version 4.0

LICENSE

@@ -1,21 +1,10 @@
-MIT License
+Copyright (c) 2009, Michael R. Brent, Ian Korf, and Paul Flicek 
+All rights reserved.
 
-Copyright (c) 2023 Brent Lab
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE

LICENSE~

@@ -0,0 +1,10 @@
+Copyright (c) 2009, Michael R. Brent and David Lu
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE

Makefile

@@ -0,0 +1,210 @@
+###############################################################################
+# Makefile for zoe
+###############################################################################
+
+###########
+# LIBRARY #
+###########
+
+LIBRARY = lib/libzoe.a
+
+OBJECTS = \
+	src/zTools.o\
+	src/zTBTree.o\
+	src/bntree/bntree.o\
+	src/bntree/cache.o\
+	src/bntree/celllistitem.o\
+	src/bntree/intlistitem.o\
+	src/bntree/node.o\
+	src/zAlignment.o\
+	src/zAlignmentScanner.o\
+	src/zAlnFeature.o\
+	src/zBNTreeModel.o\
+	src/zConseq.o\
+	src/zDistribution.o\
+	src/zDNA.o\
+	src/zDuration.o\
+	src/zEstseq.o\
+	src/zEstseqSearch.o\
+	src/zFastaFile.o\
+	src/zFeatureFactory.o\
+	src/zGTF.o\
+	src/zHardCoding.o\
+	src/zHMM.o\
+	src/zHMM_State.o\
+	src/zMath.o\
+	src/zMathTables.o\
+	src/zModel.o\
+	src/zPhasePref.o\
+	src/zProtein.o\
+	src/zScanner.o\
+	src/zSeedUtils.o\
+	src/zSequence.o\
+	src/zSfeature.o\
+	src/zStopSeq.o\
+	src/zTransition.o\
+	src/zTrellis.o\
+	src/zViterbi.o\
+	src/zPairTransition.o\
+	src/zPairTrellis.o\
+	src/zPairViterbi.o\
+
+#################
+# TEST PROGRAMS #
+#################
+
+LFLAGS = -L. -Llib -lzoe -lm 
+
+EXE12 = bin/iscan
+SRC12 = src/iscan.c
+OBJ12 = $(SRC12:.c=.o)
+
+EXE13 = bin/zoe2gtf
+SRC13 = src/zoe2gtf.c
+OBJ13 = $(SRC13:.c=.o)
+
+EXE15 = bin/pairagon
+SRC15 = src/pairagon.c
+OBJ15 = $(SRC15:.c=.o)
+
+EXE16 = bin/pairagon2estgen
+SRC16 = src/pairagon2estgen.c
+OBJ16 = $(SRC16:.c=.o)
+
+EXECUTABLES = $(EXE12) $(EXE13)
+PAIRAGON_EXECUTABLES = $(EXE15) $(EXE16)
+
+TABLE = src/zMathTables.c
+TABLEGEN = src/zFloatwiseScoreAdd
+
+########################
+# Program Options      #
+########################
+
+BUILD = 20060720RZ
+VERSION = 3.5
+PROGRAM = Twinscan
+PAIRAGON_VERSION = 0.99
+PAIRAGON_PROGRAM = Pairagon
+GCC_FLAGS = "-W -Wall -Werror -ansi -pedantic -Wwrite-strings"
+DIST_FLAGS = "-DBUILD=\\\"$(PROGRAM)\ version\ $(VERSION)\ build\ $(BUILD)\\\" -DNDEBUG -O2"
+PAIRAGON_DIST_FLAGS = "-DBUILD=\\\"$(PAIRAGON_PROGRAM)\ version\ $(PAIRAGON_VERSION)\ build\ $(BUILD)\\\" -DNDEBUG -O2"
+
+# In order to make the include file to contain header file dependencies,
+# gcc needs a flag to construct this.  In another funny SunOS stunt, this
+# is entirely different in their cc.
+INCLUDE_FLAGS = "-MM"
+
+SPARC_INCLUDE_FLAGS= "-xM1"
+
+ALPHA_FLAGS = "-c99 -msg_enable level5"
+
+SPARC_FLAGS = "-O "
+
+MACOSX_FLAGS = "-Wall -W -O2"
+MACOSX_G5_FLAGS="-fast"
+# You might have to use -mcpu=7450 if it is not a G5 processor!
+
+############################
+# End Program Options      #
