X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chopseqscommand.cpp;h=05037f6817a5a554a029a7d635460d048bf73203;hb=529ec122f7cac4af987e121d150b878d7c7a0d5d;hp=fc4327f210d04241b5c1e7a6056759525998c738;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index fc4327f..05037f6 100644
--- 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);
@@ -165,7 +185,7 @@ int ChopSeqsCommand::execute(){
 			
 			Sequence seq(in);
 			
-			if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); remove(outputFileName.c_str()); remove(outputFileNameAccnos.c_str()); return 0;  }
+			if (m->control_pressed) { outputTypes.clear(); in.close(); out.close(); outAcc.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputFileNameAccnos); return 0;  }
 			
 			if (seq.getName() != "") {
 				string newSeqString = getChopped(seq);
@@ -188,7 +208,7 @@ int ChopSeqsCommand::execute(){
 		m->mothurOut(outputFileName); m->mothurOutEndLine();	outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
 		
 		if (wroteAccnos) { m->mothurOut(outputFileNameAccnos); m->mothurOutEndLine(); outputNames.push_back(outputFileNameAccnos); outputTypes["accnos"].push_back(outputFileNameAccnos); }
-		else {  remove(outputFileNameAccnos.c_str());  }
+		else {  m->mothurRemove(outputFileNameAccnos);  }
 		
 		m->mothurOutEndLine();
 		
@@ -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++; 
 						
@@ -241,7 +261,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
 					}
 					
 					if (stopSpot == 0) { temp = ""; }
-					else {  temp = temp.substr(0, stopSpot);  }
+					else {  temp = temp.substr(0, stopSpot+1);  }
 							
 				}else { 
 					if (!Short) { temp = ""; } //sequence too short
@@ -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; }
 						}
@@ -294,7 +314,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
 					}
 					
 					if (stopSpot == 0) { temp = ""; }
-					else {  temp = temp.substr(0, stopSpot);  }
+					else {  temp = temp.substr(0, stopSpot+1);  }
 							
 				}else { 
 					if (!Short) { temp = ""; } //sequence too short
@@ -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; }
 						}
@@ -320,7 +340,7 @@ string ChopSeqsCommand::getChopped(Sequence seq) {
 					}
 				
 					if (stopSpot == 0) { temp = ""; }
-					else {  temp = temp.substr(stopSpot+1);  }
+					else {  temp = temp.substr(stopSpot);  }
 				}else { 
 					if (!Short) { temp = ""; } //sequence too short
 				}