From: westcott <westcott>
Date: Wed, 28 Jan 2009 14:38:16 +0000 (+0000)
Subject: collect.single bug in readphil.
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=8b6bc106c6dd2ae8c9b59da038f775d524f0e43e;hp=72a92a86c30876883e8af2af9803a3ecf38bdea7;p=mothur.git

collect.single bug in readphil.
---

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 6ec145b..35ea56c 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -223,6 +223,7 @@ 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; }
 			validateReadFiles();
 		}
 		
@@ -243,9 +244,9 @@ bool ErrorCheck::checkInput(string input) {
 			if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a listfile, sabundfile or rabundfile 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") || (commandName == "shared") ){ 
-			if (globaldata->getListFile() == "") { cout << "You must read a listfile and a groupfile before you can use the collect.shared, rarefaction.shared, summary.shared or shared commands." << endl; return false; }
-			else if (globaldata->getGroupFile() == "") { cout << "You must read a listfile and a groupfile before you can use the collect.shared, rarefaction.shared, summary.shared or shared commands." << endl; return false; }
+		if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") ){ 
+			if (globaldata->getListFile() == "") { cout << "You must read a listfile and a groupfile 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 listfile and a groupfile before you can use the collect.shared, rarefaction.shared or summary.shared commands." << endl; return false; }
 		}
  
 		
diff --git a/readmatrix.cpp b/readmatrix.cpp
index bd92f6c..78a4bd4 100644
--- a/readmatrix.cpp
+++ b/readmatrix.cpp
@@ -352,12 +352,12 @@ void ReadPhilFile::read(GlobalData* globaldata){
 		}
 		globaldata->ginput = input;	//saving to be used by collector and rarefact commands.
 		
-		if (globaldata->getGroupFile() == "") {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
+		if ((globaldata->getFormat() == "list") || (globaldata->getFormat() == "rabund") || (globaldata->getFormat() == "sabund")) {//you are reading a list, rabund or sabund file for collect, rarefaction or summary.
 			order = input->getOrderVector();
 			globaldata->gorder = order;	//saving to be used by collect and rarefact commands.
 			sabund = inputSabund->getSAbundVector(); 
 			globaldata->sabund = sabund; //saving to be used by summary command.
-		}else {
+		}else if (globaldata->getFormat() == "shared") {
 			SharedList = input->getSharedListVector(); //you are reading for parselist command, or shared commands.
 			globaldata->gSharedList = SharedList;
 		}