BIG_INLINE_LIMIT = 20000
CFLAG1= -static
#-mno-cygwin

CC=g++
INCLUDES = -I./ -I./pscfg -I./alifold -I./probcons/

CFLAGS = -DRELEASE0 -O3 -g3 -ggdb -Wall \
	 -finline-limit=$(BIG_INLINE_LIMIT)  $(CFLAG1)
LIBS =

CFLAGS_D = -DRELEASE0 -O0 -g3 -ggdb -Wall -DDEBUG \
	   -fkeep-inline-functions -fkeep-static-consts    \
	   -finline-limit=0 -fno-default-inline $(CFLAG1)
LIBS_D =

SRCS =                       \
Aligner.cpp		     \
AlignProbData.cpp            \
Alpha.cpp		     \
PairProbData.cpp	     \
Cluster.cpp		     \
DPDeck.cpp                   \
Dmtx.cpp		     \
DPPath.cpp		     \
DPRegion.cpp		     \
EScript.cpp		     \
GuideTree.cpp		     \
Job.cpp                      \
JobRunner.cpp		     \
LoadStat.cpp		     \
main.cpp 		     \
MSA.cpp			     \
MultiFamAligner.cpp	     \
MultipleAligner.cpp	     \
Opt.cpp			     \
Profile.cpp		     \
ProfileFreqs.cpp	     \
ProfileVectors.cpp 	     \
ProgressiveAligner.cpp	     \
Scheduler.cpp		     \
ScoreParam.cpp		     \
SeqData.cpp		     \
StripRegion.cpp              \
StripRegionIterators.cpp     \
TreeIterator.cpp             \
Util.cpp	             \
Weight.cpp 		     

SRCS +=                                \
alifold/Alifold.cpp                    \
alifold/AlifoldEnergyParam.cpp         

SRCS +=                                \
probcons/ProbCons.cpp                  

SRCS +=                                \
pscfg/DPDeckPSCFG.cpp                  \
pscfg/DPDeckPSCFGDPLocals.cpp          \
pscfg/DPDeckPSCFGDPRegion.cpp          \
pscfg/DPDeckPSCFGDPRegionRegion.cpp    \
pscfg/DPDeckPSCFGDPTask.cpp            \
pscfg/DPDeckPSCFGDPTaskSubTask.cpp     \
pscfg/DPDeckPSCFGNodes.cpp             \
pscfg/PSCFGEnergyScoreManager.cpp      \
pscfg/DPDeckPSCFGTBTree.cpp            \
pscfg/DPDeckPSCFGVectors.cpp           \
pscfg/SkipSet.cpp                      \
pscfg/StripRegionSkip.cpp              

OBJS   = ${SRCS:.cpp=.o}
OBJS_D = ${SRCS:.cpp=.o_D}

.PHONY: clean depend
.SUFFIXES: .o .cpp .hpp .o_D

murlet: $(OBJS)
	$(CC) $(CFLAGS) -o $@ $^ $(LIBS)
	strip $@
murlet_D: $(OBJS_D)
	$(CC) $(CFLAGS_D) -o $@ $^ $(LIBS_D)
murlet_cygwin: $(OBJS)
	$(CC) $(CFLAGS) -o murlet $^ $(LIBS)
	strip murlet.exe
clean:
	rm -f {.,*}/{*.o,*.o_*}

SUFLIST = o o_D
depend:
	for opt in $(SUFLIST);                     \
	do touch make_deps_$$opt;                  \
	   makedepend -o.$$opt -fmake_deps_$$opt   \
	   -I./pscfg/ -I./alifold/ -I./probcons/   \
	   -Y -- -DDEBUG -- $(SRCS);               \
	done

.cpp.o:
	$(CC) $(CFLAGS) $(INCLUDES) -o $@ -c $<
.cpp.o_D:
	$(CC) $(CFLAGS_D) $(INCLUDES) -o $@ -c $<

