added sparseDistanceMatrix class. Modified cluster commands to use the new sparse...

[mothur.git] / chopseqscommand.cpp

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index abfd8dc239b185a69e86e7641a8505761ff9766e..05037f6817a5a554a029a7d635460d048bf73203 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -51,7 +51,27 @@ string ChopSeqsCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string ChopSeqsCommand::getOutputFileNameTag(string type, string inputName=""){        
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //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 == "fasta") {  outputFileName =  "chop.fasta"; }
+            else if (type == "accnos") {  outputFileName =  "chop.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, "ChopSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 ChopSeqsCommand::ChopSeqsCommand(){    
        try {
@@ -121,7 +141,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
                        
                        string temp = validParameter.validFile(parameters, "numbases", false);  if (temp == "not found") { temp = "0"; } 
-                       convert(temp, numbases);   
+                       m->mothurConvert(temp, numbases);   
                        
                        temp = validParameter.validFile(parameters, "countgaps", false);        if (temp == "not found") { temp = "f"; } 
                        countGaps = m->isTrue(temp);  
@@ -147,8 +167,8 @@ int ChopSeqsCommand::execute(){
                
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.fasta";
-               string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "chop.accnos";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
+               string outputFileNameAccnos = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -233,7 +253,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        
                                        for (int i = 0; i < temp.length(); i++) {
                                                //eliminate N's
-                                               if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+                                               if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
                                                
                                                numBasesCounted++; 
                                                
@@ -255,7 +275,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        
                                        for (int i = (temp.length()-1); i >= 0; i--) {
                                                //eliminate N's
-                                               if (toupper(temp[i]) == 'N') { temp[i] == '.'; }
+                                               if (toupper(temp[i]) == 'N') { temp[i] = '.'; }
                                                
                                                numBasesCounted++; 
 
@@ -283,7 +303,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        for (int i = 0; i < temp.length(); i++) {
                                                //eliminate N's
                                                if (toupper(temp[i]) == 'N') { 
-                                                       temp[i] == '.'; 
+                                                       temp[i] = '.'; 
                                                        tempLength--;
                                                        if (tempLength < numbases) { stopSpot = 0; break; }
                                                }
@@ -309,7 +329,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
                                        for (int i = (temp.length()-1); i >= 0; i--) {
                                                //eliminate N's
                                                if (toupper(temp[i]) == 'N') { 
-                                                       temp[i] == '.'; 
+                                                       temp[i] = '.'; 
                                                        tempLength--;
                                                        if (tempLength < numbases) { stopSpot = 0; break; }
                                                }