*** empty log message ***

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 7330268a83ccd9b044f38fa28f58386132562e2d..e8c96b3a42b88b6dbd4a003fe3a2454d2bbb4cb3 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -16,7 +16,7 @@ FilterSeqsCommand::FilterSeqsCommand(){
        
        if(globaldata->getFastaFile() == "")            {       cout << "You must enter a fasta formatted file" << endl;        }
        trump = globaldata->getTrump()[0];
-       vertical = 
+//     vertical = 
 //     readSeqs->read();
 //     db = readSeqs->getDB();
 //     numSeqs = db->size();
@@ -30,43 +30,43 @@ FilterSeqsCommand::FilterSeqsCommand(){
 
 void FilterSeqsCommand::doHard() {
        
-//     string hardName = globaldata->getHard();
-//     string hardFilter = "";
-//             
-//     ifstream fileHandle;
-//     openInputFile(hardName, fileHandle);
-//     
-//     fileHandle >> hardFilter;
-//     
-//     if(hardFilter.length() != filter.length()){
-//             cout << "The hard filter is not the same length as the alignment: Hard filter will not be applied." << endl;
-//     }
-//     else{
-//             filter = hardFilter;
-//     }
+       string hardName = globaldata->getHard();
+       string hardFilter = "";
+               
+       ifstream fileHandle;
+       openInputFile(hardName, fileHandle);
+       
+       fileHandle >> hardFilter;
+       
+       if(hardFilter.length() != filter.length()){
+               cout << "The hard filter is not the same length as the alignment: Hard filter will not be applied." << endl;
+       }
+       else{
+               filter = hardFilter;
+       }
 
 }
 
 /**************************************************************************************/
 
-void FilterSeqsCommand::doTrump() {
+void FilterSeqsCommand::doTrump(Sequence seq) {
 
        
-       for(int i = 0; i < numSeqs; i++) {
-               string curAligned = db->get(i).getAligned();;
-
-               for(int j = 0; j < alignmentLength; j++) {
-                       if(curAligned[j] == trump){
-                               filter[j] = '0';
-                       }
-               }
-       }
+//     for(int i = 0; i < numSeqs; i++) {
+//             string curAligned = db->get(i).getAligned();;
+//
+//             for(int j = 0; j < alignmentLength; j++) {
+//                     if(curAligned[j] == trump){
+//                             filter[j] = '0';
+//                     }
+//             }
+//     }
 
 }
 
 /**************************************************************************************/
 
-void FilterSeqsCommand::doVertical() {
+void FilterSeqsCommand::doVertical(Sequence seq) {
 
 //     vector<int> counts(alignmentLength, 0);
 //     
@@ -86,7 +86,7 @@ void FilterSeqsCommand::doVertical() {
 
 /**************************************************************************************/
 
-void FilterSeqsCommand::doSoft() {
+void FilterSeqsCommand::doSoft(Sequence seq) {
 
 //     int softThreshold = numSeqs * (float)atoi(globaldata->getSoft().c_str()) / 100.0;
 //
@@ -121,16 +121,20 @@ int FilterSeqsCommand::execute() {
                ifstream inFASTA;
                openInputFile(globaldata->getFastaFile(), inFASTA);
                
-               Sequence currSequence(inFASTA);
-               alignmentLength = currSequence.getAlignLength();
-               
-               //while
+               Sequence testSeq(inFASTA);
+               alignmentLength = testSeq.getAlignLength();
+               inFASTA.seekg(0);
+               int numSeqs = 0;
                
-               
-               if(globaldata->getHard().compare("") != 0)      {       doHard();               }       //      has to be applied first!
-               if(globaldata->getTrump().compare("") != 0)     {       doTrump();              }
-               if(isTrue(globaldata->getVertical()) == true)           {       doVertical();   }
-               if(globaldata->getSoft().compare("") != 0)      {       doSoft();               }
+               if(globaldata->getHard().compare("") != 0)      {       doHard();                                                               }
+               else                                                                            {       filter = string(alignmentLength, '1');  }
+               while(!inFASTA.eof()){
+                       Sequence seq(inFASTA);
+                       if(globaldata->getTrump().compare("") != 0)     {       doTrump(seq);           }
+                       if(isTrue(globaldata->getVertical()) == 1)      {       doVertical(seq);        }
+//                     if(globaldata->getSoft().compare("") != 0)      {       doSoft(seq);            }                       
+                       numSeqs++;
+               }
                
                ofstream outfile;
                string filterFile = getRootName(globaldata->inputFileName) + "filter";
@@ -142,17 +146,17 @@ int FilterSeqsCommand::execute() {
                string filteredFasta = getRootName(globaldata->inputFileName) + "filter.fasta";
                openOutputFile(filteredFasta, outfile);
 
-               for(int i=0;i<numSeqs;i++){
-                       string curAligned = db->get(i).getAligned();
-                       outfile << '>' << db->get(i).getName() << endl;
-                       for(int j=0;j<alignmentLength;j++){
-                               if(filter[j] == '1'){
-                                       outfile << curAligned[j];
-                               }
-                       }
-                       outfile << endl;
-               }
-               outfile.close();
+//             for(int i=0;i<numSeqs;i++){
+//                     string curAligned = db->get(i).getAligned();
+//                     outfile << '>' << db->get(i).getName() << endl;
+//                     for(int j=0;j<alignmentLength;j++){
+//                             if(filter[j] == '1'){
+//                                     outfile << curAligned[j];
+//                             }
+//                     }
+//                     outfile << endl;
+//             }
+//             outfile.close();
                
                int filteredLength = 0;
                for(int i=0;i<alignmentLength;i++){

diff --git a/filterseqscommand.h b/filterseqscommand.h
index 6fe171a1ee7f3027377e0e02e6a78e2831a86a0b..924c36627fec65abd777c5ae530bf154583e954f 100644 (file)
--- a/filterseqscommand.h
+++ b/filterseqscommand.h
@@ -26,10 +26,10 @@ public:
        int execute();  
        
 private:
-       void doTrump();
-       void doSoft();
        void doHard();
-       void doVertical();
+       void doTrump(Sequence);
+       void doSoft(Sequence);
+       void doVertical(Sequence);
        string filter;  
        int alignmentLength;