#include make_deps_o
# DO NOT DELETE

Aligner.o: LoadStat.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
Aligner.o: UpTriMtx.hpp EScript.hpp Alpha.hpp SeqData.hpp MSA.hpp
Aligner.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
Aligner.o: Rect.hpp DPPath.hpp DPRegion.hpp StripRegion.hpp Trapezoid.hpp
Aligner.o: StripRegionIterators.cpp DPDeck.hpp ./pscfg/DPDeckPSCFG.hpp
Aligner.o: DPScore.hpp ./pscfg/PSCFG_Energy.hpp
Aligner.o: ./pscfg/PSCFGEnergyScoreManager.hpp Profile.hpp ProfileFreqs.hpp
Aligner.o: ProfileVectors.hpp ./alifold/Alifold.hpp Aligner.hpp
Aligner.o: AlignProbData.hpp SparseProb.hpp PairProbData.hpp
Aligner.o: ./probcons/ProbCons.hpp
AlignProbData.o: SeqData.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
AlignProbData.o: Matrix.hpp UpTriMtx.hpp EScript.hpp MSA.hpp DPPath.hpp
AlignProbData.o: Rect.hpp GuideTree.hpp Weight.hpp Aligner.hpp DPRegion.hpp
AlignProbData.o: StripRegion.hpp Trapezoid.hpp StripRegionIterators.cpp
AlignProbData.o: DPDeck.hpp AlignProbData.hpp SparseProb.hpp PairProbData.hpp
AlignProbData.o: Job.hpp Scheduler.hpp JobRunner.hpp
Alpha.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
Alpha.o: Alpha.hpp
PairProbData.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
PairProbData.o: UpTriMtx.hpp SeqData.hpp EScript.hpp ScoreParam.hpp Alpha.hpp
PairProbData.o: pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp Rect.hpp
PairProbData.o: GuideTree.hpp Weight.hpp MSA.hpp Profile.hpp ProfileFreqs.hpp
PairProbData.o: ProfileVectors.hpp PairProbData.hpp SparseProb.hpp
PairProbData.o: Aligner.hpp DPRegion.hpp StripRegion.hpp Trapezoid.hpp
PairProbData.o: StripRegionIterators.cpp DPPath.hpp DPDeck.hpp
PairProbData.o: AlignProbData.hpp Job.hpp Scheduler.hpp JobRunner.hpp
Cluster.o: Dmtx.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
Cluster.o: UpTriMtx.hpp GuideTree.hpp SeqData.hpp EScript.hpp Cluster.hpp
DPDeck.o: DPDeck.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
DPDeck.o: UpTriMtx.hpp
Dmtx.o: EScript.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
Dmtx.o: UpTriMtx.hpp SeqData.hpp MSA.hpp Dmtx.hpp Scheduler.hpp Job.hpp
Dmtx.o: JobRunner.hpp DPPath.hpp Rect.hpp
DPPath.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
DPPath.o: Rect.hpp EScript.hpp DPPath.hpp Trapezoid.hpp DPRegion.hpp
DPPath.o: StripRegion.hpp StripRegionIterators.cpp SeqData.hpp MSA.hpp
DPPath.o: Weight.hpp Profile.hpp ProfileFreqs.hpp Alpha.hpp
DPPath.o: ProfileVectors.hpp
DPRegion.o: DPRegion.hpp StripRegion.hpp Util.hpp Vector.hpp Array.hpp
DPRegion.o: IntPairs.hpp Matrix.hpp UpTriMtx.hpp Rect.hpp Trapezoid.hpp
DPRegion.o: StripRegionIterators.cpp
EScript.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
EScript.o: Alpha.hpp EScript.hpp SeqData.hpp MSA.hpp
GuideTree.o: GuideTree.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
GuideTree.o: Matrix.hpp UpTriMtx.hpp SeqData.hpp EScript.hpp TreeIterator.hpp
GuideTree.o: TreeIterator.cpp MSA.hpp Dmtx.hpp Cluster.hpp Scheduler.hpp
GuideTree.o: Job.hpp JobRunner.hpp DPPath.hpp Rect.hpp
Job.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
Job.o: Rect.hpp EScript.hpp SeqData.hpp MSA.hpp Weight.hpp DPPath.hpp
Job.o: GuideTree.hpp Job.hpp SparseProb.hpp
JobRunner.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
JobRunner.o: UpTriMtx.hpp LoadStat.hpp Rect.hpp Trapezoid.hpp EScript.hpp
JobRunner.o: Alpha.hpp ScoreParam.hpp pscfg/PSCFG_Energy.hpp
JobRunner.o: pscfg/PSCFG_Base.hpp Dmtx.hpp Weight.hpp SeqData.hpp
JobRunner.o: GuideTree.hpp Cluster.hpp PairProbData.hpp SparseProb.hpp
JobRunner.o: DPPath.hpp MSA.hpp DPRegion.hpp StripRegion.hpp
JobRunner.o: StripRegionIterators.cpp DPDeck.hpp Aligner.hpp
JobRunner.o: AlignProbData.hpp Job.hpp JobRunner.hpp
LoadStat.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
LoadStat.o: UpTriMtx.hpp LoadStat.hpp
main.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
main.o: Alpha.hpp Opt.hpp LoadStat.hpp Rect.hpp SeqData.hpp EScript.hpp
main.o: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp MSA.hpp
main.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
main.o: PairProbData.hpp SparseProb.hpp Dmtx.hpp Weight.hpp GuideTree.hpp
main.o: Cluster.hpp Trapezoid.hpp DPPath.hpp DPRegion.hpp StripRegion.hpp
main.o: StripRegionIterators.cpp DPDeck.hpp Aligner.hpp AlignProbData.hpp
main.o: Scheduler.hpp Job.hpp JobRunner.hpp SeqFamAligner.hpp
main.o: ProgressiveAligner.hpp MultipleAligner.hpp MultiFamAligner.hpp
main.o: ScoreParamDefault.hpp
MSA.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
MSA.o: Alpha.hpp Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
MSA.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp Rect.hpp
MSA.o: SeqData.hpp EScript.hpp Weight.hpp MSA.hpp DPPath.hpp
MultiFamAligner.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
MultiFamAligner.o: UpTriMtx.hpp Alpha.hpp Rect.hpp SeqData.hpp EScript.hpp
MultiFamAligner.o: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp MSA.hpp
MultiFamAligner.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
MultiFamAligner.o: Dmtx.hpp Weight.hpp GuideTree.hpp Cluster.hpp
MultiFamAligner.o: Trapezoid.hpp DPPath.hpp DPRegion.hpp StripRegion.hpp
MultiFamAligner.o: StripRegionIterators.cpp DPDeck.hpp Aligner.hpp
MultiFamAligner.o: AlignProbData.hpp SparseProb.hpp PairProbData.hpp Job.hpp
MultiFamAligner.o: Scheduler.hpp JobRunner.hpp SeqFamAligner.hpp
MultiFamAligner.o: ProgressiveAligner.hpp MultipleAligner.hpp
MultiFamAligner.o: MultiFamAligner.hpp
MultipleAligner.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
MultipleAligner.o: UpTriMtx.hpp Alpha.hpp Rect.hpp SeqData.hpp EScript.hpp
MultipleAligner.o: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp MSA.hpp
MultipleAligner.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
MultipleAligner.o: Dmtx.hpp Weight.hpp GuideTree.hpp Cluster.hpp
MultipleAligner.o: Trapezoid.hpp DPPath.hpp DPRegion.hpp StripRegion.hpp
MultipleAligner.o: StripRegionIterators.cpp DPDeck.hpp Aligner.hpp
MultipleAligner.o: AlignProbData.hpp SparseProb.hpp PairProbData.hpp Job.hpp
MultipleAligner.o: Scheduler.hpp JobRunner.hpp SeqFamAligner.hpp
MultipleAligner.o: ProgressiveAligner.hpp MultipleAligner.hpp
Opt.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
Opt.o: Opt.hpp
Profile.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
Profile.o: Rect.hpp Alpha.hpp EScript.hpp SeqData.hpp MSA.hpp DPPath.hpp
Profile.o: Weight.hpp Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
Profile.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
Profile.o: BasePairData.hpp SparseProb.hpp
ProfileFreqs.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
ProfileFreqs.o: UpTriMtx.hpp Rect.hpp Alpha.hpp Profile.hpp ProfileFreqs.hpp
ProfileFreqs.o: ProfileVectors.hpp ScoreParam.hpp pscfg/PSCFG_Energy.hpp
ProfileFreqs.o: pscfg/PSCFG_Base.hpp
