }