Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / multipleAlign / MSA.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/multipleAlign/MSA.h b/website/archive/binaries/mac/src/clustalw/src/multipleAlign/MSA.h
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+/**
+ * Author: Mark Larkin
+ * 
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
+ */
+#ifndef MSA_H
+#define MSA_H
+
+#include <iomanip>
+#include "ProfileBase.h"
+#include "../alignment/Alignment.h"
+//#include "../calcAlignSteps/Tree.h"
+#include "../tree/AlignmentSteps.h"
+#include "ProfileAlignAlgorithm.h"
+
+namespace clustalw
+{
+//using tree::AlignmentSteps;
+
+class MSA
+{
+    public:
+        /* Functions */
+        int multiSeqAlign(Alignment* alnPtr, DistMatrix* distMat, 
+            vector<int>* seqWeight, AlignmentSteps* progSteps, int iStart);
+        int seqsAlignToProfile(Alignment* alnPtr, DistMatrix* distMat, vector<int>* seqWeight, int iStart, 
+                              string phylipName);
+        int calcPairwiseForProfileAlign(Alignment* alnPtr, DistMatrix* distMat);
+        int doProfileAlign(Alignment* alnPtr, DistMatrix* distMat, vector<int>* prof1Weight,
+                           vector<int>* prof2Weight);
+
+        /* Attributes */
+
+    private:
+        /* Functions */
+        
+        /* Attributes */
+};
+
+}
+#endif