ProfileVectors.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
ProfileVectors.o: UpTriMtx.hpp Rect.hpp Alpha.hpp EScript.hpp SeqData.hpp
ProfileVectors.o: MSA.hpp DPPath.hpp Weight.hpp Profile.hpp ProfileFreqs.hpp
ProfileVectors.o: ProfileVectors.hpp ScoreParam.hpp pscfg/PSCFG_Energy.hpp
ProfileVectors.o: pscfg/PSCFG_Base.hpp
ProgressiveAligner.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
ProgressiveAligner.o: UpTriMtx.hpp Alpha.hpp Rect.hpp SeqData.hpp EScript.hpp
ProgressiveAligner.o: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp MSA.hpp
ProgressiveAligner.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
ProgressiveAligner.o: pscfg/PSCFG_Base.hpp Dmtx.hpp Weight.hpp GuideTree.hpp
ProgressiveAligner.o: Cluster.hpp Trapezoid.hpp DPPath.hpp DPRegion.hpp
ProgressiveAligner.o: StripRegion.hpp StripRegionIterators.cpp DPDeck.hpp
ProgressiveAligner.o: Aligner.hpp AlignProbData.hpp SparseProb.hpp
ProgressiveAligner.o: PairProbData.hpp Job.hpp Scheduler.hpp JobRunner.hpp
ProgressiveAligner.o: SeqFamAligner.hpp ProgressiveAligner.hpp
Scheduler.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
Scheduler.o: UpTriMtx.hpp LoadStat.hpp Rect.hpp Trapezoid.hpp EScript.hpp
Scheduler.o: Alpha.hpp Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
Scheduler.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
Scheduler.o: Dmtx.hpp Weight.hpp SeqData.hpp GuideTree.hpp Cluster.hpp
Scheduler.o: BasePairData.hpp SparseProb.hpp DPPath.hpp MSA.hpp DPRegion.hpp
Scheduler.o: StripRegion.hpp StripRegionIterators.cpp DPDeck.hpp Aligner.hpp
Scheduler.o: AlignProbData.hpp PairProbData.hpp Job.hpp JobRunner.hpp
Scheduler.o: Scheduler.hpp
ScoreParam.o: ScoreParam.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
ScoreParam.o: Matrix.hpp UpTriMtx.hpp Alpha.hpp pscfg/PSCFG_Energy.hpp
ScoreParam.o: pscfg/PSCFG_Base.hpp Rect.hpp
SeqData.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
SeqData.o: Alpha.hpp SeqData.hpp EScript.hpp
StripRegion.o: StripRegion.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
StripRegion.o: Matrix.hpp UpTriMtx.hpp Rect.hpp Trapezoid.hpp
StripRegion.o: StripRegionIterators.cpp
StripRegionIterators.o: StripRegion.hpp Util.hpp Vector.hpp Array.hpp
StripRegionIterators.o: IntPairs.hpp Matrix.hpp UpTriMtx.hpp Rect.hpp
StripRegionIterators.o: Trapezoid.hpp StripRegionIterators.cpp
TreeIterator.o: TreeIterator.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
TreeIterator.o: Matrix.hpp UpTriMtx.hpp TreeIterator.cpp
Util.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
Weight.o: SeqData.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
Weight.o: UpTriMtx.hpp EScript.hpp Weight.hpp TreeIterator.hpp
Weight.o: TreeIterator.cpp GuideTree.hpp
alifold/Alifold.o: ./alifold/Alifold.hpp DPDeck.hpp Util.hpp Vector.hpp
alifold/Alifold.o: Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp Profile.hpp
alifold/Alifold.o: ProfileFreqs.hpp Alpha.hpp ProfileVectors.hpp DPPath.hpp
alifold/Alifold.o: Rect.hpp EScript.hpp ScoreParam.hpp pscfg/PSCFG_Energy.hpp
alifold/Alifold.o: pscfg/PSCFG_Base.hpp MSA.hpp SeqData.hpp
alifold/AlifoldEnergyParam.o: ./alifold/Alifold.hpp DPDeck.hpp Util.hpp
alifold/AlifoldEnergyParam.o: Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
alifold/AlifoldEnergyParam.o: UpTriMtx.hpp Profile.hpp ProfileFreqs.hpp
alifold/AlifoldEnergyParam.o: Alpha.hpp ProfileVectors.hpp DPPath.hpp
alifold/AlifoldEnergyParam.o: Rect.hpp EScript.hpp ScoreParam.hpp
alifold/AlifoldEnergyParam.o: pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
probcons/ProbCons.o: ./probcons/ProbCons.hpp DPDeck.hpp Util.hpp Vector.hpp
probcons/ProbCons.o: Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
probcons/ProbCons.o: Profile.hpp ProfileFreqs.hpp Alpha.hpp
probcons/ProbCons.o: ProfileVectors.hpp DPPath.hpp Rect.hpp EScript.hpp
probcons/ProbCons.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
probcons/ProbCons.o: pscfg/PSCFG_Base.hpp MSA.hpp SeqData.hpp
pscfg/DPDeckPSCFG.o: pscfg/SkipSet.hpp Rect.hpp Util.hpp Vector.hpp Array.hpp
pscfg/DPDeckPSCFG.o: IntPairs.hpp Matrix.hpp UpTriMtx.hpp DPRegion.hpp
pscfg/DPDeckPSCFG.o: StripRegion.hpp Trapezoid.hpp StripRegionIterators.cpp
pscfg/DPDeckPSCFG.o: DPPath.hpp EScript.hpp TreeIterator.hpp TreeIterator.cpp
pscfg/DPDeckPSCFG.o: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFG.o: pscfg/PSCFG_Base.hpp ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFG.o: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFG.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFG.o: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFG.o: pscfg/DPDeckPSCFGNodes.hpp pscfg/DPDeckPSCFGVectors.hpp
pscfg/DPDeckPSCFG.o: pscfg/DPDeckPSCFGDPRegion.hpp
pscfg/DPDeckPSCFG.o: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFG.o: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFG.o: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFG.o: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFG.o: pscfg/DPDeckPSCFGDPTask.hpp pscfg/DPDeckPSCFGTBTree.hpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGDPLocals.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGDPLocals.o: Rect.hpp Util.hpp Vector.hpp Array.hpp
pscfg/DPDeckPSCFGDPLocals.o: IntPairs.hpp Matrix.hpp UpTriMtx.hpp
pscfg/DPDeckPSCFGDPLocals.o: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/PSCFG_Base.hpp ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPLocals.o: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGDPLocals.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPLocals.o: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGDPRegion.hpp pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGDPLocals.o: StripRegion.hpp StripRegionIterators.cpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGVectors.hpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGDPTask.hpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGTBTree.hpp DPPath.hpp
pscfg/DPDeckPSCFGDPLocals.o: EScript.hpp pscfg/DPDeckPSCFGDPTaskSubTask.cpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGDPTaskSubTask.hpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGDPLocals.cpp
pscfg/DPDeckPSCFGDPLocals.o: pscfg/DPDeckPSCFGDPLocalsTest.cpp
pscfg/DPDeckPSCFGDPRegion.o: pscfg/DPDeckPSCFGDPRegion.hpp Util.hpp
pscfg/DPDeckPSCFGDPRegion.o: Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
pscfg/DPDeckPSCFGDPRegion.o: UpTriMtx.hpp Rect.hpp pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGDPRegion.o: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGDPRegion.o: pscfg/PSCFG_Base.hpp ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPRegion.o: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGDPRegion.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPRegion.o: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGDPRegion.o: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGDPRegion.o: StripRegion.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGDPRegion.o: StripRegionIterators.cpp
pscfg/DPDeckPSCFGDPRegion.o: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGDPRegion.o: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGDPRegion.o: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFGDPRegionRegion.o: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: StripRegion.hpp Util.hpp Vector.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: Array.hpp IntPairs.hpp Matrix.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: UpTriMtx.hpp Rect.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: StripRegionIterators.cpp
pscfg/DPDeckPSCFGDPRegionRegion.o: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGDPRegionRegion.o: pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: pscfg/DPDeckPSCFGDPRegion.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: DPScore.hpp pscfg/PSCFG_Base.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: ./pscfg/PSCFGEnergyScoreManager.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: Alpha.hpp ScoreParam.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGVectors.hpp Util.hpp Vector.hpp
pscfg/DPDeckPSCFGDPTask.o: Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
pscfg/DPDeckPSCFGDPTask.o: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/PSCFG_Base.hpp Rect.hpp
pscfg/DPDeckPSCFGDPTask.o: ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPTask.o: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGDPTask.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFGDPTask.o: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGDPRegion.hpp pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGDPTask.o: StripRegion.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGDPTask.o: StripRegionIterators.cpp pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGDPTask.hpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGTBTree.hpp DPPath.hpp EScript.hpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGDPTaskSubTask.hpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGDPTaskSubTask.cpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGDPLocals.cpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGDPLocals.hpp
pscfg/DPDeckPSCFGDPTask.o: pscfg/DPDeckPSCFGDPLocalsTest.cpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/DPDeckPSCFGDPTaskSubTask.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: ./pscfg/DPDeckPSCFG.hpp Util.hpp Vector.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: Array.hpp IntPairs.hpp Matrix.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: UpTriMtx.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/PSCFG_Base.hpp Rect.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: ./pscfg/PSCFGEnergyScoreManager.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: Alpha.hpp ScoreParam.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/DPDeckPSCFGDPTask.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/DPDeckPSCFGDPRegion.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: StripRegion.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: StripRegionIterators.cpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/DPDeckPSCFGTBTree.hpp DPPath.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: EScript.hpp pscfg/DPDeckPSCFGVectors.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o: pscfg/DPDeckPSCFGDPLocals.cpp
pscfg/DPDeckPSCFGNodes.o: Util.hpp Vector.hpp Array.hpp IntPairs.hpp
pscfg/DPDeckPSCFGNodes.o: Matrix.hpp UpTriMtx.hpp pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFGNodes.o: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGNodes.o: pscfg/PSCFG_Base.hpp Rect.hpp
pscfg/DPDeckPSCFGNodes.o: ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGNodes.o: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGNodes.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFGNodes.o: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/PSCFGEnergyScoreManager.o: ./pscfg/PSCFGEnergyScoreManager.hpp
pscfg/PSCFGEnergyScoreManager.o: ./pscfg/PSCFG_Energy.hpp Alpha.hpp Util.hpp
pscfg/PSCFGEnergyScoreManager.o: Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
pscfg/PSCFGEnergyScoreManager.o: UpTriMtx.hpp DPScore.hpp ScoreParam.hpp
pscfg/PSCFGEnergyScoreManager.o: pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
pscfg/PSCFGEnergyScoreManager.o: Rect.hpp Profile.hpp ProfileFreqs.hpp
pscfg/PSCFGEnergyScoreManager.o: ProfileVectors.hpp DPDeck.hpp EScript.hpp
pscfg/PSCFGEnergyScoreManager.o: Weight.hpp SeqData.hpp MSA.hpp
pscfg/PSCFGEnergyScoreManager.o: AlignProbData.hpp SparseProb.hpp
pscfg/PSCFGEnergyScoreManager.o: PairProbData.hpp DPPath.hpp
pscfg/DPDeckPSCFGTBTree.o: EScript.hpp Util.hpp Vector.hpp Array.hpp
pscfg/DPDeckPSCFGTBTree.o: IntPairs.hpp Matrix.hpp UpTriMtx.hpp
pscfg/DPDeckPSCFGTBTree.o: pscfg/DPDeckPSCFGTBTree.hpp DPPath.hpp Rect.hpp
pscfg/DPDeckPSCFGTBTree.o: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGTBTree.o: pscfg/PSCFG_Base.hpp ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGTBTree.o: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGTBTree.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFGTBTree.o: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGTBTree.o: TreeIterator.hpp TreeIterator.cpp
pscfg/DPDeckPSCFGVectors.o: pscfg/DPDeckPSCFGVectors.hpp Util.hpp Vector.hpp
pscfg/DPDeckPSCFGVectors.o: Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
pscfg/DPDeckPSCFGVectors.o: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGVectors.o: pscfg/PSCFG_Base.hpp Rect.hpp
pscfg/DPDeckPSCFGVectors.o: ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGVectors.o: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGVectors.o: ScoreParam.hpp pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFGVectors.o: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGVectors.o: pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFGVectors.o: pscfg/DPDeckPSCFGDPRegion.hpp pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGVectors.o: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGVectors.o: StripRegion.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGVectors.o: StripRegionIterators.cpp
pscfg/DPDeckPSCFGVectors.o: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGVectors.o: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGVectors.o: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/SkipSet.o: pscfg/SkipSet.hpp Rect.hpp Util.hpp Vector.hpp Array.hpp
pscfg/SkipSet.o: IntPairs.hpp Matrix.hpp UpTriMtx.hpp DPPath.hpp EScript.hpp
pscfg/StripRegionSkip.o: pscfg/StripRegionSkip.hpp StripRegion.hpp Util.hpp
pscfg/StripRegionSkip.o: Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
pscfg/StripRegionSkip.o: UpTriMtx.hpp Rect.hpp Trapezoid.hpp
pscfg/StripRegionSkip.o: StripRegionIterators.cpp
pscfg/StripRegionSkip.o: pscfg/StripRegionSkipIterators.cpp pscfg/SkipSet.hpp

