diff --git a/src/IntaRNA/Makefile.am b/src/IntaRNA/Makefile.am index 23a3e8ef..81b35c0e 100644 --- a/src/IntaRNA/Makefile.am +++ b/src/IntaRNA/Makefile.am @@ -1,150 +1,151 @@ - -### std-options -# check that installed programs support the --help and --version options -# basic check that the program's run-time dependencies are satisfied -### subdir-objects -# Place generated object files (.o) into the same directory as their source -# files, in order to avoid collisions when non-recursive make is used. -AUTOMAKE_OPTIONS = std-options subdir-objects - -AM_DEFAULT_SOURCE_EXT = .cpp - -############################################################################### -# THE INTARNA LIBRARY -############################################################################### - -# the library names to build (note we are building static libs only) -lib_LIBRARIES = libIntaRNA.a - -# where to install the headers on the system -libIntaRNA_adir = $(includedir)/IntaRNA - -# the list of header files that belong to the library (to be installed later) -libIntaRNA_a_HEADERS = \ - intarna_config.h \ - general.h \ - Accessibility.h \ - AccessibilityConstraint.h \ - AccessibilityDisabled.h \ - AccessibilityFromStream.h \ - AccessibilityVrna.h \ - AccessibilityBasePair.h \ + +### std-options +# check that installed programs support the --help and --version options +# basic check that the program's run-time dependencies are satisfied +### subdir-objects +# Place generated object files (.o) into the same directory as their source +# files, in order to avoid collisions when non-recursive make is used. +AUTOMAKE_OPTIONS = std-options subdir-objects + +AM_DEFAULT_SOURCE_EXT = .cpp + +############################################################################### +# THE INTARNA LIBRARY +############################################################################### + +# the library names to build (note we are building static libs only) +lib_LIBRARIES = libIntaRNA.a + +# where to install the headers on the system +libIntaRNA_adir = $(includedir)/IntaRNA + +# the list of header files that belong to the library (to be installed later) +libIntaRNA_a_HEADERS = \ + intarna_config.h \ + general.h \ + Accessibility.h \ + AccessibilityConstraint.h \ + AccessibilityDisabled.h \ + AccessibilityFromStream.h \ + AccessibilityVrna.h \ + AccessibilityBasePair.h \ + HelixConstraint.h \ HelixHandler.h \ HelixHandlerIdxOffset.h \ HelixHandlerStackingOnly.h \ HelixHandlerUnpaired.h \ - IndexRange.h \ - IndexRangeList.h \ - Interaction.h \ - InteractionEnergy.h \ - InteractionEnergyBasePair.h \ - InteractionEnergyIdxOffset.h \ - InteractionEnergyVrna.h \ - InteractionRange.h \ - NussinovHandler.h \ - OutputConstraint.h \ - OutputHandler.h \ - OutputHandlerCsv.h \ - OutputHandlerHub.h \ - OutputHandlerIntaRNA1.h \ - OutputHandlerInteractionList.h \ - OutputHandlerRangeOnly.h \ - OutputHandlerText.h \ - PredictionTracker.h \ - PredictionTrackerHub.h \ - PredictionTrackerPairMinE.h \ - PredictionTrackerProfileMinE.h \ - PredictionTrackerSpotProb.h \ - PredictionTrackerSpotProbAll.h \ - PredictionTrackerProfileSpotProb.h \ - Predictor.h \ - PredictorMaxProb.h \ - PredictorMfe.h \ - PredictorMfe2d.h \ - PredictorMfe2dSeed.h \ - PredictorMfe2dHeuristic.h \ - PredictorMfe2dHeuristicSeed.h \ + IndexRange.h \ + IndexRangeList.h \ + Interaction.h \ + InteractionEnergy.h \ + InteractionEnergyBasePair.h \ + InteractionEnergyIdxOffset.h \ + InteractionEnergyVrna.h \ + InteractionRange.h \ + NussinovHandler.h \ + OutputConstraint.h \ + OutputHandler.h \ + OutputHandlerCsv.h \ + OutputHandlerHub.h \ + OutputHandlerIntaRNA1.h \ + OutputHandlerInteractionList.h \ + OutputHandlerRangeOnly.h \ + OutputHandlerText.h \ + PredictionTracker.h \ + PredictionTrackerHub.h \ + PredictionTrackerPairMinE.h \ + PredictionTrackerProfileMinE.h \ + PredictionTrackerSpotProb.h \ + PredictionTrackerSpotProbAll.h \ + PredictionTrackerProfileSpotProb.h \ + Predictor.h \ + PredictorMaxProb.h \ + PredictorMfe.h \ + PredictorMfe2d.h \ + PredictorMfe2dSeed.h \ + PredictorMfe2dHeuristic.h \ + PredictorMfe2dHeuristicSeed.h \ PredictorMfe2dHelixHeuristic.h \ PredictorMfe2dHelixHeuristicSeed.h \ - PredictorMfe4d.h \ - PredictorMfe4dSeed.h \ - ReverseAccessibility.h \ - RnaSequence.h \ - SeedConstraint.h \ - SeedHandler.h \ - SeedHandlerExplicit.h \ - SeedHandlerIdxOffset.h \ - SeedHandlerMfe.h \ - SeedHandlerNoBulge.h \ - VrnaHandler.h - -# the sources to add to the library and to add to the source distribution -libIntaRNA_a_SOURCES = \ - $(libmylib_a_HEADERS) \ - general.cpp \ - Accessibility.cpp \ - AccessibilityConstraint.cpp \ - AccessibilityFromStream.cpp \ - AccessibilityVrna.cpp \ - AccessibilityBasePair.cpp \ + PredictorMfe4d.h \ + PredictorMfe4dSeed.h \ + ReverseAccessibility.h \ + RnaSequence.h \ + SeedConstraint.h \ + SeedHandler.h \ + SeedHandlerExplicit.h \ + SeedHandlerIdxOffset.h \ + SeedHandlerMfe.h \ + SeedHandlerNoBulge.h \ + VrnaHandler.h + +# the sources to add to the library and to add to the source distribution +libIntaRNA_a_SOURCES = \ + $(libmylib_a_HEADERS) \ + general.cpp \ + Accessibility.cpp \ + AccessibilityConstraint.cpp \ + AccessibilityFromStream.cpp \ + AccessibilityVrna.cpp \ + AccessibilityBasePair.cpp \ HelixHandler.cpp \ HelixHandlerStackingOnly.cpp \ HelixHandlerStackingOnlySeed.cpp \ HelixHandlerUnpaired.cpp \ HelixHandlerUnpairedSeed.cpp \ - IndexRange.cpp \ - IndexRangeList.cpp \ - Interaction.cpp \ - InteractionEnergy.cpp \ - InteractionEnergyBasePair.cpp \ - InteractionEnergyIdxOffset.cpp \ - InteractionEnergyVrna.cpp \ - InteractionRange.cpp \ - NussinovHandler.cpp \ - OutputConstraint.cpp \ - OutputHandler.cpp \ - OutputHandlerCsv.cpp \ - OutputHandlerIntaRNA1.cpp \ - OutputHandlerInteractionList.cpp \ - OutputHandlerRangeOnly.cpp \ - OutputHandlerText.cpp \ - PredictionTrackerPairMinE.cpp \ - PredictionTrackerProfileMinE.cpp \ - PredictionTrackerSpotProb.cpp \ - PredictionTrackerSpotProbAll.cpp \ - PredictionTrackerProfileSpotProb.cpp \ - PredictorMaxProb.cpp \ - PredictorMfe.cpp \ - PredictorMfe2d.cpp \ - PredictorMfe2dSeed.cpp \ - PredictorMfe2dHeuristic.cpp \ - PredictorMfe2dHeuristicSeed.cpp \ + IndexRange.cpp \ + IndexRangeList.cpp \ + Interaction.cpp \ + InteractionEnergy.cpp \ + InteractionEnergyBasePair.cpp \ + InteractionEnergyIdxOffset.cpp \ + InteractionEnergyVrna.cpp \ + InteractionRange.cpp \ + NussinovHandler.cpp \ + OutputConstraint.cpp \ + OutputHandler.cpp \ + OutputHandlerCsv.cpp \ + OutputHandlerIntaRNA1.cpp \ + OutputHandlerInteractionList.cpp \ + OutputHandlerRangeOnly.cpp \ + OutputHandlerText.cpp \ + PredictionTrackerPairMinE.cpp \ + PredictionTrackerProfileMinE.cpp \ + PredictionTrackerSpotProb.cpp \ + PredictionTrackerSpotProbAll.cpp \ + PredictionTrackerProfileSpotProb.cpp \ + PredictorMaxProb.cpp \ + PredictorMfe.cpp \ + PredictorMfe2d.cpp \ + PredictorMfe2dSeed.cpp \ + PredictorMfe2dHeuristic.cpp \ + PredictorMfe2dHeuristicSeed.cpp \ PredictorMfe2dHelixHeuristic.cpp \ PredictorMfe2dHelixHeuristicSeed.cpp \ - PredictorMfe4d.cpp \ - PredictorMfe4dSeed.cpp \ - ReverseAccessibility.cpp \ - RnaSequence.cpp \ - SeedConstraint.cpp \ - SeedHandlerExplicit.cpp \ - SeedHandlerMfe.cpp \ - SeedHandlerNoBulge.cpp \ - VrnaHandler.cpp - - -# generated intaRNA sources -nodist_libIntaRNA_a_SOURCES = \ - ../config.h \ - intarna_config.h - -################################################################ -# pkg-config -################################################################ - -if enable_pkg_config -pkgconfigdir = $(libdir)/pkgconfig -pkgconfig_DATA = $(top_srcdir)/IntaRNA.pc -endif - -############################################################################### - + PredictorMfe4d.cpp \ + PredictorMfe4dSeed.cpp \ + ReverseAccessibility.cpp \ + RnaSequence.cpp \ + SeedConstraint.cpp \ + SeedHandlerExplicit.cpp \ + SeedHandlerMfe.cpp \ + SeedHandlerNoBulge.cpp \ + VrnaHandler.cpp + + +# generated intaRNA sources +nodist_libIntaRNA_a_SOURCES = \ + ../config.h \ + intarna_config.h + +################################################################ +# pkg-config +################################################################ + +if enable_pkg_config +pkgconfigdir = $(libdir)/pkgconfig +pkgconfig_DATA = $(top_srcdir)/IntaRNA.pc +endif + +############################################################################### +