+
+Mussa* MussaSetupWidget::getMussaObject()
+{
+ Mussa *mussa = new Mussa;
+
+
+
+ std::string seqFile;
+ std::string annotFile;
+ int fastaIndex;
+ int start;
+ int end;
+
+ std::list<SetupInfo *> setupInfoList = seqSetupFrame->getSetupInfo();
+
+ const int count = setupInfoList.size();
+
+ SetupInfo *setupInfo = 0;
+ for (int i=0; i < count; i++)
+ {
+ setupInfo = setupInfoList.back();
+ setupInfoList.pop_back();
+
+ seqFile = setupInfo->getSeqFile();
+ annotFile = setupInfo->getAnnotFile();
+ fastaIndex = setupInfo->getFastaIndex();
+ start = setupInfo->getSubSeqStart();
+ end = setupInfo->getSubSeqEnd();
+
+ mussa->load_sequence(seqFile, annotFile, fastaIndex, start, end);
+ delete setupInfo;
+ }
+
+ mussa->analyze(0, 0, Mussa::TransitiveNway, 0.0);
+
+ return mussa;
+}
+
+//MussaSetupWidget::MussaSetupWidget(const MussaSetupWidget& msw)
+// : analysisNameLineEdit(msw.analysisNameLineEdit),
+// windowLineEdit(msw.windowLineEdit),
+// thresholdLineEdit(msw.thresholdLineEdit),
+// numOfSequencesLineEdit(msw.numOfSequencesLineEdit),
+// seqSetupFrame(msw.seqSetupFrame)
+//{
+//}