#include make_deps_o_D
# DO NOT DELETE

Aligner.o_D: LoadStat.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
Aligner.o_D: Matrix.hpp UpTriMtx.hpp EScript.hpp Alpha.hpp SeqData.hpp
Aligner.o_D: MSA.hpp ScoreParam.hpp pscfg/PSCFG_Energy.hpp
Aligner.o_D: pscfg/PSCFG_Base.hpp Rect.hpp DPPath.hpp DPRegion.hpp
Aligner.o_D: StripRegion.hpp Trapezoid.hpp StripRegionIterators.cpp
Aligner.o_D: DPDeck.hpp ./pscfg/DPDeckPSCFG.hpp DPScore.hpp
Aligner.o_D: ./pscfg/PSCFG_Energy.hpp ./pscfg/PSCFGEnergyScoreManager.hpp
Aligner.o_D: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
Aligner.o_D: ./alifold/Alifold.hpp Aligner.hpp AlignProbData.hpp
Aligner.o_D: SparseProb.hpp PairProbData.hpp ./probcons/ProbCons.hpp
AlignProbData.o_D: SeqData.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
AlignProbData.o_D: Matrix.hpp UpTriMtx.hpp EScript.hpp MSA.hpp DPPath.hpp
AlignProbData.o_D: Rect.hpp GuideTree.hpp Weight.hpp Aligner.hpp DPRegion.hpp
AlignProbData.o_D: StripRegion.hpp Trapezoid.hpp StripRegionIterators.cpp
AlignProbData.o_D: DPDeck.hpp AlignProbData.hpp SparseProb.hpp
AlignProbData.o_D: PairProbData.hpp Job.hpp Scheduler.hpp JobRunner.hpp
Alpha.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
Alpha.o_D: Alpha.hpp
PairProbData.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
PairProbData.o_D: UpTriMtx.hpp SeqData.hpp EScript.hpp ScoreParam.hpp
PairProbData.o_D: Alpha.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
PairProbData.o_D: Rect.hpp GuideTree.hpp Weight.hpp MSA.hpp Profile.hpp
PairProbData.o_D: ProfileFreqs.hpp ProfileVectors.hpp PairProbData.hpp
PairProbData.o_D: SparseProb.hpp Aligner.hpp DPRegion.hpp StripRegion.hpp
PairProbData.o_D: Trapezoid.hpp StripRegionIterators.cpp DPPath.hpp
PairProbData.o_D: DPDeck.hpp AlignProbData.hpp Job.hpp Scheduler.hpp
PairProbData.o_D: JobRunner.hpp
Cluster.o_D: Dmtx.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
Cluster.o_D: UpTriMtx.hpp GuideTree.hpp SeqData.hpp EScript.hpp Cluster.hpp
DPDeck.o_D: DPDeck.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
DPDeck.o_D: UpTriMtx.hpp
Dmtx.o_D: EScript.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
Dmtx.o_D: UpTriMtx.hpp SeqData.hpp MSA.hpp Dmtx.hpp Scheduler.hpp Job.hpp
Dmtx.o_D: JobRunner.hpp DPPath.hpp Rect.hpp
DPPath.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
DPPath.o_D: UpTriMtx.hpp Rect.hpp EScript.hpp DPPath.hpp Trapezoid.hpp
DPPath.o_D: DPRegion.hpp StripRegion.hpp StripRegionIterators.cpp SeqData.hpp
DPPath.o_D: MSA.hpp Weight.hpp Profile.hpp ProfileFreqs.hpp Alpha.hpp
DPPath.o_D: ProfileVectors.hpp
DPRegion.o_D: DPRegion.hpp StripRegion.hpp Util.hpp Vector.hpp Array.hpp
DPRegion.o_D: IntPairs.hpp Matrix.hpp UpTriMtx.hpp Rect.hpp Trapezoid.hpp
DPRegion.o_D: StripRegionIterators.cpp
EScript.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
EScript.o_D: UpTriMtx.hpp Alpha.hpp EScript.hpp SeqData.hpp MSA.hpp
GuideTree.o_D: GuideTree.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
GuideTree.o_D: Matrix.hpp UpTriMtx.hpp SeqData.hpp EScript.hpp
GuideTree.o_D: TreeIterator.hpp TreeIterator.cpp MSA.hpp Dmtx.hpp Cluster.hpp
GuideTree.o_D: Scheduler.hpp Job.hpp JobRunner.hpp DPPath.hpp Rect.hpp
Job.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
Job.o_D: Rect.hpp EScript.hpp SeqData.hpp MSA.hpp Weight.hpp DPPath.hpp
Job.o_D: GuideTree.hpp Job.hpp SparseProb.hpp
JobRunner.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
JobRunner.o_D: UpTriMtx.hpp LoadStat.hpp Rect.hpp Trapezoid.hpp EScript.hpp
JobRunner.o_D: Alpha.hpp ScoreParam.hpp pscfg/PSCFG_Energy.hpp
JobRunner.o_D: pscfg/PSCFG_Base.hpp Dmtx.hpp Weight.hpp SeqData.hpp
JobRunner.o_D: GuideTree.hpp Cluster.hpp PairProbData.hpp SparseProb.hpp
JobRunner.o_D: DPPath.hpp MSA.hpp DPRegion.hpp StripRegion.hpp
JobRunner.o_D: StripRegionIterators.cpp DPDeck.hpp Aligner.hpp
JobRunner.o_D: AlignProbData.hpp Job.hpp JobRunner.hpp
LoadStat.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
LoadStat.o_D: UpTriMtx.hpp LoadStat.hpp
main.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
main.o_D: Alpha.hpp Opt.hpp LoadStat.hpp Rect.hpp SeqData.hpp EScript.hpp
main.o_D: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp MSA.hpp
main.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
main.o_D: PairProbData.hpp SparseProb.hpp Dmtx.hpp Weight.hpp GuideTree.hpp
main.o_D: Cluster.hpp Trapezoid.hpp DPPath.hpp DPRegion.hpp StripRegion.hpp
main.o_D: StripRegionIterators.cpp DPDeck.hpp Aligner.hpp AlignProbData.hpp
main.o_D: Scheduler.hpp Job.hpp JobRunner.hpp SeqFamAligner.hpp
main.o_D: ProgressiveAligner.hpp MultipleAligner.hpp MultiFamAligner.hpp
main.o_D: ScoreParamDefault.hpp
MSA.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
MSA.o_D: Alpha.hpp Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
MSA.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp Rect.hpp
MSA.o_D: SeqData.hpp EScript.hpp Weight.hpp MSA.hpp DPPath.hpp
MultiFamAligner.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
MultiFamAligner.o_D: UpTriMtx.hpp Alpha.hpp Rect.hpp SeqData.hpp EScript.hpp
MultiFamAligner.o_D: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp MSA.hpp
MultiFamAligner.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
MultiFamAligner.o_D: pscfg/PSCFG_Base.hpp Dmtx.hpp Weight.hpp GuideTree.hpp
