Minor modifications to output filenames

#792

source/commands/aligncommand.cpp

@@ -114,7 +114,7 @@ string AlignCommand::getOutputPattern(string type) {
         string pattern = "";
 
         if (type == "fasta") {  pattern = "[filename],align"; } //makes file like: amazon.align
-        else if (type == "alignreport") {  pattern = "[filename],align.report"; }
+        else if (type == "alignreport") {  pattern = "[filename],align_report"; }
         else if (type == "accnos") {  pattern = "[filename],flip.accnos"; }
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true);  }
 

source/commands/getseqscommand.h

@@ -13,6 +13,9 @@
 #include "command.hpp"
 #include "sequencedb.h"
 
+//**********************************************************************************************************************
+
+
 class GetSeqsCommand : public Command {
 
 	public:
@@ -26,7 +29,8 @@ class GetSeqsCommand : public Command {
 		string getCommandCategory()		{ return "Sequence Processing";		}
 
 	string getHelpString();	
-    string getOutputPattern(string);	
+    string getOutputPattern(string);
+    string getCommonQuestions();
 		string getCitation() { return "http://www.mothur.org/wiki/Get.seqs"; }
 		string getDescription()		{ return "gets sequences from a list, fasta, count, name, group, alignreport, quality, fastq, contigsreport or taxonomy file"; }
 
@@ -36,29 +40,29 @@ class GetSeqsCommand : public Command {
 
 	private:
 		set<string> names;
-		vector<string> outputNames;
-		string accnosfile, accnosfile2, fastafile, fastqfile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile,  format, contigsreportfile;
+        vector<string> fastafiles, namefiles, groupfiles, countfiles, alignfiles, listfiles, taxfiles, fastqfiles, contigsreportfiles, qualityfiles, outputNames;
+		string accnosfile, accnosfile2, format, inputFileName;
 		bool abort, dups;
         map<string, string> uniqueMap;
-        //for debug
-        map<string, set<string> > sanity; //maps file type to names chosen for file. something like "fasta" -> vector<string>. If running in debug mode this is filled and we check to make sure all the files have the same names. If they don't we output the differences for the user.
+        map<string, set<string> > sanity; //for debug //maps file type to names chosen for file. something like "fasta" -> vector<string>. If running in debug mode this is filled and we check to make sure all the files have the same names. If they don't we output the differences for the user.
 
-		void readFasta();
-        void readFastq();
-		void readName();
-		void readGroup();
-        void readCount();
-		void readAlign();
-		void readList();
-		void readTax();
-		void readQual();
-        void readContigs();
-		int compareAccnos();
-        int runSanityCheck();
+        void readFasta(string);
+        void readFastq(string);
+        void readName(string);
+        void readGroup(string);
+        void readCount(string);
+        void readAlign(string);
+        void readList(string);
+        void readTax(string);
+        void readQual(string);
+        void readContigs(string);
+		int compareAccnos(string);
+        int runSanityCheck(string, string, string, string, string, string);
         int createMisMatchFile(ofstream&, string, string, set<string>, set<string>);
 
 
 };
+//**********************************************************************************************************************
 
 #endif
 

source/commands/listseqscommand.cpp

@@ -87,9 +87,6 @@ ListSeqsCommand::ListSeqsCommand(string option) : Command()  {
 			map<string,string> parameters = parser.getParameters();
 
 			ValidParameters validParameter;
-
-
-			//check for required parameters
 			fastafiles = validParameter.validFiles(parameters, "fasta");
             if (fastafiles.size() != 0) {
                 if (fastafiles[0] == "not open") { abort = true; }

source/commands/makecontigscommand.cpp

@@ -195,7 +195,7 @@ string MakeContigsCommand::getOutputPattern(string type) {
         if (type == "fasta") {  pattern = "[filename],[tag],contigs.fasta"; }
         else if (type == "qfile") {  pattern = "[filename],[tag],contigs.qual"; }
         else if (type == "count") {  pattern = "[filename],[tag],contigs.count_table"; }
-        else if (type == "report") {  pattern = "[filename],[tag],contigs.report"; }
+        else if (type == "report") {  pattern = "[filename],[tag],contigs_report"; }
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true);  }
 
