BitSequenceRGK, Tests and WaveletTree Top-K Implementation

Makefile

@@ -1,45 +1,72 @@
 
-# CPPFLAGS=-g3 -Wall -O0 -fPIC -DVERBOSE
-CPPFLAGS=-O9 -Wall -DNDEBUG -fPIC
-
-all: libcompact tests
-
-doc:
-	@echo " [DOC] Generating documentation"
-	@doxygen
-
-libcompact:
-	@echo " [MSG] Entering directory src"
-	@CPPFLAGS="$(CPPFLAGS)" make --no-print-directory -C src
-
-tests: libcompact
-	@echo " [MSG] Entering directory tests"
-	@CPPFLAGS="$(CPPFLAGS)" make --no-print-directory -C tests
-
-shared_lib: libcompact
-	@echo " [C++] Compiling shared library"
-	@g++ -shared $(CPPFLAGS) -w -o lib/libcds.so ./lib/libcds.a
-
-shared_lib_install:
-	@cp ./lib/libcds.so /usr/lib
-	@cp ./lib/libcds.a /usr/lib
-	@echo " [MSG] Library copied to /usr/lib"
-	@mkdir -p /usr/include/libcds
-	@cp -rf ./includes /usr/include/libcds
-	@echo " [MSG] Headers copied to /usr/include/libcds"
+CPP=g++
 
-clean:
-	@echo " [MSG] Entering directory src"
-	@make --no-print-directory -C src clean
-	@echo " [MSG] Entering directory tests"
-	@make --no-print-directory -C tests clean
-	@echo " [CLN] Cleaning docs folder"
-	@rm -rf docs/*
-	@touch docs/delete_me
-	@echo " [CLN] Cleaning lib folder"
-	@rm -f lib/*
-	@touch lib/delete_me
-	@echo " [CLN] Cleaning includes folder"
-	@rm -f includes/*
-	@touch includes/delete_me
+#CPPFLAGS=-g3 -Wall -O0 -I../includes/ 
+#CPPFLAGS=-O3 -Wall -DNDEBUG -I../includes/
+INCS=-I../includes/
+LIB=../lib/libcds.a
+
+OBJECTS= testArray.o testBitSequence.o testSequence.o testQuantile.o testHuffman.o timeSequence.o toArray.o toArray2.o
+BIN= testArray testBitSequence testSequence testHuffman timeSequence toArray toArray2 testQuantile
+
+%.o: %.cpp
+	@echo " [C++] Compiling $<"
+	@$(CPP) $(CPPFLAGS) $(INCS) -c $< -o $@
+
+all: clean $(OBJECTS) $(BIN)
+	@echo " [MSG] Done compiling tests"
+	@echo " [FLG] $(CPPFLAGS)"
+
+testHuffman:
+	@echo " [LNK] Building testHuffman"
+	@$(CPP) $(CPPFLAGS) -o testHuffman testHuffman.o $(LIB)
+
+testSequence:
+	@echo " [LNK] Building testSequence"
+	@$(CPP) $(CPPFLAGS) -o testSequence testSequence.o $(LIB)
+
+testQuantile:
+	@echo " [LNK] Building testSequence"
+	@$(CPP) $(CPPFLAGS) -o testQuantile testQuantile.o $(LIB)
+
+testBitSequence:
+	@echo " [LNK] Building testBitSequence"
+	@$(CPP) $(CPPFLAGS) -o testBitSequence testBitSequence.o $(LIB)
+
+testArray:
+	@echo " [LNK] Building testArray"
+	@$(CPP) $(CPPFLAGS) -o testArray testArray.o $(LIB)
+
+testTextIndex:
+	 @echo " [LNK] Building testTextIndex"
+	 @$(CPP) $(CPPFLAGS) -o testTextIndex testTextIndex.o $(LIB)
 