MultiFamAligner.o_D: Cluster.hpp Trapezoid.hpp DPPath.hpp DPRegion.hpp
MultiFamAligner.o_D: StripRegion.hpp StripRegionIterators.cpp DPDeck.hpp
MultiFamAligner.o_D: Aligner.hpp AlignProbData.hpp SparseProb.hpp
MultiFamAligner.o_D: PairProbData.hpp Job.hpp Scheduler.hpp JobRunner.hpp
MultiFamAligner.o_D: SeqFamAligner.hpp ProgressiveAligner.hpp
MultiFamAligner.o_D: MultipleAligner.hpp MultiFamAligner.hpp
MultipleAligner.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
MultipleAligner.o_D: UpTriMtx.hpp Alpha.hpp Rect.hpp SeqData.hpp EScript.hpp
MultipleAligner.o_D: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp MSA.hpp
MultipleAligner.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
MultipleAligner.o_D: pscfg/PSCFG_Base.hpp Dmtx.hpp Weight.hpp GuideTree.hpp
MultipleAligner.o_D: Cluster.hpp Trapezoid.hpp DPPath.hpp DPRegion.hpp
MultipleAligner.o_D: StripRegion.hpp StripRegionIterators.cpp DPDeck.hpp
MultipleAligner.o_D: Aligner.hpp AlignProbData.hpp SparseProb.hpp
MultipleAligner.o_D: PairProbData.hpp Job.hpp Scheduler.hpp JobRunner.hpp
MultipleAligner.o_D: SeqFamAligner.hpp ProgressiveAligner.hpp
MultipleAligner.o_D: MultipleAligner.hpp
Opt.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
Opt.o_D: Opt.hpp
Profile.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
Profile.o_D: UpTriMtx.hpp Rect.hpp Alpha.hpp EScript.hpp SeqData.hpp MSA.hpp
Profile.o_D: DPPath.hpp Weight.hpp Profile.hpp ProfileFreqs.hpp
Profile.o_D: ProfileVectors.hpp ScoreParam.hpp pscfg/PSCFG_Energy.hpp
Profile.o_D: pscfg/PSCFG_Base.hpp BasePairData.hpp SparseProb.hpp
ProfileFreqs.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
ProfileFreqs.o_D: UpTriMtx.hpp Rect.hpp Alpha.hpp Profile.hpp
ProfileFreqs.o_D: ProfileFreqs.hpp ProfileVectors.hpp ScoreParam.hpp
ProfileFreqs.o_D: pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
ProfileVectors.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
ProfileVectors.o_D: UpTriMtx.hpp Rect.hpp Alpha.hpp EScript.hpp SeqData.hpp
ProfileVectors.o_D: MSA.hpp DPPath.hpp Weight.hpp Profile.hpp
ProfileVectors.o_D: ProfileFreqs.hpp ProfileVectors.hpp ScoreParam.hpp
ProfileVectors.o_D: pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
ProgressiveAligner.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
ProgressiveAligner.o_D: UpTriMtx.hpp Alpha.hpp Rect.hpp SeqData.hpp
ProgressiveAligner.o_D: EScript.hpp Profile.hpp ProfileFreqs.hpp
ProgressiveAligner.o_D: ProfileVectors.hpp MSA.hpp ScoreParam.hpp
ProgressiveAligner.o_D: pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp Dmtx.hpp
ProgressiveAligner.o_D: Weight.hpp GuideTree.hpp Cluster.hpp Trapezoid.hpp
ProgressiveAligner.o_D: DPPath.hpp DPRegion.hpp StripRegion.hpp
ProgressiveAligner.o_D: StripRegionIterators.cpp DPDeck.hpp Aligner.hpp
ProgressiveAligner.o_D: AlignProbData.hpp SparseProb.hpp PairProbData.hpp
ProgressiveAligner.o_D: Job.hpp Scheduler.hpp JobRunner.hpp SeqFamAligner.hpp
ProgressiveAligner.o_D: ProgressiveAligner.hpp
Scheduler.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
Scheduler.o_D: UpTriMtx.hpp LoadStat.hpp Rect.hpp Trapezoid.hpp EScript.hpp
Scheduler.o_D: Alpha.hpp Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
Scheduler.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
Scheduler.o_D: Dmtx.hpp Weight.hpp SeqData.hpp GuideTree.hpp Cluster.hpp
Scheduler.o_D: BasePairData.hpp SparseProb.hpp DPPath.hpp MSA.hpp
Scheduler.o_D: DPRegion.hpp StripRegion.hpp StripRegionIterators.cpp
Scheduler.o_D: DPDeck.hpp Aligner.hpp AlignProbData.hpp PairProbData.hpp
Scheduler.o_D: Job.hpp JobRunner.hpp Scheduler.hpp
ScoreParam.o_D: ScoreParam.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
ScoreParam.o_D: Matrix.hpp UpTriMtx.hpp Alpha.hpp pscfg/PSCFG_Energy.hpp
ScoreParam.o_D: pscfg/PSCFG_Base.hpp Rect.hpp
SeqData.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
SeqData.o_D: UpTriMtx.hpp Alpha.hpp SeqData.hpp EScript.hpp
StripRegion.o_D: StripRegion.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
StripRegion.o_D: Matrix.hpp UpTriMtx.hpp Rect.hpp Trapezoid.hpp
StripRegion.o_D: StripRegionIterators.cpp
StripRegionIterators.o_D: StripRegion.hpp Util.hpp Vector.hpp Array.hpp
StripRegionIterators.o_D: IntPairs.hpp Matrix.hpp UpTriMtx.hpp Rect.hpp
StripRegionIterators.o_D: Trapezoid.hpp StripRegionIterators.cpp
TreeIterator.o_D: TreeIterator.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp
TreeIterator.o_D: Matrix.hpp UpTriMtx.hpp TreeIterator.cpp
Util.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
Weight.o_D: SeqData.hpp Util.hpp Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
Weight.o_D: UpTriMtx.hpp EScript.hpp Weight.hpp TreeIterator.hpp
Weight.o_D: TreeIterator.cpp GuideTree.hpp
alifold/Alifold.o_D: ./alifold/Alifold.hpp DPDeck.hpp Util.hpp Vector.hpp
alifold/Alifold.o_D: Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
alifold/Alifold.o_D: Profile.hpp ProfileFreqs.hpp Alpha.hpp
alifold/Alifold.o_D: ProfileVectors.hpp DPPath.hpp Rect.hpp EScript.hpp
alifold/Alifold.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
alifold/Alifold.o_D: pscfg/PSCFG_Base.hpp MSA.hpp SeqData.hpp
alifold/AlifoldEnergyParam.o_D: ./alifold/Alifold.hpp DPDeck.hpp Util.hpp
alifold/AlifoldEnergyParam.o_D: Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
