Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / clustalw / src / fileInput / ClustalFileParser.h

diff --git a/website/archive/binaries/mac/src/clustalw/src/fileInput/ClustalFileParser.h b/website/archive/binaries/mac/src/clustalw/src/fileInput/ClustalFileParser.h
new file mode 100644 (file)
index 0000000..299b7da
--- /dev/null
+++ b/website/archive/binaries/mac/src/clustalw/src/fileInput/ClustalFileParser.h
@@ -0,0 +1,39 @@
+/**
+ * Author: Mark Larkin
+ * 
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
+ */
+#ifndef CLUSTALFILEPARSER_H
+#define CLUSTALFILEPARSER_H
+
+#include <string>
+#include "FileParser.h"
+
+namespace clustalw
+{
+
+class ClustalFileParser : public FileParser
+{
+    public:
+        /* Functions */
+        ClustalFileParser(string filePath);
+        ~ClustalFileParser();
+        virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
+        virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
+        virtual int countSeqs();
+        virtual void getSecStructure(vector<char>& gapPenaltyMask, 
+                vector<char>& secStructMask,
+               string& secStructName, int &structPenalties, int length); 
+
+        /* Attributes */
+
+    private:
+        /* Functions */
+        bool clustalBlankline(char* line); // Only used in this class!
+        string fileName;
+        /* Attributes */
+        
+};
+
+}
+#endif