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fixed bug in phylo.diversity rooting. added filename patterns and create filename...
[mothur.git] / prcseqscommand.cpp
diff --git a/prcseqscommand.cpp b/prcseqscommand.cpp
index de2cb2058a064b043f424921f599edd6f7f8bf24..5fc9f988be038bb02a724e38cc11b2d9ddf1fa3e 100644 (file)
--- a/prcseqscommand.cpp
+++ b/prcseqscommand.cpp
@@ -11,21 +11,21 @@
 //**********************************************************************************************************************
 vector<string> PcrSeqsCommand::setParameters(){        
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               CommandParameter poligos("oligos", "InputTypes", "", "", "ecolioligos", "none", "none",false,false); parameters.push_back(poligos);
-        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 ptax("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptax);
-        CommandParameter pecoli("ecoli", "InputTypes", "", "", "ecolioligos", "none", "none",false,false); parameters.push_back(pecoli);
-               CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
-               CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
-               CommandParameter pnomatch("nomatch", "Multiple", "reject-keep", "reject", "", "", "",false,false); parameters.push_back(pnomatch);
-               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepprimer);
-        CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pkeepdots);
-        CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,true,true); parameters.push_back(pfasta);
+               CommandParameter poligos("oligos", "InputTypes", "", "", "ecolioligos", "none", "none","",false,false,true); parameters.push_back(poligos);
+        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","name",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","count",false,false,true); parameters.push_back(pcount);
+               CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","group",false,false,true); parameters.push_back(pgroup);
+        CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none","taxonomy",false,false,true); parameters.push_back(ptax);
+        CommandParameter pecoli("ecoli", "InputTypes", "", "", "ecolioligos", "none", "none","",false,false); parameters.push_back(pecoli);
+               CommandParameter pstart("start", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pstart);
+               CommandParameter pend("end", "Number", "", "-1", "", "", "","",false,false); parameters.push_back(pend);
+               CommandParameter pnomatch("nomatch", "Multiple", "reject-keep", "reject", "", "", "","",false,false); parameters.push_back(pnomatch);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+               CommandParameter pkeepprimer("keepprimer", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkeepprimer);
+        CommandParameter pkeepdots("keepdots", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pkeepdots);
+        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);          }
@@ -58,31 +58,25 @@ string PcrSeqsCommand::getHelpString(){
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
-string PcrSeqsCommand::getOutputFileNameTag(string type, string inputName=""){ 
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string PcrSeqsCommand::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 == "fasta") {  outputFileName =  "pcr.fasta"; }
-            else if (type == "taxonomy") {  outputFileName =  "pcr" + m->getExtension(inputName); }
-            else if (type == "group") {  outputFileName =  "pcr" + m->getExtension(inputName); }
-            else if (type == "name") {  outputFileName =  "pcr" + m->getExtension(inputName); }
-            else if (type == "count") {  outputFileName =  "pcr" + m->getExtension(inputName); }
-            else if (type == "accnos") {  outputFileName =  "bad.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, "PcrSeqsCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "fasta")            {   pattern = "[filename],pcr,[extension]-[filename],[tag],pcr,[extension]";    }
+        else if (type == "taxonomy")    {   pattern = "[filename],pcr,[extension]";    }
+        else if (type == "name")        {   pattern = "[filename],pcr,[extension]";    }
+        else if (type == "group")       {   pattern = "[filename],pcr,[extension]";    }
+        else if (type == "count")       {   pattern = "[filename],pcr,[extension]";    }
+        else if (type == "accnos")      {   pattern = "[filename],bad.accnos";    }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "PcrSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 
@@ -315,10 +309,13 @@ int PcrSeqsCommand::execute(){
         
         string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
-               string trimSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("fasta");
+        map<string, string> variables; 
+        variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+        variables["[extension]"] = m->getExtension(fastafile);
+               string trimSeqFile = getOutputFileName("fasta",variables);
                outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
-        
-        string badSeqFile = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "scrap." + getOutputFileNameTag("fasta");
+        variables["[tag]"] = "scrap";
+        string badSeqFile = getOutputFileName("fasta",variables);
                
                
         length = 0;
@@ -914,7 +911,9 @@ int PcrSeqsCommand::writeAccnos(set<string> badNames){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(fastafile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("accnos");
+        map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(fastafile));
+               string outputFileName = getOutputFileName("accnos",variables);
         outputNames.push_back(outputFileName); outputTypes["accnos"].push_back(outputFileName);
         
         ofstream out;
@@ -976,7 +975,10 @@ int PcrSeqsCommand::readName(set<string>& names){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(namefile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + getOutputFileNameTag("name", namefile);
+               map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(namefile));
+        variables["[extension]"] = m->getExtension(namefile);
+               string outputFileName = getOutputFileName("name", variables);
         
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -1034,7 +1036,10 @@ int PcrSeqsCommand::readGroup(set<string> names){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(groupfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + getOutputFileNameTag("group", groupfile);
+               map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(groupfile));
+        variables["[extension]"] = m->getExtension(groupfile);
+               string outputFileName = getOutputFileName("group", variables);
                
                ofstream out;
                m->openOutputFile(outputFileName, out);
@@ -1081,7 +1086,11 @@ int PcrSeqsCommand::readTax(set<string> names){
        try {
                string thisOutputDir = outputDir;
                if (outputDir == "") {  thisOutputDir += m->hasPath(taxfile);  }
-               string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + getOutputFileNameTag("taxonomy", taxfile);
+               map<string, string> variables; 
+               variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(taxfile));
+        variables["[extension]"] = m->getExtension(taxfile);
+               string outputFileName = getOutputFileName("taxonomy", variables);
+
                ofstream out;
                m->openOutputFile(outputFileName, out);
         
@@ -1128,7 +1137,11 @@ int PcrSeqsCommand::readCount(set<string> badSeqNames){
                m->openInputFile(countfile, in);
                set<string>::iterator it;
                
-               string goodCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + getOutputFileNameTag("count", countfile);
+               map<string, string> variables; 
+               variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(countfile));
+        variables["[extension]"] = m->getExtension(countfile);
+               string goodCountFile = getOutputFileName("count", variables);
+
         outputNames.push_back(goodCountFile);  outputTypes["count"].push_back(goodCountFile);
                ofstream goodCountOut;  m->openOutputFile(goodCountFile, goodCountOut);
                
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