alifold/AlifoldEnergyParam.o_D: UpTriMtx.hpp Profile.hpp ProfileFreqs.hpp
alifold/AlifoldEnergyParam.o_D: Alpha.hpp ProfileVectors.hpp DPPath.hpp
alifold/AlifoldEnergyParam.o_D: Rect.hpp EScript.hpp ScoreParam.hpp
alifold/AlifoldEnergyParam.o_D: pscfg/PSCFG_Energy.hpp pscfg/PSCFG_Base.hpp
probcons/ProbCons.o_D: ./probcons/ProbCons.hpp DPDeck.hpp Util.hpp Vector.hpp
probcons/ProbCons.o_D: Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
probcons/ProbCons.o_D: Profile.hpp ProfileFreqs.hpp Alpha.hpp
probcons/ProbCons.o_D: ProfileVectors.hpp DPPath.hpp Rect.hpp EScript.hpp
probcons/ProbCons.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
probcons/ProbCons.o_D: pscfg/PSCFG_Base.hpp MSA.hpp SeqData.hpp
pscfg/DPDeckPSCFG.o_D: pscfg/SkipSet.hpp Rect.hpp Util.hpp Vector.hpp
pscfg/DPDeckPSCFG.o_D: Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
pscfg/DPDeckPSCFG.o_D: DPRegion.hpp StripRegion.hpp Trapezoid.hpp
pscfg/DPDeckPSCFG.o_D: StripRegionIterators.cpp DPPath.hpp EScript.hpp
pscfg/DPDeckPSCFG.o_D: TreeIterator.hpp TreeIterator.cpp
pscfg/DPDeckPSCFG.o_D: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFG.o_D: pscfg/PSCFG_Base.hpp ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFG.o_D: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFG.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFG.o_D: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFG.o_D: pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFG.o_D: pscfg/DPDeckPSCFGVectors.hpp
pscfg/DPDeckPSCFG.o_D: pscfg/DPDeckPSCFGDPRegion.hpp
pscfg/DPDeckPSCFG.o_D: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFG.o_D: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFG.o_D: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFG.o_D: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFG.o_D: pscfg/DPDeckPSCFGDPTask.hpp
pscfg/DPDeckPSCFG.o_D: pscfg/DPDeckPSCFGTBTree.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/DPDeckPSCFGDPLocals.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: Rect.hpp Util.hpp Vector.hpp Array.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: IntPairs.hpp Matrix.hpp UpTriMtx.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/PSCFG_Base.hpp ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: Profile.hpp ProfileFreqs.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: ProfileVectors.hpp pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/DPDeckPSCFGDPRegion.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: StripRegion.hpp StripRegionIterators.cpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/DPDeckPSCFGVectors.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/DPDeckPSCFGDPTask.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/DPDeckPSCFGTBTree.hpp DPPath.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: EScript.hpp pscfg/DPDeckPSCFGDPTaskSubTask.cpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/DPDeckPSCFGDPTaskSubTask.hpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/DPDeckPSCFGDPLocals.cpp
pscfg/DPDeckPSCFGDPLocals.o_D: pscfg/DPDeckPSCFGDPLocalsTest.cpp
pscfg/DPDeckPSCFGDPRegion.o_D: pscfg/DPDeckPSCFGDPRegion.hpp Util.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: UpTriMtx.hpp Rect.hpp pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: pscfg/PSCFG_Base.hpp ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: Profile.hpp ProfileFreqs.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: ProfileVectors.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: StripRegion.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: StripRegionIterators.cpp
pscfg/DPDeckPSCFGDPRegion.o_D: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGDPRegion.o_D: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGDPRegion.o_D: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: StripRegion.hpp Util.hpp Vector.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: Array.hpp IntPairs.hpp Matrix.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: UpTriMtx.hpp Rect.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: StripRegionIterators.cpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: pscfg/DPDeckPSCFGDPRegion.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: DPScore.hpp pscfg/PSCFG_Base.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: ./pscfg/PSCFGEnergyScoreManager.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: Alpha.hpp ScoreParam.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGDPRegionRegion.o_D: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGVectors.hpp Util.hpp Vector.hpp
pscfg/DPDeckPSCFGDPTask.o_D: Array.hpp IntPairs.hpp Matrix.hpp UpTriMtx.hpp
pscfg/DPDeckPSCFGDPTask.o_D: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/PSCFG_Base.hpp Rect.hpp
pscfg/DPDeckPSCFGDPTask.o_D: ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPTask.o_D: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGDPTask.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPTask.o_D: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGDPRegion.hpp pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGDPTask.o_D: StripRegion.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGDPTask.o_D: StripRegionIterators.cpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGDPTask.hpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGTBTree.hpp DPPath.hpp
