X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=errorchecking.cpp;h=f8b34bba53ef6260d0c0756dfeec109cc946c9e8;hb=81a77fdce5e9b060c71b162305ddd9fa4308f78a;hp=8aaa8b04fbeeb80b4c727396bab06f9899840a7e;hpb=b01e4c8527e66f227eff16cf296eeadf060306b6;p=mothur.git

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 8aaa8b0..f8b34bb 100644
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -118,7 +118,15 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "scale" )			{ scale = value;	}
 				if (parameter == "ends" )			{ ends = value; }
 				if (parameter == "processors" )		{ processors = value;	}
-
+				if (parameter == "size" )			{ size = value; }
+				if (parameter == "template")		{ templatefile = value;	}
+				if (parameter == "search")			{ search = value;		}
+				if (parameter == "ksize")			{ ksize = value;		}
+				if (parameter == "align")		    { align = value;		}
+				if (parameter == "match")			{ match = value;		}
+				if (parameter == "mismatch")		{ mismatch = value;	    }
+				if (parameter == "gapopen")			{ gapopen = value;		}
+				if (parameter == "gapextend" )		{ gapextend = value;	}
 			}
 			
 			//gets the last parameter and value
@@ -160,7 +168,16 @@ bool ErrorCheck::checkInput(string input) {
 				if (parameter == "scale" )			{ scale = value;	}
 				if (parameter == "ends" )			{ ends = value; }
 				if (parameter == "processors" )		{ processors = value;	}
-
+				if (parameter == "size" )			{ size = value; }
+				if (parameter == "template")		{ templatefile = value;	}
+				if (parameter == "search")			{ search = value;		}
+				if (parameter == "ksize")			{ ksize = value;		}
+				if (parameter == "align")		    { align = value;		}
+				if (parameter == "match")			{ match = value;		}
+				if (parameter == "mismatch")		{ mismatch = value;	    }
+				if (parameter == "gapopen")			{ gapopen = value;		}
+				if (parameter == "gapextend" )		{ gapextend = value;	}
+				
 			}
 		}
 		
@@ -233,10 +250,10 @@ 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") || (commandName == "tree.shared") || (commandName == "bootstrap.shared")){ 
+		if ((commandName == "collect.shared") || (commandName == "rarefaction.shared") || (commandName == "summary.shared") || (commandName == "tree.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 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 (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; }
+				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, bootstrap.shared or dist.shared commands." << endl; return false; }
 			}
 		}
 		
@@ -246,18 +263,21 @@ bool ErrorCheck::checkInput(string input) {
 			}
 		}
 		
-		if ((commandName == "filter.seqs") || (commandName == "dist.seqs")) { 
+		if ((commandName == "filter.seqs") || (commandName == "dist.seqs") || (commandName == "align.seqs")) { 
 			if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) {
-				 cout << "You must read either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs command." << endl; return false; 
+				 cout << "You must enter either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs, dist.seqs or align.seqs command." << endl; return false; 
+			}else if ((commandName == "align.seqs") && (templatefile == "")) {
+				cout << "You must enter a template to use the align.seqs command." << endl; return false; 
 			}
 			validateSeqsFiles();
 		}
 		
 		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; }
+			if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the bin.seqs commands." << 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; 
@@ -558,9 +578,15 @@ void ErrorCheck::validateSeqsFiles() {
 					errorFree = false;
 				}
 			}
-
+		}else if (templatefile != "") {
+			ableToOpen = openInputFile(templatefile, filehandle);
+			filehandle.close();
+			if (ableToOpen == 1) { //unable to open
+				errorFree = false;
+			}
 		}
 		
+		
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -583,7 +609,7 @@ void ErrorCheck::validateBinFiles() {
 		int ableToOpen;
 		
 		if (fastafile == "") {
-				cout << "fasta is a required parameter for bin.seqs and get.oturep commands." << endl; errorFree = false; 
+				cout << "fasta is a required parameter for bin.seqs, get.oturep and get.repseqs commands." << endl; errorFree = false; 
 		}else if (fastafile != "") {
 			//is it a valid filename'
 			ableToOpen = openInputFile(fastafile, filehandle);
@@ -610,9 +636,17 @@ void ErrorCheck::validateBinFiles() {
 			filehandle.close();
 			//unable to open
 			if (ableToOpen == 1) {  errorFree = false; }
+		}else if (groupfile != "") {
+			//is it a valid filename'
+			ifstream filehandle;
+			int ableToOpen = openInputFile(groupfile, 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";
@@ -642,6 +676,7 @@ void ErrorCheck::clear() {
 	fastafile       =   "";
 	nexusfile       =   "";
 	clustalfile     =   "";
+	templatefile	=	"";
 	line			=	"";
 	label			=	"";
 	method			=   "furthest";