+############################
+
+################################################################################
+# TARGETS 
+################################################################################
+
+
+all: include $(LIBRARY) $(EXECUTABLES) symlinks
+
+symlinks:
+	ln -s iscan bin/nscan || :
+	ln -s iscan bin/twinscan || :
+
+$(LIBRARY): $(OBJECTS)
+	rm -f $(LIBRARY)
+	ar cr $(LIBRARY) $(OBJECTS)
+	ranlib $(LIBRARY)
+
+include:
+	$(CC) $(INCLUDE_FLAGS) src/*.c > Makefile.include
+	src/get-glib-flags.sh >> Makefile.include
+
+pairagon-exe: $(LIBRARY) $(PAIRAGON_EXECUTABLES)
+
+clean:
+	rm -f src/*.o src/bntree/*.o $(LIBRARY) $(PAIRAGON_EXECUTABLES) $(EXECUTABLES) $(TABLE) $(TABLEGEN)
+	rm -f bin/twinscan bin/nscan
+
+product:
+	make all CC="gcc" CFLAGS+=$(GCC_FLAGS) CFLAGS+=-march=i686 CFLAGS+=-DNDEBUG CFLAGS+=-O2 CFLAGS+=$(DIST_FLAGS)
+
+gcc-distribution:
+	make all CC="gcc" CFLAGS+=$(GCC_FLAGS) CFLAGS+=-march=i686 CFLAGS+=-DNDEBUG CFLAGS+=-O2 CFLAGS+=$(DIST_FLAGS)
+
+linux:
+	make all CC="gcc" CFLAGS+=$(GCC_FLAGS) CFLAGS+=-march=i686 CFLAGS+=-DNDEBUG CFLAGS+=-O2 CFLAGS+=$(DIST_FLAGS)
+
+alpha:
+	make all CC="cc" CFLAGS+=$(ALPHA_FLAGS) CFLAGS+=$(DIST_FLAGS)
+
+macosx:
+	make all CC="gcc" CFLAGS+=$(MACOSX_FLAGS) CFLAGS+=$(DIST_FLAGS)
+
+macosxg5:
+	make all CC="gcc" CFLAGS+=$(MACOSX_FLAGS) CFLAGS+=$(MACOSX_G5_FLAGS) CFLAGS+=$(DIST_FLAGS)
+
+sparc:
+	make all CC="cc" INCLUDE_FLAGS=$(SPARC_INCLUDE_FLAGS) CFLAGS+=$(SPARC_FLAGS) CFLAGS+=$(DIST_FLAGS)
+
+pairagon-linux:
+	make pairagon-exe CC="gcc" CFLAGS+=$(GCC_FLAGS) CFLAGS+=$(PAIRAGON_DIST_FLAGS) $(GLIB_FLAGS)
+
+pairagon-sparc:
+	make pairagon-exe CC="cc" CFLAGS+=$(SPARC_FLAGS) CFLAGS+=$(PAIRAGON_DIST_FLAGS)
+
+pairagon-macosx:
+	make pairagon-exe CC="cc" CFLAGS+=$(MACOSX_FLAGS) CFLAGS+=$(PAIRAGON_DIST_FLAGS)
+
+pairagon-distro:
+	make pairagon-exe CC="gcc" CFLAGS+=$(GCC_FLAGS) CFLAGS+=-march=i686 CFLAGS+=$(PAIRAGON_DIST_FLAGS)
+
+.PHONY:include all pairagon-exe clean product gcc-distribution alpha macosx sparc pairagon-linux pairagon-sparc pairagon-macosx pairagon-distro
+
+#######################
+# Excecutable Section #
+#######################
+
+$(EXE12): $(OBJ12) $(LIBRARY)
+	$(CC) -o $(EXE12) $(CFLAGS) $(OBJ12) $(LFLAGS) $(GLIB_LFLAGS)
+
+$(EXE13): $(OBJ13) $(LIBRARY)
+	$(CC) -o $(EXE13) $(CFLAGS) $(OBJ13) $(LFLAGS) $(GLIB_LFLAGS)
+
+$(EXE15): $(OBJ15) $(LIBRARY)
+	$(CC) -o $(EXE15) $(CFLAGS) $(OBJ15) $(LFLAGS) $(GLIB_LFLAGS)
+
+$(EXE16): $(OBJ16) $(LIBRARY)
+	$(CC) -o $(EXE16) $(CFLAGS) $(OBJ16) $(LFLAGS) $(GLIB_LFLAGS)
+
+###################
+# Inference Rules #
+###################
+
+.SUFFIXES : .c .o
+
+.c.o:
+	$(CC) $(CFLAGS) -c -o $@ $<
+
+
+#######################
+# Source Dependencies #
+#######################
+
+$(TABLEGEN): src/zFloatwiseScoreAdd.c
+	$(CC) $(CFLAGS) -o $(TABLEGEN) src/zFloatwiseScoreAdd.c -lm
+
+$(TABLE): $(TABLEGEN)
+	./$(TABLEGEN) > $(TABLE)
+
+include Makefile.include
+