pscfg/DPDeckPSCFGDPTask.o_D: EScript.hpp pscfg/DPDeckPSCFGDPTaskSubTask.hpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGDPTaskSubTask.cpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGDPLocals.cpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGDPLocals.hpp
pscfg/DPDeckPSCFGDPTask.o_D: pscfg/DPDeckPSCFGDPLocalsTest.cpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/DPDeckPSCFGDPTaskSubTask.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: ./pscfg/DPDeckPSCFG.hpp Util.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: Vector.hpp Array.hpp IntPairs.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: Matrix.hpp UpTriMtx.hpp DPDeck.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: DPScore.hpp pscfg/PSCFG_Base.hpp Rect.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: ./pscfg/PSCFGEnergyScoreManager.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: Alpha.hpp ScoreParam.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/DPDeckPSCFGDPTask.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/DPDeckPSCFGDPRegion.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: StripRegion.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: StripRegionIterators.cpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/DPDeckPSCFGTBTree.hpp DPPath.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: EScript.hpp pscfg/DPDeckPSCFGVectors.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFGDPTaskSubTask.o_D: pscfg/DPDeckPSCFGDPLocals.cpp
pscfg/DPDeckPSCFGNodes.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp
pscfg/DPDeckPSCFGNodes.o_D: Matrix.hpp UpTriMtx.hpp
pscfg/DPDeckPSCFGNodes.o_D: pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFGNodes.o_D: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGNodes.o_D: pscfg/PSCFG_Base.hpp Rect.hpp
pscfg/DPDeckPSCFGNodes.o_D: ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGNodes.o_D: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGNodes.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp Profile.hpp
pscfg/DPDeckPSCFGNodes.o_D: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/PSCFGEnergyScoreManager.o_D: ./pscfg/PSCFGEnergyScoreManager.hpp
pscfg/PSCFGEnergyScoreManager.o_D: ./pscfg/PSCFG_Energy.hpp Alpha.hpp
pscfg/PSCFGEnergyScoreManager.o_D: Util.hpp Vector.hpp Array.hpp IntPairs.hpp
pscfg/PSCFGEnergyScoreManager.o_D: Matrix.hpp UpTriMtx.hpp DPScore.hpp
pscfg/PSCFGEnergyScoreManager.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
pscfg/PSCFGEnergyScoreManager.o_D: pscfg/PSCFG_Base.hpp Rect.hpp Profile.hpp
pscfg/PSCFGEnergyScoreManager.o_D: ProfileFreqs.hpp ProfileVectors.hpp
pscfg/PSCFGEnergyScoreManager.o_D: DPDeck.hpp EScript.hpp Weight.hpp
pscfg/PSCFGEnergyScoreManager.o_D: SeqData.hpp MSA.hpp AlignProbData.hpp
pscfg/PSCFGEnergyScoreManager.o_D: SparseProb.hpp PairProbData.hpp DPPath.hpp
pscfg/DPDeckPSCFGTBTree.o_D: EScript.hpp Util.hpp Vector.hpp Array.hpp
pscfg/DPDeckPSCFGTBTree.o_D: IntPairs.hpp Matrix.hpp UpTriMtx.hpp
pscfg/DPDeckPSCFGTBTree.o_D: pscfg/DPDeckPSCFGTBTree.hpp DPPath.hpp Rect.hpp
pscfg/DPDeckPSCFGTBTree.o_D: ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp DPScore.hpp
pscfg/DPDeckPSCFGTBTree.o_D: pscfg/PSCFG_Base.hpp ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGTBTree.o_D: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGTBTree.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGTBTree.o_D: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGTBTree.o_D: TreeIterator.hpp TreeIterator.cpp
pscfg/DPDeckPSCFGVectors.o_D: pscfg/DPDeckPSCFGVectors.hpp Util.hpp
pscfg/DPDeckPSCFGVectors.o_D: Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
pscfg/DPDeckPSCFGVectors.o_D: UpTriMtx.hpp ./pscfg/DPDeckPSCFG.hpp DPDeck.hpp
pscfg/DPDeckPSCFGVectors.o_D: DPScore.hpp pscfg/PSCFG_Base.hpp Rect.hpp
pscfg/DPDeckPSCFGVectors.o_D: ./pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGVectors.o_D: ./pscfg/PSCFGEnergyScoreManager.hpp Alpha.hpp
pscfg/DPDeckPSCFGVectors.o_D: ScoreParam.hpp pscfg/PSCFG_Energy.hpp
pscfg/DPDeckPSCFGVectors.o_D: Profile.hpp ProfileFreqs.hpp ProfileVectors.hpp
pscfg/DPDeckPSCFGVectors.o_D: pscfg/DPDeckPSCFGNodes.hpp
pscfg/DPDeckPSCFGVectors.o_D: pscfg/DPDeckPSCFGDPRegion.hpp pscfg/SkipSet.hpp
pscfg/DPDeckPSCFGVectors.o_D: pscfg/DPDeckPSCFGDPRegionRegion.hpp
pscfg/DPDeckPSCFGVectors.o_D: StripRegion.hpp Trapezoid.hpp
pscfg/DPDeckPSCFGVectors.o_D: StripRegionIterators.cpp
pscfg/DPDeckPSCFGVectors.o_D: pscfg/StripRegionSkip.hpp
pscfg/DPDeckPSCFGVectors.o_D: pscfg/StripRegionSkipIterators.cpp
pscfg/DPDeckPSCFGVectors.o_D: pscfg/DPDeckPSCFGDPRegionRegionIterators.cpp
pscfg/SkipSet.o_D: pscfg/SkipSet.hpp Rect.hpp Util.hpp Vector.hpp Array.hpp
pscfg/SkipSet.o_D: IntPairs.hpp Matrix.hpp UpTriMtx.hpp DPPath.hpp
pscfg/SkipSet.o_D: EScript.hpp
pscfg/StripRegionSkip.o_D: pscfg/StripRegionSkip.hpp StripRegion.hpp Util.hpp
pscfg/StripRegionSkip.o_D: Vector.hpp Array.hpp IntPairs.hpp Matrix.hpp
pscfg/StripRegionSkip.o_D: UpTriMtx.hpp Rect.hpp Trapezoid.hpp
pscfg/StripRegionSkip.o_D: StripRegionIterators.cpp
pscfg/StripRegionSkip.o_D: pscfg/StripRegionSkipIterators.cpp
pscfg/StripRegionSkip.o_D: pscfg/SkipSet.hpp










