X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=secondarystructurecommand.h;h=c1cc057cd190cd4570b57d9bcc9f622a8f6bf0f4;hb=6d12ed0ba66fb35e9e2781fe3ca361e2293f2476;hp=2e6191ca67f47f92f38bb8c030a8ad3e32920af6;hpb=f89b6501b7d80e705b6c50ff2c8bdd8bb5d2edf7;p=mothur.git diff --git a/secondarystructurecommand.h b/secondarystructurecommand.h index 2e6191c..c1cc057 100644 --- a/secondarystructurecommand.h +++ b/secondarystructurecommand.h @@ -33,7 +33,12 @@ class AlignCheckCommand : public Command { public: AlignCheckCommand(string); - ~AlignCheckCommand(){}; + AlignCheckCommand(); + ~AlignCheckCommand(){} + vector getRequiredParameters(); + vector getValidParameters(); + vector getRequiredFiles(); + map > getOutputFiles() { return outputTypes; } int execute(); void help(); @@ -42,6 +47,8 @@ class AlignCheckCommand : public Command { string mapfile, fastafile, outputDir; bool abort; int seqLength, haderror; + vector outputNames; + map > outputTypes; void readMap(); statData getStats(string sequence);