X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifytreecommand.cpp;h=79a82454d14304d997a2a46efbc62ffbeac63f60;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=69da8e0d74e58d54d7ae59c78c7ad7f91e9f4b29;hpb=90708fe9701e3827e477c82fb3652539c3bf2a0d;p=mothur.git

diff --git a/classifytreecommand.cpp b/classifytreecommand.cpp
index 69da8e0..79a8245 100644
--- a/classifytreecommand.cpp
+++ b/classifytreecommand.cpp
@@ -13,14 +13,14 @@
 //**********************************************************************************************************************
 vector<string> ClassifyTreeCommand::setParameters(){	
 	try {
-		CommandParameter ptree("tree", "InputTypes", "", "", "", "", "none",false,true); parameters.push_back(ptree);
-        CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "", "", "none",false,true); parameters.push_back(ptaxonomy);
-        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
-		CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
-        CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "",false,true); parameters.push_back(pcutoff);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter ptree("tree", "InputTypes", "", "", "", "", "none","tree-summary",false,true,true); parameters.push_back(ptree);
+        CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "", "", "none","",false,true,true); parameters.push_back(ptaxonomy);
+        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+		CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+        CommandParameter pcutoff("cutoff", "Number", "", "51", "", "", "","",false,true); parameters.push_back(pcutoff);
+		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);		}
@@ -52,25 +52,20 @@ string ClassifyTreeCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
-string ClassifyTreeCommand::getOutputFileNameTag(string type, string inputName=""){	
-	try {
-        string outputFileName = "";
-		map<string, vector<string> >::iterator it;
+string ClassifyTreeCommand::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 == "tree") {  outputFileName =  "taxonomy.tre"; }
-            else if (type == "summary") {  outputFileName =  "taxonomy.summary"; }
-            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, "ClassifyTreeCommand", "getOutputFileNameTag");
-		exit(1);
-	}
+        if (type == "summary") {  pattern = "[filename],taxonomy.summary"; } //makes file like: amazon.0.03.fasta
+        else if (type == "tree") {  pattern = "[filename],taxonomy.tre"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "ClassifyTreeCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 ClassifyTreeCommand::ClassifyTreeCommand(){	
@@ -286,7 +281,9 @@ int ClassifyTreeCommand::getClassifications(Tree*& T){
 		
 		string thisOutputDir = outputDir;
 		if (outputDir == "") {  thisOutputDir += m->hasPath(treefile);  }
-		string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("summary");
+        map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(treefile));
+		string outputFileName = getOutputFileName("summary", variables);
 		outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
 		
 		ofstream out;
@@ -300,12 +297,13 @@ int ClassifyTreeCommand::getClassifications(Tree*& T){
 		
 		string treeOutputDir = outputDir;
 		if (outputDir == "") {  treeOutputDir += m->hasPath(treefile);  }
-		string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + getOutputFileNameTag("tree");
+        variables["[filename]"] = treeOutputDir + m->getRootName(m->getSimpleName(treefile));
+		string outputTreeFileName = getOutputFileName("tree", variables);
 		
 		//create a map from tree node index to names of descendants, save time later
 		map<int, map<string, set<string> > > nodeToDescendants; //node# -> (groupName -> groupMembers)
 		for (int i = 0; i < T->getNumNodes(); i++) {
-			if (m->control_pressed) { return 0; }
+            if (m->control_pressed) { return 0; }
 			
 			nodeToDescendants[i] = getDescendantList(T, i, nodeToDescendants);
 		}
@@ -329,7 +327,7 @@ int ClassifyTreeCommand::getClassifications(Tree*& T){
                 tax = getTaxonomy(nodeToDescendants[i][group], size);
                 out << (i+1) << '\t' << size << '\t' << tax << endl;
             }
-           			
+           	
 			T->tree[i].setLabel((i+1));
 		}
 		out.close();
@@ -358,7 +356,6 @@ string ClassifyTreeCommand::getTaxonomy(set<string> names, int& size) {
 		
 		for (set<string>::iterator it = names.begin(); it != names.end(); it++) {
             
-            
 			//if namesfile include the names
 			if (namefile != "") {
                 
@@ -379,7 +376,7 @@ string ClassifyTreeCommand::getTaxonomy(set<string> names, int& size) {
 					}else{
 						//add seq to tree
                         int num = nameCount[(*it)]; // we know its there since we found it in nameMap
-						for (int i = 0; i < num; i++) {  phylo->addSeqToTree((*it)+toString(i), it2->second);  }
+						for (int i = 0; i < num; i++) {  phylo->addSeqToTree((*it)+toString(i), itTax->second);  }
                         size += num;
 					}
 				}