changes to dist.seqs and pairwise.seqs and cluster.classic no longer resizes

[mothur.git] / parselistscommand.cpp

diff --git a/parselistscommand.cpp b/parselistscommand.cpp
index d09910b48de9003865f06fd21d165a71e989dde9..9cf5a73a56802b65bae10d1c28187f214ebcfb56 100644 (file)
--- a/parselistscommand.cpp
+++ b/parselistscommand.cpp
@@ -9,6 +9,55 @@
 
 #include "parselistscommand.h"
 
+//**********************************************************************************************************************
+vector<string> ParseListCommand::getValidParameters(){ 
+       try {
+               string Array[] =  {"list","group", "label", "outputdir","inputdir"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseListCommand", "getValidParameters");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+ParseListCommand::ParseListCommand(){  
+       try {
+               abort = true;
+               //initialize outputTypes
+               vector<string> tempOutNames;
+               outputTypes["list"] = tempOutNames;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseListCommand", "ParseListCommand");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ParseListCommand::getRequiredParameters(){      
+       try {
+               string Array[] =  {"list","group"};
+               vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseListCommand", "getRequiredParameters");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
+vector<string> ParseListCommand::getRequiredFiles(){   
+       try {
+               vector<string> myArray;
+               return myArray;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ParseListCommand", "getRequiredFiles");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 ParseListCommand::ParseListCommand(string option)  {
        try {
@@ -33,7 +82,11 @@ ParseListCommand::ParseListCommand(string option)  {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-                                               
+                       
+                       //initialize outputTypes
+                       vector<string> tempOutNames;
+                       outputTypes["list"] = tempOutNames;                     
+                                                                                               
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
                        if (inputDir == "not found"){   inputDir = "";          }
@@ -42,7 +95,7 @@ ParseListCommand::ParseListCommand(string option)  {
                                it = parameters.find("list");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["list"] = inputDir + it->second;             }
                                }
@@ -50,7 +103,7 @@ ParseListCommand::ParseListCommand(string option)  {
                                it = parameters.find("group");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["group"] = inputDir + it->second;            }
                                }
@@ -83,7 +136,7 @@ ParseListCommand::ParseListCommand(string option)  {
                        label = validParameter.validFile(parameters, "label", false);                   
                        if (label == "not found") { label = "";  allLines = 1; }
                        else { 
-                               if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
+                               if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
                                else { allLines = 1;  }
                        }
                }
@@ -120,8 +173,7 @@ int ParseListCommand::execute(){
                if (abort == true) {    return 0;       }
                
                //set fileroot
-               string fileroot = outputDir + getRootName(getSimpleName(listfile));
-               vector<string> outputNames;
+               string fileroot = outputDir + m->getRootName(m->getSimpleName(listfile));
                
                //fill filehandles with neccessary ofstreams
                int i;
@@ -131,8 +183,8 @@ int ParseListCommand::execute(){
                        filehandles[groupMap->namesOfGroups[i]] = temp;
                        
                        string filename = fileroot +  groupMap->namesOfGroups[i] + ".list";
-                       outputNames.push_back(filename);
-                       openOutputFile(filename, *temp);
+                       outputNames.push_back(filename); outputTypes["list"].push_back(filename);
+                       m->openOutputFile(filename, *temp);
                }
                
                //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
@@ -146,7 +198,7 @@ int ParseListCommand::execute(){
                if (m->control_pressed) { 
                        delete input; delete list; delete groupMap;
                        for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
                        return 0;
                }
                
@@ -155,7 +207,7 @@ int ParseListCommand::execute(){
                        if (m->control_pressed) { 
                                delete input; delete list; delete groupMap;
                                for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
                                return 0;
                        }
                        
@@ -168,7 +220,7 @@ int ParseListCommand::execute(){
                                        userLabels.erase(list->getLabel());
                        }
                        
-                       if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+                       if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
                                        string saveLabel = list->getLabel();
                                        
                                        delete list;
@@ -194,7 +246,7 @@ int ParseListCommand::execute(){
                if (m->control_pressed) { 
                                delete input; delete groupMap;
                                for (i=0; i<groupMap->namesOfGroups.size(); i++) { (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
                                return 0;
                }
                
@@ -215,7 +267,7 @@ int ParseListCommand::execute(){
                if (m->control_pressed) { 
                                delete input; delete groupMap;
                                for (i=0; i<groupMap->namesOfGroups.size(); i++) {  (*(filehandles[groupMap->namesOfGroups[i]])).close();  delete filehandles[groupMap->namesOfGroups[i]]; } 
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
                                return 0;
                }
                
@@ -240,7 +292,7 @@ int ParseListCommand::execute(){
                delete input;
                
                if (m->control_pressed) { 
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
+                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
                        return 0;
                }
                
@@ -278,7 +330,7 @@ int ParseListCommand::parse(ListVector* thisList) {
                        string bin = list->get(i); 
                        
                        vector<string> names;
-                       splitAtComma(bin, names);  //parses bin into individual sequence names
+                       m->splitAtComma(bin, names);  //parses bin into individual sequence names
                        
                        //parse bin into list of sequences in each group
                        for (int j = 0; j < names.size(); j++) {