fixed project

[mothur.git] / removeseqscommand.cpp

diff --git a/removeseqscommand.cpp b/removeseqscommand.cpp
index 07e946b78eb8d7d56c7d09a91fd2fb90fc8564a5..a61e467e0bd5820060c052acffefe5fe7983294f 100644 (file)
--- a/removeseqscommand.cpp
+++ b/removeseqscommand.cpp
@@ -125,13 +125,13 @@ RemoveSeqsCommand::RemoveSeqsCommand(string option)  {
                        
                        if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == ""))  { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport or list."); m->mothurOutEndLine(); abort = true; }
                        
-                       int okay = 2;
-                       if (outputDir != "") { okay++; }
-                       if (usedDups != "") { okay++;  }
+                       //int okay = 2;
+                       //if (outputDir != "") { okay++; }
+                       //if (usedDups != "") { okay++;  }
                        
                        if ((usedDups != "") && (namefile == "")) {  m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine();  abort = true; }
                        
-                       if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); m->mothurOutEndLine(); abort = true;  }
+                       //if (parameters.size() > okay) { m->mothurOut("You may only enter one of the following: fasta, name, group, alignreport, or list."); m->mothurOutEndLine(); abort = true;  }
                }
 
        }
@@ -172,10 +172,10 @@ int RemoveSeqsCommand::execute(){
                
                //read through the correct file and output lines you want to keep
                if (fastafile != "")            {               readFasta();    }
-               else if (namefile != "")        {               readName();             }
-               else if (groupfile != "")       {               readGroup();    }
-               else if (alignfile != "")       {               readAlign();    }
-               else if (listfile != "")        {               readList();             }
+               if (namefile != "")                     {               readName();             }
+               if (groupfile != "")            {               readGroup();    }
+               if (alignfile != "")            {               readAlign();    }
+               if (listfile != "")                     {               readList();             }
                
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
                
@@ -199,7 +199,7 @@ int RemoveSeqsCommand::execute(){
 int RemoveSeqsCommand::readFasta(){
        try {
                if (outputDir == "") {  outputDir += hasPath(fastafile);  }
-               string outputFileName = getRootName(fastafile) + "pick" + getExtension(fastafile);
+               string outputFileName = outputDir + getRootName(getSimpleName(fastafile)) + "pick" + getExtension(fastafile);
                ofstream out;
                openOutputFile(outputFileName, out);
                
@@ -221,7 +221,7 @@ int RemoveSeqsCommand::readFasta(){
                                        wroteSomething = true;
                                        
                                        currSeq.printSequence(out);
-                               }else {         names.erase(name);              }
+                               }//else {               names.erase(name);              }
                        }
                        gobble(in);
                }
@@ -245,7 +245,7 @@ int RemoveSeqsCommand::readFasta(){
 int RemoveSeqsCommand::readList(){
        try {
                if (outputDir == "") {  outputDir += hasPath(listfile);  }
-               string outputFileName = getRootName(listfile) + "pick" +  getExtension(listfile);
+               string outputFileName = outputDir + getRootName(getSimpleName(listfile)) + "pick" +  getExtension(listfile);
                ofstream out;
                openOutputFile(outputFileName, out);
                
@@ -316,8 +316,8 @@ int RemoveSeqsCommand::readList(){
 int RemoveSeqsCommand::readName(){
        try {
                if (outputDir == "") {  outputDir += hasPath(namefile);  }
-               string outputFileName = getRootName(namefile) + "pick" + getExtension(namefile);
-               string outputFileName2 = getRootName(namefile) + "dups.accnos";
+               string outputFileName = outputDir + getRootName(getSimpleName(namefile)) + "pick" + getExtension(namefile);
+               string outputFileName2 = outputDir + getRootName(getSimpleName(namefile)) + "dups.accnos";
 
                ofstream out2;
                if (dups) {      openOutputFile(outputFileName2, out2); }
@@ -415,7 +415,7 @@ int RemoveSeqsCommand::readName(){
 int RemoveSeqsCommand::readGroup(){
        try {
                if (outputDir == "") {  outputDir += hasPath(groupfile);  }
-               string outputFileName = getRootName(groupfile) + "pick" + getExtension(groupfile);
+               string outputFileName = outputDir + getRootName(getSimpleName(groupfile)) + "pick" + getExtension(groupfile);
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -435,7 +435,7 @@ int RemoveSeqsCommand::readGroup(){
                        if (names.count(name) == 0) {
                                wroteSomething = true;
                                out << name << '\t' << group << endl;
-                       }else {         names.erase(name);              }
+                       }//else {               names.erase(name);              }
                                        
                        gobble(in);
                }
@@ -460,7 +460,7 @@ int RemoveSeqsCommand::readGroup(){
 int RemoveSeqsCommand::readAlign(){
        try {
                if (outputDir == "") {  outputDir += hasPath(alignfile);  }
-               string outputFileName = getRootName(getRootName(alignfile)) + "pick.align.report";
+               string outputFileName = outputDir + getRootName(getSimpleName(alignfile)) + "pick.align.report";
                ofstream out;
                openOutputFile(outputFileName, out);
 
@@ -496,7 +496,7 @@ int RemoveSeqsCommand::readAlign(){
                                out << endl;
                                
                        }else {//still read just don't do anything with it
-                               names.erase(name);      
+                               //names.erase(name);    
                                
                                //read rest
                                for (int i = 0; i < 15; i++) {