X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=listseqscommand.cpp;h=cf884705cb26f341ef08713b118af32fd49c5bdf;hp=7c3f07f96e092d81c307673192dad29a31fee091;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=ea4f373c28543cd1002b0dd7dc6e55c526647d59

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 7c3f07f..cf88470 100644
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -16,15 +16,15 @@
 //**********************************************************************************************************************
 vector<string> ListSeqsCommand::setParameters(){	
 	try {
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pfasta);
-		CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pcount);
-		CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(pgroup);
-		CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(plist);
-		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(ptaxonomy);
-		CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none",false,false); parameters.push_back(palignreport);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pfasta);
+		CommandParameter pname("name", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pcount);
+		CommandParameter pgroup("group", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(pgroup);
+		CommandParameter plist("list", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(plist);
+		CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false,true); parameters.push_back(ptaxonomy);
+		CommandParameter palignreport("alignreport", "InputTypes", "", "", "FNGLT", "FNGLT", "none","accnos",false,false); parameters.push_back(palignreport);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -52,24 +52,19 @@ string ListSeqsCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
-string ListSeqsCommand::getOutputFileNameTag(string type, string inputName=""){	
-	try {
-        string outputFileName = "";
-		map<string, vector<string> >::iterator it;
+string ListSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //is this a type this command creates
-        it = outputTypes.find(type);
-        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
-        else {
-            if (type == "accnos")             {   outputFileName =  "accnos";       }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
-        }
-        return outputFileName;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "ListSeqsCommand", "getOutputFileNameTag");
-		exit(1);
-	}
+        if (type == "accnos") {  pattern = "[filename],accnos"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ListSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 ListSeqsCommand::ListSeqsCommand(){	
@@ -249,7 +244,9 @@ int ListSeqsCommand::execute(){
 		
 		if (outputDir == "") {  outputDir += m->hasPath(inputFileName);  }
 		
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + getOutputFileNameTag("accnos");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+		string outputFileName = getOutputFileName("accnos", variables);
 
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
@@ -269,7 +266,7 @@ int ListSeqsCommand::execute(){
 		m->setAccnosFile(outputFileName);
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOut(outputFileName); m->mothurOutEndLine();	
 		m->mothurOutEndLine();
 		
@@ -300,7 +297,7 @@ int ListSeqsCommand::readFasta(){
 		//ofstream out;
 		//string newFastaName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "numsAdded.fasta";
 		//m->openOutputFile(newFastaName, out);
-		//int count = 1;
+		int count = 1;
 		//string lastName = "";
 		
 		while(!in.eof()){
@@ -313,7 +310,7 @@ int ListSeqsCommand::readFasta(){
 			if (name != "") {  names.push_back(name);  }
 			
 			m->gobble(in);
-			//count++;
+			if (m->debug) { count++; cout << "[DEBUG]: count = " + toString(count) + ", name = " + currSeq.getName() + "\n"; }
 		}
 		in.close();	
 		//out.close();
@@ -418,7 +415,7 @@ int ListSeqsCommand::readGroup(){
 int ListSeqsCommand::readCount(){
 	try {
 		CountTable ct;
-		ct.readTable(countfile);
+		ct.readTable(countfile, false);
         
         if (m->control_pressed) { return 0; }