WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / RNAforester / src / progressive_align.h

diff --git a/binaries/src/ViennaRNA/RNAforester/src/progressive_align.h b/binaries/src/ViennaRNA/RNAforester/src/progressive_align.h
new file mode 100644 (file)
index 0000000..1648519
--- /dev/null
+++ b/binaries/src/ViennaRNA/RNAforester/src/progressive_align.h
@@ -0,0 +1,32 @@
+/*
+  Copyright by Matthias Hoechsmann (C) 2002-2004
+  =====================================                                   
+  You may use, copy and distribute this file freely as long as you
+  - do not change the file,
+  - leave this copyright notice in the file,
+  - do not make any profit with the distribution of this file
+  - give credit where credit is due
+  You are not allowed to copy or distribute this file otherwise
+  The commercial usage and distribution of this file is prohibited
+  Please report bugs and suggestions to <mhoechsm@TechFak.Uni-Bielefeld.DE>
+*/
+
+#include "graphtypes.h"
+#include "matrix.h"
+#include "rnaforester_options.h"
+#include "rna_profile_alignment.h"
+#include "wmatch.h"
+
+/* ****************************************** */
+/*          Definitions and typedefs          */
+/* ****************************************** */
+
+typedef map<long,RNAProfileAlignment*> RNAProfileAliMapType;
+typedef pair<long,RNAProfileAlignment*> RNAProfileAliKeyPairType;
+
+/* ****************************************** */
+/*            Function prototypes             */
+/* ****************************************** */
+
+void progressiveAlign(deque<RNAProfileAlignment*> &inputList, deque<pair<double,RNAProfileAlignment*> > &resultList, const DoubleScoreProfileAlgebraType *alg,const RNAforesterOptions &options);
+Graph makePairsGraph(const RNAProfileAliMapType &inputListProfile, const DoubleScoreProfileAlgebraType *alg, const Matrix<double> *score_mtrx, double threshold);