added sharedotu parameter to venn command. working of make.contigs.

[mothur.git] / sequence.cpp

diff --git a/sequence.cpp b/sequence.cpp
index d877f4b93f33d8123ff6a1a9f7f839dc680fcf61..96662bc36d4b77e1cb8b7a884f4e8460969033f4 100644 (file)
--- a/sequence.cpp
+++ b/sequence.cpp
@@ -300,7 +300,7 @@ string Sequence::getSequenceString(ifstream& fastaFile, int& numAmbig) {
                        if(letter == '>'){
                                fastaFile.putback(letter);
                                break;
-                       }
+                       }else if (letter == ' ') {;}
                        else if(isprint(letter)){
                                letter = toupper(letter);
                                if(letter == 'U'){letter = 'T';}
@@ -354,7 +354,7 @@ string Sequence::getSequenceString(istringstream& fastaFile, int& numAmbig) {
                        if(letter == '>'){
                                fastaFile.putback(letter);
                                break;
-                       }
+                       }else if (letter == ' ') {;}
                        else if(isprint(letter)){
                                letter = toupper(letter);
                                if(letter == 'U'){letter = 'T';}
@@ -603,7 +603,7 @@ int Sequence::getLongHomoPolymer(){
 int Sequence::getStartPos(){
        if(startPos == -1){
                for(int j = 0; j < alignmentLength; j++) {
-                       if(aligned[j] != '.'){
+                       if((aligned[j] != '.')&&(aligned[j] != '-')){
                                startPos = j + 1;
                                break;
                        }
@@ -668,7 +668,7 @@ int Sequence::filterFromPos(int end){
 int Sequence::getEndPos(){
        if(endPos == -1){
                for(int j=alignmentLength-1;j>=0;j--){
-                       if(aligned[j] != '.'){
+                       if((aligned[j] != '.')&&(aligned[j] != '-')){
                                endPos = j + 1;
                                break;
                        }
@@ -682,7 +682,7 @@ int Sequence::getEndPos(){
 //********************************************************************************************************************
 
 void Sequence::padFromPos(int end){
-       cout << end << '\t' << endPos << endl;
+       //cout << end << '\t' << endPos << endl;
        for(int j = end; j < endPos; j++) {
                aligned[j] = '.';
        }