Commit 9da60314 authored by Neil Kindlon's avatar Neil Kindlon
Browse files

forgot src/utils/ToolBase directory

parent ed59faae
OBJ_DIR = ../../../obj/
BIN_DIR = ../../../bin/
UTILITIES_DIR = ../../utils/
# -------------------
# define our includes
# -------------------
INCLUDES = -I$(UTILITIES_DIR)/general/ \
-I$(UTILITIES_DIR)/fileType/ \
-I$(UTILITIES_DIR)/Contexts/ \
-I$(UTILITIES_DIR)/GenomeFile/ \
-I$(UTILITIES_DIR)/FileRecordTools/ \
-I$(UTILITIES_DIR)/FileRecordTools/FileReaders/ \
-I$(UTILITIES_DIR)/FileRecordTools/Records/ \
-I$(UTILITIES_DIR)/RecordOutputMgr/ \
-I$(UTILITIES_DIR)/KeyListOps/ \
-I$(UTILITIES_DIR)/BamTools/include \
-I$(UTILITIES_DIR)/BamTools/src/ \
-I$(UTILITIES_DIR)/version/
# ----------------------------------
# define our source and object files
# ----------------------------------
SOURCES= ToolBase.h
OBJECTS= ToolBase.o
_EXT_OBJECTS=
EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
$(BUILT_OBJECTS): $(SOURCES)
@echo " * compiling" $(*F).cpp
@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
$(EXT_OBJECTS):
@$(MAKE) --no-print-directory -C $(INCLUDES)
clean:
@echo "Cleaning up."
@rm -f $(OBJ_DIR)/ToolBase.o
.PHONY: clean
\ No newline at end of file
#include "ToolBase.h"
// All methods are currently purely abstract, so this file is only a placeholder for any future
// methods that may be added.
/*
* ToolBase.h
*
* Created on: Mar 25, 2015
* Author: nek3d
*/
#ifndef TOOLBASE_H_
#define TOOLBASE_H_
using namespace std;
#include "RecordKeyVector.h"
#include "RecordOutputMgr.h"
class ContextBase;
class ToolBase {
public:
ToolBase(ContextBase *context) {_context = context; }
virtual ~ToolBase() {}
virtual bool init() = 0; // after construction
virtual bool findNext(RecordKeyVector &hits) = 0;
virtual void processHits(RecordOutputMgr *outputMgr, RecordKeyVector &hits) = 0;
virtual void cleanupHits(RecordKeyVector &hits) = 0;
//do any last things needed to wrap up.
virtual bool finalizeCalculations() = 0;
virtual void giveFinalReport(RecordOutputMgr *outputMgr) = 0;
protected:
ContextBase *_context;
};
#endif /* TOOLBASE_H_ */
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