Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / tree / ClusterTreeOutput.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/tree/ClusterTreeOutput.h b/website/archive/binaries/mac/src/clustalw/src/tree/ClusterTreeOutput.h
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+++ b/website/archive/binaries/mac/src/clustalw/src/tree/ClusterTreeOutput.h
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+/**
+ * Author: Mark Larkin
+ * 
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
+ */
+#ifndef CLUSTERTREEOUTPUT_H
+#define CLUSTERTREEOUTPUT_H
+
+#include <memory>
+#include <fstream>
+#include "../alignment/Alignment.h"
+#include "../general/clustalw.h"
+
+namespace clustalw
+{
+
+class ClusterTreeOutput
+{
+    public:
+        ClusterTreeOutput(clustalw::SeqInfo* seqInfo, int boot);
+        void printNexusTree(clustalw::PhyloTree* phyloTree, ofstream* tree,
+                   clustalw::Alignment *alignPtr, clustalw::DistMatrix* distMat, vector<int>* bootTotals);
+        void printTree(clustalw::PhyloTree* phyloTree, ofstream* tree, vector<int>* totals);
+        void printPhylipTree(clustalw::PhyloTree* phyloTree, ofstream* tree,
+                   clustalw::Alignment *alignPtr, clustalw::DistMatrix* distMat, vector<int>* bootTotals);
+        void printTreeDesc(clustalw::PhyloTree* phyloTree);
+          
+    private:
+        ClusterTreeOutput(); // Dont allow contruction with default!!!!
+        int twoWaySplit(clustalw::PhyloTree* phyloTree, ofstream* tree, int startRow, 
+                    int flag, clustalw::Alignment *alignPtr, vector<int>* bootTotals);
+        int twoWaySplitNexus(clustalw::PhyloTree* phyloTree, ofstream* tree, int startRow,
+                    int flag, clustalw::Alignment *alignPtr, vector<int>* bootTotals);
+        /* Attributes! */
+        int firstSeq;
+        int lastSeq;
+        int numSeqs;
+        int bootstrap;
+};
+
+}
+
+#endif