+testLCP:
+	@echo " [LNK] Building testLCP"
+	@$(CPP) $(CPPFLAGS) -o testLCP testLCP.o $(LIB)
+
+testNPR:
+	@echo " [LNK] Building testNPR"
+	@$(CPP) $(CPPFLAGS) -o testNPR testNPR.o $(LIB)
+
+toArray2:
+	@echo " [LNK] Building toArray2"
+	@$(CPP) $(CPPFLAGS) -o toArray2 toArray2.o $(LIB)
+
+toArray:
+	@echo " [LNK] Building toArray"
+	@$(CPP) $(CPPFLAGS) -o toArray toArray.o $(LIB)
+
+testSuffixTree:
+	@echo " [LNK] Building testSuffixTree"
+	@$(CPP) $(CPPFLAGS) -o testSuffixTree testSuffixTree.o $(LIB)
+
+timeSequence:
+	@echo " [LNK] Building timeSequence"
+	@$(CPP) $(CPPFLAGS) -o timeSequence timeSequence.o $(LIB)
+
+
+
+clean:
+	@echo " [CLN] Cleaning object and binary files"
+	@rm -f $(OBJECTS) $(BIN)

src/Makefile

@@ -8,7 +8,7 @@ UTILS_OBJ=utils/Array.o utils/libcdsBitString.o utils/cppUtils.o utils/timing.o
 
 # OBJECTS FROM cds_static PACKAGE
 STATIC_MAPPER_OBJ=static/mapper/Mapper.o static/mapper/MapperNone.o static/mapper/MapperCont.o static/mapper/MapperRev.o
-STATIC_BITSEQ_OBJ= static/bitsequence/BitSequence.o static/bitsequence/BitSequenceRG.o static/bitsequence/BitSequenceSDArray.o static/bitsequence/sdarraySadakane.o static/bitsequence/BitSequenceDArray.o static/bitsequence/BitSequenceRRR.o static/bitsequence/BitSequenceBuilderRG.o static/bitsequence/BitSequenceBuilderRRR.o static/bitsequence/BitSequenceBuilderSDArray.o static/bitsequence/BitSequenceBuilderDArray.o static/bitsequence/TableOffsetRRR.o
+STATIC_BITSEQ_OBJ= static/bitsequence/BitSequence.o static/bitsequence/BitSequenceRG.o static/bitsequence/BitSequenceSDArray.o static/bitsequence/sdarraySadakane.o static/bitsequence/BitSequenceDArray.o static/bitsequence/BitSequenceRRR.o static/bitsequence/BitSequenceBuilderRG.o static/bitsequence/BitSequenceBuilderRRR.o static/bitsequence/BitSequenceBuilderSDArray.o static/bitsequence/BitSequenceBuilderDArray.o static/bitsequence/TableOffsetRRR.o static/bitsequence/BitSequenceRGK.o
 STATIC_CODER_OBJ=static/coders/huff.o static/coders/HuffmanCoder.o
 STATIC_SEQ_OBJ=static/sequence/Sequence.o static/sequence/BitmapsSequence.o static/sequence/wt_coder.o static/sequence/wt_coder_binary.o static/sequence/wt_coder_huff.o static/sequence/wt_node.o static/sequence/wt_node_internal.o static/sequence/wt_node_leaf.o static/sequence/WaveletTree.o static/sequence/WaveletTreeNoptrs.o static/sequence/WaveletTreeNoptrsS.o static/sequence/WaveletMatrix.o static/sequence/SequenceGMR.o static/sequence/SequenceGMRChunk.o static/sequence/SequenceBuilderWaveletTreeNoptrs.o static/sequence/SequenceBuilderWaveletTreeNoptrsS.o static/sequence/SequenceBuilderWaveletTree.o static/sequence/SequenceBuilderGMR.o static/sequence/SequenceBuilderGMRChunk.o static/sequence/SequenceAlphPart.o static/sequence/SequenceBuilderStr.o static/sequence/SequenceBuilderAlphPart.o static/sequence/SequenceBuilderWaveletMatrix.o