modified sequence class to read fasta files with comments. this required modification...

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index 68450fb15a7b140803aab2d54d8c5bc84e7ce688..a689704131d32ae7e8a244babc672695cb432384 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -121,10 +121,12 @@ int FilterSeqsCommand::execute() {
                if(trump != '*' || isTrue(vertical) || soft != 0){
                        while(!inFASTA.eof()){  //read through and create the filter...
                                Sequence seq(inFASTA);
-                               if(trump != '*'){       F.doTrump(seq); }
-                               if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
-                               numSeqs++;
-                               cout.flush();
+                               if (seq.getName() != "") {
+                                       if(trump != '*'){       F.doTrump(seq); }
+                                       if(isTrue(vertical) || soft != 0){      F.getFreqs(seq);        }
+                                       numSeqs++;
+                                       cout.flush();
+                               }
                        }
                
                }
@@ -152,17 +154,19 @@ int FilterSeqsCommand::execute() {
                numSeqs = 0;
                while(!inFasta2.eof()){
                        Sequence seq(inFasta2);
-                       string align = seq.getAligned();
-                       string filterSeq = "";
-       
-                       for(int j=0;j<alignmentLength;j++){
-                               if(filter[j] == '1'){
-                                       filterSeq += align[j];
+                       if (seq.getName() != "") {
+                               string align = seq.getAligned();
+                               string filterSeq = "";
+                               
+                               for(int j=0;j<alignmentLength;j++){
+                                       if(filter[j] == '1'){
+                                               filterSeq += align[j];
+                                       }
                                }
+                               
+                               outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
+                               numSeqs++;
                        }
-
-                       outFASTA << '>' << seq.getName() << endl << filterSeq << endl;
-                       numSeqs++;
                        gobble(inFasta2);
                }
                outFASTA.close();