- }
-}
-
-/**************************************************************************************/
-
-void FilterSeqsCommand::doHard() {
-
- ifstream fileHandle;
- openInputFile(hard, fileHandle);
-
- fileHandle >> filter;
-
-}
-
-/**************************************************************************************/
-
-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);
- bool keep = 0;
-
- for(int i=0;i<alignmentLength;i++){
- if(a[i] >= threshold) { keep = 1; }
- else if(t[i] >= threshold) { keep = 1; }
- else if(g[i] >= threshold) { keep = 1; }
- else if(c[i] >= threshold) { keep = 1; }
-
- if(keep == 0) { 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]++; }