- void doTrump();
- void doSoft();
- void doFilter();
-
- GlobalData* globaldata;
- string filename, trump, filter;
-
- ReadFasta* readFasta;
- ReadNexus* readNexus;
- ReadClustal* readClustal;
- ReadPhylip* readPhylip;
+ struct linePair {
+ int start;
+ int numSeqs;
+ linePair(long int i, int j) : start(i), numSeqs(j) {}
+ };
+ vector<linePair*> lines;
+
+
+ string vertical, filter, fasta, hard, outputDir, filterFileName;
+ vector<string> fastafileNames;
+ int alignmentLength, processors;
+
+ char trump;
+ bool abort;
+ float soft;
+ int numSeqs;