X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=secondarystructurecommand.cpp;h=3354665852ce1b5a95b9ecc7cc673d5083b25d8b;hp=4d04270ce649f8b2e579625eae7c074b322d10cb;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=ea4f373c28543cd1002b0dd7dc6e55c526647d59

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index 4d04270..3354665 100644
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -14,12 +14,12 @@
 //**********************************************************************************************************************
 vector<string> AlignCheckCommand::setParameters(){	
 	try {
-		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-		CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pmap);
-		CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
-        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","aligncheck",false,true,true); parameters.push_back(pfasta);
+		CommandParameter pmap("map", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pmap);
+		CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false); parameters.push_back(pcount);
+        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);		}
@@ -48,24 +48,19 @@ string AlignCheckCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
-string AlignCheckCommand::getOutputFileNameTag(string type, string inputName=""){	
-	try {
-        string outputFileName = "";
-		map<string, vector<string> >::iterator it;
+string AlignCheckCommand::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 == "aligncheck")            {   outputFileName =  "align.check";   }
-            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, "AlignCheckCommand", "getOutputFileNameTag");
-		exit(1);
-	}
+        if (type == "aligncheck") {  pattern = "[filename],align.check"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "AlignCheckCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 AlignCheckCommand::AlignCheckCommand(){	
@@ -205,7 +200,7 @@ int AlignCheckCommand::execute(){
 		if (namefile != "") { nameMap = m->readNames(namefile); }
         else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             nameMap = ct.getNameMap();
         }
 		
@@ -215,7 +210,9 @@ int AlignCheckCommand::execute(){
 		m->openInputFile(fastafile, in);
 		
 		ofstream out;
-		string outfile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("aligncheck");
+        map<string, string> variables; 
+		variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafile));
+		string outfile = getOutputFileName("aligncheck",variables);
 		m->openOutputFile(outfile, out);
 		
 				
@@ -303,7 +300,7 @@ int AlignCheckCommand::execute(){
 		
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOut(outfile); m->mothurOutEndLine();	outputNames.push_back(outfile); outputTypes["aligncheck"].push_back(outfile);
 		m->mothurOutEndLine();