merged pat's trim seqs edits with sarah's major overhaul of global data; also added...

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 1363216ffe56267adf628c42fe9ede4065c8f626..95d51f329f30d8a639d0772844e54be5246e5005 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -8,12 +8,12 @@
  */
 
 #include "filterseqscommand.h"
+#include "sequence.hpp"
 
 /**************************************************************************************/
 
 FilterSeqsCommand::FilterSeqsCommand(string option){
        try {
-               globaldata = GlobalData::getInstance();
                abort = false;
                
                //allow user to run help
@@ -24,40 +24,35 @@ FilterSeqsCommand::FilterSeqsCommand(string option){
                        string Array[] =  {"fasta", "trump", "soft", "hard", "vertical"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
-                       parser = new OptionParser();
-                       parser->parse(option, parameters);  delete parser;
+                       OptionParser parser(option);
+                       map<string,string> parameters = parser.getParameters();
+                       
+                       ValidParameters validParameter;
                        
-                       ValidParameters* validParameter = new ValidParameters();
-               
                        //check to make sure all parameters are valid for command
-                       for (it = parameters.begin(); it != parameters.end(); it++) { 
-                               if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+                       for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+                               if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
                        
                        //check for required parameters
-                       fastafile = validParameter->validFile(parameters, "fasta", true);
+                       fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not found") { cout << "fasta is a required parameter for the filter.seqs command." << endl; abort = true; }
                        else if (fastafile == "not open") { abort = true; }     
-                       else { 
-                               globaldata->setFastaFile(fastafile);
-                       }
-                       
+
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
                        
                        string temp;
-                       temp = validParameter->validFile(parameters, "trump", false);                           if (temp == "not found") { temp = "."; }
+                       temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
                        trump = temp[0];
                        
-                       temp = validParameter->validFile(parameters, "soft", false);                            if (temp == "not found") { soft = 0; }
+                       temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
                        else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
                        
-                       hard = validParameter->validFile(parameters, "hard", true);                                     if (hard == "not found") { hard = ""; }
+                       hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
                        else if (hard == "not open") { abort = true; }  
                        
-                       vertical = validParameter->validFile(parameters, "vertical", false);            if (vertical == "not found") { vertical = "F"; }
-       
-                       delete validParameter;
+                       vertical = validParameter.validFile(parameters, "vertical", false);             if (vertical == "not found") { vertical = "T"; }
                        
                        numSeqs = 0;
                        
@@ -81,10 +76,10 @@ void FilterSeqsCommand::help(){
                cout << "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file." << "\n";
                cout << "The filter.seqs command parameters are fasta, trump, soft, hard and vertical.  " << "\n";
                cout << "The fasta parameter is required." << "\n";
-               cout << "The trump parameter .... The default is '.'" << "\n";
+               cout << "The trump parameter .... The default is ..." << "\n";
                cout << "The soft parameter .... The default is ...." << "\n";
                cout << "The hard parameter .... The default is ...." << "\n";
-               cout << "The vertical parameter .... The default is F." << "\n";
+               cout << "The vertical parameter .... The default is T." << "\n";
                cout << "The filter.seqs command should be in the following format: " << "\n";
                cout << "filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) " << "\n";
                cout << "Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T)." << "\n";
@@ -117,7 +112,7 @@ void FilterSeqsCommand::doHard() {
 void FilterSeqsCommand::doTrump(Sequence seq) {
        
        string curAligned = seq.getAligned();
-       
+
        for(int j = 0; j < alignmentLength; j++) {
                if(curAligned[j] == trump){
                        filter[j] = '0';
@@ -141,15 +136,9 @@ void FilterSeqsCommand::doVertical() {
 void FilterSeqsCommand::doSoft() {
        
        int threshold = int (soft * numSeqs);
-       bool keep = 0;
        
        for(int i=0;i<alignmentLength;i++){
-               if(a[i] >= threshold)           {       keep = 1;       }
-               else if(t[i] >= threshold)      {       keep = 1;       }
-               else if(g[i] >= threshold)      {       keep = 1;       }
-               else if(c[i] >= threshold)      {       keep = 1;       }
-               
-               if(keep == 0)   {       filter[i] = 0;          }
+               if(a[i] < threshold && t[i] < threshold && g[i] < threshold && c[i] < threshold){       filter[i] = 0;  }
        }
 }
 
@@ -194,11 +183,10 @@ int FilterSeqsCommand::execute() {
                if(hard.compare("") != 0)       {       doHard();               }
                else                                            {       filter = string(alignmentLength, '1');  }
 
-               if(isTrue(vertical) || soft != 0){
-               
-                       while(!inFASTA.eof()){
+               if(trump != '*' || isTrue(vertical) || soft != 0){
+                       while(!inFASTA.eof()){  //read through and create the filter...
                                Sequence seq(inFASTA);
-                               doTrump(seq);   
+                               if(trump != '*'){       doTrump(seq);   }
                                if(isTrue(vertical) || soft != 0){      getFreqs(seq);  }
                                numSeqs++;
                                cout.flush();
@@ -253,8 +241,6 @@ int FilterSeqsCommand::execute() {
                cout << "Length of the original alignment: " << alignmentLength << endl;
                cout << "Number of sequences used to construct filter: " << numSeqs << endl;
                
-               globaldata->clear();
-               
                return 0;
                
        }