fixed bug in phylo.diversity rooting. added filename patterns and create filename...

[mothur.git] / aligncommand.cpp

diff --git a/aligncommand.cpp b/aligncommand.cpp
index efc8ce489e79ac5e1d17084f5e952b39590894ba..9d4a609963316d31bcf0740649b88f4b798747ba 100644 (file)
--- a/aligncommand.cpp
+++ b/aligncommand.cpp
@@ -20,21 +20,21 @@
 //**********************************************************************************************************************
 vector<string> AlignCommand::setParameters(){  
        try {
-               CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
-               CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate);
-               CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch);
-               CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
-               CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
-               CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
-               CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
-               CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
-               CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
-               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-               CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
-               CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
-               CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(ptemplate);
+               CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none","fasta-alignreport-accnos",false,true,true); parameters.push_back(pcandidate);
+               CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "","",false,false,true); parameters.push_back(psearch);
+               CommandParameter pksize("ksize", "Number", "", "8", "", "", "","",false,false); parameters.push_back(pksize);
+               CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
+               CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "","",false,false,true); parameters.push_back(palign);
+               CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
+               CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
+               CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
+               CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+               CommandParameter pflip("flip", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pflip);
+               CommandParameter psave("save", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psave);
+               CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(pthreshold);
+               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);          }
@@ -76,28 +76,22 @@ string AlignCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string AlignCommand::getOutputFileNameTag(string type, string inputName=""){   
-       try {
-        string tag = "";
-               map<string, vector<string> >::iterator it;
+string AlignCommand::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") {  tag = "align"; }
-            else if (type == "alignreport") {  tag = "align.report"; }
-            else if (type == "accnos") {  tag = "flip.accnos"; }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
-        }
-        return tag;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "AlignCommand", "getOutputFileName");
-               exit(1);
-       }
+        if (type == "fasta") {  pattern = "[filename],align"; } //makes file like: amazon.align
+        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->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "AlignCommand", "getOutputPattern");
+        exit(1);
+    }
 }
-
 //**********************************************************************************************************************
 AlignCommand::AlignCommand(){  
        try {
@@ -328,9 +322,11 @@ int AlignCommand::execute(){
                        m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
                        
                        if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
-                       string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("fasta");  
-                       string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("alignreport");
-                       string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("accnos");
+            map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s]));
+                       string alignFileName = getOutputFileName("fasta", variables);  
+                       string reportFileName = getOutputFileName("alignreport", variables);
+                       string accnosFileName = getOutputFileName("accnos", variables);
+            
                        bool hasAccnos = true;
                        
                        int numFastaSeqs = 0;