made changes to concensus to find a better tree. also fixed minor bug in venn with...

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index ad491aa1252ccb28553b12daf0f353533428d531..68450fb15a7b140803aab2d54d8c5bc84e7ce688 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -56,6 +56,13 @@ FilterSeqsCommand::FilterSeqsCommand(string option){
                        
                        numSeqs = 0;
                        
+                       if (abort == false) {
+                       
+                               if (soft != 0)                  {  F.setSoft(soft);             }
+                               if (trump != '*')               {  F.setTrump(trump);   }
+                       
+                       }
+                                               
                }
                
        }
@@ -90,70 +97,6 @@ void FilterSeqsCommand::help(){
 
 /**************************************************************************************/
 
-void FilterSeqsCommand::doHard() {
-       
-       ifstream fileHandle;
-       openInputFile(hard, fileHandle);
-       
-       fileHandle >> filter;
-       
-       fileHandle.close();
-
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doTrump(Sequence seq) {
-       
-       string curAligned = seq.getAligned();
-
-       for(int j = 0; j < alignmentLength; j++) {
-               if(curAligned[j] == trump){
-                       filter[j] = '0';
-               }
-       }
-
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doVertical() {
-
-       for(int i=0;i<alignmentLength;i++){
-               if(gap[i] == numSeqs)   {       filter[i] = '0';        }
-       }
-       
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doSoft() {
-       
-       int threshold = int (soft * numSeqs);
-       
-       for(int i=0;i<alignmentLength;i++){
-               if(a[i] < threshold && t[i] < threshold && g[i] < threshold && c[i] < threshold){       filter[i] = 0;  }
-       }
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::getFreqs(Sequence seq) {
-
-       string curAligned = seq.getAligned();;
-       
-       for(int j=0;j<alignmentLength;j++){
-               if(toupper(curAligned[j]) == 'A')                                                                               {       a[j]++;         }
-               else if(toupper(curAligned[j]) == 'T' || toupper(curAligned[j]) == 'U') {       t[j]++;         }
-               else if(toupper(curAligned[j]) == 'G')                                                                  {       g[j]++;         }
-               else if(toupper(curAligned[j]) == 'C')                                                                  {       c[j]++;         }
-               else if(curAligned[j] == '-' || curAligned[j] == '.')                                   {       gap[j]++;       }
-       }
-       
-}
-
-/**************************************************************************************/
-
 int FilterSeqsCommand::execute() {     
        try {
        
@@ -166,31 +109,33 @@ int FilterSeqsCommand::execute() {
                alignmentLength = testSeq.getAlignLength();
                inFASTA.seekg(0);
                
+               F.setLength(alignmentLength);
+               
                if(soft != 0 || isTrue(vertical)){
-                       a.assign(alignmentLength, 0);
-                       t.assign(alignmentLength, 0);
-                       g.assign(alignmentLength, 0);
-                       c.assign(alignmentLength, 0);
-                       gap.assign(alignmentLength, 0);
+                       F.initialize();
                }
                
-               if(hard.compare("") != 0)       {       doHard();               }
-               else                                            {       filter = string(alignmentLength, '1');  }
+               if(hard.compare("") != 0)       {       F.doHard(hard);         }
+               else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 
                if(trump != '*' || isTrue(vertical) || soft != 0){
                        while(!inFASTA.eof()){  //read through and create the filter...
                                Sequence seq(inFASTA);
-                               if(trump != '*'){       doTrump(seq);   }
-                               if(isTrue(vertical) || soft != 0){      getFreqs(seq);  }
+                               if(trump != '*'){       F.doTrump(seq); }
+                               if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
                                numSeqs++;
                                cout.flush();
                        }
                
                }
                inFASTA.close();
+               F.setNumSeqs(numSeqs);
+               
+               
+               if(isTrue(vertical) == 1)       {       F.doVertical(); }
+               if(soft != 0)                           {       F.doSoft();             }
                
-               if(isTrue(vertical) == 1)       {       doVertical();   }
-               if(soft != 0)   {       doSoft();               }                       
+               filter = F.getFilter();
 
                ofstream outFilter;
                string filterFile = getRootName(fastafile) + "filter";