Mac binaries

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

diff --git a/website/archive/binaries/mac/src/clustalw/src/Clustal.h b/website/archive/binaries/mac/src/clustalw/src/Clustal.h
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+/**
+ * Author: Mark Larkin
+ *
+ * Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.  
+ */
+/**
+ * The class Clustal is the main class in the program. It is used by the interactive
+ * menu, command line parser and clustal x to perform the algorithmic part of the
+ * program. 
+ */
+#ifndef CLUSTAL_H
+#define CLUSTAL_H
+
+#include <string>
+#include "general/clustalw.h"
+#include "general/utils.h"
+#include "general/userparams.h"
+#include "fileInput/FileReader.h"
+#include "alignment/Alignment.h"
+#include "alignment/AlignmentOutput.h"
+
+using namespace std;
+
+namespace clustalw
+{
+
+class Clustal
+{
+    public:
+        /* Functions */
+        Clustal();
+        void align(string* phylipName, bool createOutput = true);
+        void sequencesAlignToProfile(string* phylipName);
+        void profileAlign(string* p1TreeName, string* p2TreeName);
+        void doGuideTreeOnly(string* phylipName);
+        void doAlignUseOldTree(string* phylipName);        
+        void getHelp(string helpPointer, bool printTitle = false);
+        void getHelp(char helpPointer, bool printTitle = false);
+        void getFullHelp();
+        int sequenceInput(bool append, string *offendingSeq);
+        int profile1Input(string profile1Name = "");
+        int profile2Input(string profile2Name = "");
+        int commandLineReadSeq(int firstSeq);
+        void outputNow();
+        void phylogeneticTree(string* phylip_name, string* clustal_name, string* dist_name,
+                              string* nexus_name, string pimName);
+        void bootstrapTree(string* phylip_name, string* clustal_name, string* nexus_name);
+        Alignment* getAlignmentPtr(){return &alignmentObj;} 
+        void QTcalcLowScoreSegments(LowScoreSegParams* params);
+        void QTcalcWeightsForLowScoreSeg(LowScoreSegParams* params);
+        void QTremoveShortSegments(LowScoreSegParams* params);
+        void QTSetFileNamesForOutput(AlignmentFileNames fileNames);
+        bool QTRealignSelectedRange(AlignmentFileNames fileNames, int beginPos, int endPos,
+                                    bool realignEndGapPen);
+        void test();
+        /* Attributes */
+
+    private:
+        /* Functions */
+        void initInterface();
+        void calcGapPenaltyMask(int prfLength, vector<char>* mask, vector<char>* gapMask);
+        bool useExistingGuideTree(int type, string* phylipName, const string& path);
+        void promptForNewGuideTreeName(int type, string* treeName, const string& path);
+        //bool removeFirstIterate(Alignment* alnPtr, DistMatrix* distMat);
+        /* Attributes */
+        enum{Sequences, Profile1, Profile2};
+        string sequencesMsg, profile1Msg, profile2Msg;
+        string newProfile1TreePrompt, newProfile2TreePrompt;
+        
+        Alignment alignmentObj;
+        string helpFileName;
+        int newSeq;
+        bool checkTree;
+        AlignmentFileNames QTFileNames;
+};
+}
+#endif