         return pattern;

source/commands/removelineagecommand.cpp

@@ -93,7 +93,7 @@ string RemoveLineageCommand::getOutputPattern(string type) {
         else if (type == "count")           {   pattern = "[filename],pick,[extension]";    }
         else if (type == "list")            {   pattern = "[filename],[distance],pick,[extension]";    }
         else if (type == "shared")          {   pattern = "[filename],[distance],pick,[extension]";    }
-        else if (type == "alignreport")     {   pattern = "[filename],pick.align.report";       }
+        else if (type == "alignreport")     {   pattern = "[filename],pick.[extension]";       }
         else if (type == "accnos")          {   pattern = "[filename],accnos";                  }
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true);  }
 

source/commands/removeseqscommand.cpp

@@ -91,8 +91,8 @@ string RemoveSeqsCommand::getOutputPattern(string type) {
         else if (type == "count")       {   pattern = "[filename],pick,[extension]";    }
         else if (type == "list")        {   pattern = "[filename],[distance],pick,[extension]";    }
         else if (type == "qfile")       {   pattern = "[filename],pick,[extension]";    }
-        else if (type == "alignreport")      {   pattern = "[filename],pick.align.report";    }
-        else if (type == "contigsreport")    {   pattern = "[filename],pick.contigs.report";  }
+        else if (type == "alignreport")      {   pattern = "[filename],pick.[extension]";    }
+        else if (type == "contigsreport")    {   pattern = "[filename],pick.[extension]";  }
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true);  }
 
         return pattern;
@@ -845,6 +845,7 @@ void RemoveSeqsCommand::readAlign(){
 		if (outputdir == "") {  thisOutputDir += util.hasPath(alignfile);  }
 		map<string, string> variables; 
 		variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(alignfile));
+        variables["[extension]"] = util.getExtension(alignfile);
 		string outputFileName = getOutputFileName("alignreport", variables);
 
 		ofstream out; util.openOutputFile(outputFileName, out);
@@ -904,6 +905,7 @@ void RemoveSeqsCommand::readContigs(){
         if (outputdir == "") {  thisOutputDir += util.hasPath(contigsreportfile);  }
         map<string, string> variables;
         variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(contigsreportfile));
+        variables["[extension]"] = util.getExtension(contigsreportfile);
         string outputFileName = getOutputFileName("contigsreport", variables);
         ofstream out; util.openOutputFile(outputFileName, out);
 

source/commands/screenseqscommand.cpp

@@ -145,8 +145,8 @@ string ScreenSeqsCommand::getOutputPattern(string type) {
         else if (type == "count")       {   pattern = "[filename],good,[extension]";    }
         else if (type == "accnos")      {   pattern = "[filename],bad.accnos";          }
         else if (type == "qfile")       {   pattern = "[filename],good,[extension]";    }
-        else if (type == "alignreport")      {   pattern = "[filename],good.align.report";    }
-        else if (type == "contigsreport")      {   pattern = "[filename],good.contigs.report";    }
+        else if (type == "alignreport")      {   pattern = "[filename],good.[extension]";    }
+        else if (type == "contigsreport")      {   pattern = "[filename],good.[extension]";    }
         else if (type == "summary")      {   pattern = "[filename],good.summary";    }
         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true);  }
 
@@ -575,6 +575,7 @@ int ScreenSeqsCommand::screenAlignReport(map<string, string>& badSeqNames){
 
         map<string, string> variables;
         variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(alignreport));
+        variables["[extension]"] = util.getExtension(alignreport);
         string outSummary =  getOutputFileName("alignreport",variables);
         outputNames.push_back(outSummary); outputTypes["alignreport"].push_back(outSummary);
 
@@ -657,6 +658,7 @@ int ScreenSeqsCommand::screenContigs(map<string, string>& badSeqNames){
     try{
         map<string, string> variables;
         variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(contigsreport));
+        variables["[extension]"] = util.getExtension(contigsreport);
         string outSummary =  getOutputFileName("contigsreport",variables);
         outputNames.push_back(outSummary); outputTypes["contigsreport"].push_back(outSummary);