From 7a8fc1115b3871107c09a4b9b307b1f2ab7d3fcf Mon Sep 17 00:00:00 2001 From: westcott Date: Tue, 15 Jun 2010 13:59:28 +0000 Subject: [PATCH] changed how we count sequences in a fastafile to allow for '>' in sequence names --- sequence.cpp | 139 ++++++++++++++++++++++++++++----------------------- 1 file changed, 76 insertions(+), 63 deletions(-) diff --git a/sequence.cpp b/sequence.cpp index 0afe3a9..b9e1c4b 100644 --- a/sequence.cpp +++ b/sequence.cpp @@ -54,29 +54,34 @@ Sequence::Sequence(istringstream& fastaString){ initialize(); fastaString >> name; - name = name.substr(1); - string sequence; - - //read comments - while ((name[0] == '#') && fastaString) { - while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there - sequence = getCommentString(fastaString); - - if (fastaString) { - fastaString >> name; - name = name.substr(1); - }else { - name = ""; - break; - } - } - while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + if (name.length() != 0) { + + name = name.substr(1); + string sequence; - sequence = getSequenceString(fastaString); - setAligned(sequence); - //setUnaligned removes any gap characters for us - setUnaligned(sequence); + //read comments + while ((name[0] == '#') && fastaString) { + while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + sequence = getCommentString(fastaString); + + if (fastaString) { + fastaString >> name; + name = name.substr(1); + }else { + name = ""; + break; + } + } + + while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + + sequence = getSequenceString(fastaString); + setAligned(sequence); + //setUnaligned removes any gap characters for us + setUnaligned(sequence); + }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); } + } catch(exception& e) { m->errorOut(e, "Sequence", "Sequence"); @@ -91,29 +96,33 @@ Sequence::Sequence(istringstream& fastaString, string JustUnaligned){ initialize(); fastaString >> name; - name = name.substr(1); - string sequence; - - //read comments - while ((name[0] == '#') && fastaString) { - while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there - sequence = getCommentString(fastaString); - - if (fastaString) { - fastaString >> name; - name = name.substr(1); - }else { - name = ""; - break; - } - } - while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + if (name.length() != 0) { - sequence = getSequenceString(fastaString); + name = name.substr(1); + string sequence; - //setUnaligned removes any gap characters for us - setUnaligned(sequence); + //read comments + while ((name[0] == '#') && fastaString) { + while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + sequence = getCommentString(fastaString); + + if (fastaString) { + fastaString >> name; + name = name.substr(1); + }else { + name = ""; + break; + } + } + + while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + + sequence = getSequenceString(fastaString); + + //setUnaligned removes any gap characters for us + setUnaligned(sequence); + }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); } } catch(exception& e) { m->errorOut(e, "Sequence", "Sequence"); @@ -158,7 +167,7 @@ Sequence::Sequence(ifstream& fastaFile){ setAligned(sequence); //setUnaligned removes any gap characters for us setUnaligned(sequence); - } + }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); } } catch(exception& e) { @@ -173,30 +182,34 @@ Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){ m = MothurOut::getInstance(); initialize(); fastaFile >> name; - name = name.substr(1); - string sequence; - //read comments - while ((name[0] == '#') && fastaFile) { - while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there - sequence = getCommentString(fastaFile); + if (name.length() != 0) { + name = name.substr(1); + string sequence; - if (fastaFile) { - fastaFile >> name; - name = name.substr(1); - }else { - name = ""; - break; + //read comments + while ((name[0] == '#') && fastaFile) { + while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + sequence = getCommentString(fastaFile); + + if (fastaFile) { + fastaFile >> name; + name = name.substr(1); + }else { + name = ""; + break; + } } - } - - //read real sequence - while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there - - sequence = getSequenceString(fastaFile); - - //setUnaligned removes any gap characters for us - setUnaligned(sequence); + + //read real sequence + while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there + + sequence = getSequenceString(fastaFile); + + //setUnaligned removes any gap characters for us + setUnaligned(sequence); + }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); } + } catch(exception& e) { m->errorOut(e, "Sequence", "Sequence"); -- 2.39.2