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# This is a GNU Makefile for Artemis
# $Header: //tmp/pathsoft/artemis/Makefile,v 1.47 2009-09-21 15:32:03 tjc Exp $
SHELL=/bin/sh
#OPT_FLAGS = -g -deprecation
JAVAC := javac -source 1.5 -target 1.5 $(OPT_FLAGS) $(EXTRA_FLAGS)
REAL_CLASSPATH := CLASSPATH=lib/biojava.jar:lib/jemAlign.jar:lib/j2ssh/j2ssh-core.jar:lib/ibatis/ibatis-2.3.4.726.jar:lib/ibatis/log4j-1.2.14.jar:lib/postgresql-8.4-701.jdbc3.jar:lib/picard/picard.jar:lib/picard/sam.jar:lib/commons-net-2.2.jar:.
NAMES:= \
uk/ac/sanger/artemis/OptionChangeListener \
uk/ac/sanger/artemis/OptionChangeEvent \
uk/ac/sanger/artemis/Options \
uk/ac/sanger/artemis/Selection \
uk/ac/sanger/artemis/components/ArtemisMain \
uk/ac/sanger/artemis/components/ActMain \
uk/ac/sanger/artemis/components/Splash \
uk/ac/sanger/artemis/components/ListDialog \
uk/ac/sanger/artemis/components/FeatureListFrame \
uk/ac/sanger/artemis/components/FeatureList \
uk/ac/sanger/artemis/components/FeatureDisplay \
uk/ac/sanger/artemis/components/CanvasPanel \
uk/ac/sanger/artemis/components/EntryGroupDisplay \
uk/ac/sanger/artemis/components/EntryHeaderEdit \
uk/ac/sanger/artemis/components/BasePlotGroup \
uk/ac/sanger/artemis/components/EntryEditVector \
uk/ac/sanger/artemis/components/EntryEdit \
uk/ac/sanger/artemis/components/WritableEMBLCorbaEntrySource \
uk/ac/sanger/artemis/components/DbfetchEntrySource \
uk/ac/sanger/artemis/components/EMBLCorbaEntrySource \
uk/ac/sanger/artemis/components/CorbaEntrySource \
uk/ac/sanger/artemis/components/BioJavaEntrySource \
uk/ac/sanger/artemis/components/FileDialogEntrySource \
uk/ac/sanger/artemis/components/EntryActionListener \
uk/ac/sanger/artemis/components/DisplayComponent \
uk/ac/sanger/artemis/components/EntryFileDialog \
uk/ac/sanger/artemis/components/StickyFileChooser \
uk/ac/sanger/artemis/components/LogReadListener \
uk/ac/sanger/artemis/components/Selector \
uk/ac/sanger/artemis/components/Navigator \
uk/ac/sanger/artemis/components/EntryGroupPanel \
uk/ac/sanger/artemis/components/FeaturePopup \
uk/ac/sanger/artemis/components/WriteMenu \
uk/ac/sanger/artemis/components/SelectMenu \
uk/ac/sanger/artemis/components/GraphMenu \
uk/ac/sanger/artemis/components/RunMenu \
uk/ac/sanger/artemis/components/AddMenu \
uk/ac/sanger/artemis/components/ViewMenu \
uk/ac/sanger/artemis/components/GotoMenu \
uk/ac/sanger/artemis/components/EditMenu \
uk/ac/sanger/artemis/components/SelectionMenu \
uk/ac/sanger/artemis/components/SelectionViewer \
uk/ac/sanger/artemis/components/FeaturePlotGroup \
uk/ac/sanger/artemis/components/FeaturePlot \
uk/ac/sanger/artemis/components/FeatureEdit \
uk/ac/sanger/artemis/components/FeatureViewer \
uk/ac/sanger/artemis/components/SearchResultViewer \
uk/ac/sanger/artemis/components/LogViewer \
uk/ac/sanger/artemis/components/FileViewer \
uk/ac/sanger/artemis/components/MessageFrame \
uk/ac/sanger/artemis/components/MessageDialog \
uk/ac/sanger/artemis/components/YesNoDialog \
uk/ac/sanger/artemis/components/KeyChooser \
uk/ac/sanger/artemis/components/KeyChoice \
uk/ac/sanger/artemis/components/QualifierEditor \
uk/ac/sanger/artemis/components/QualifierTextArea \
uk/ac/sanger/artemis/components/QualifierChoice \
uk/ac/sanger/artemis/components/ChoiceFrame \
uk/ac/sanger/artemis/components/SelectionInfoDisplay \
uk/ac/sanger/artemis/components/EntryGroupMenu \
uk/ac/sanger/artemis/components/EntryGroupInfoDisplay \
uk/ac/sanger/artemis/components/Utilities \
uk/ac/sanger/artemis/components/MarkerRangeRequester \
uk/ac/sanger/artemis/components/MarkerRangeRequesterListener \
uk/ac/sanger/artemis/components/MarkerRangeRequesterEvent \
uk/ac/sanger/artemis/components/TextRequester \
uk/ac/sanger/artemis/components/TextRequesterListener \
uk/ac/sanger/artemis/components/TextRequesterEvent \
uk/ac/sanger/artemis/components/TextDialog \
uk/ac/sanger/artemis/components/BasePlot \
uk/ac/sanger/artemis/components/ProcessWatcher \
uk/ac/sanger/artemis/components/ProcessWatcherEvent \
uk/ac/sanger/artemis/components/ProcessWatcherListener \
uk/ac/sanger/artemis/components/ExternalProgramOptions \
uk/ac/sanger/artemis/components/Plot \
uk/ac/sanger/artemis/components/PlotMouseListener \
uk/ac/sanger/artemis/components/FeatureAminoAcidViewer \
uk/ac/sanger/artemis/components/FeatureBaseViewer \
uk/ac/sanger/artemis/components/SequenceViewer \
uk/ac/sanger/artemis/components/FeatureInfo \
uk/ac/sanger/artemis/components/DisplayAdjustmentListener \
uk/ac/sanger/artemis/components/DisplayAdjustmentEvent \
uk/ac/sanger/artemis/components/ScoreChanger \
uk/ac/sanger/artemis/components/ScoreScrollbar \
uk/ac/sanger/artemis/components/ScoreChangeListener \
uk/ac/sanger/artemis/components/ScoreChangeEvent \
uk/ac/sanger/artemis/components/InputStreamProgressDialog \
uk/ac/sanger/artemis/plot/KarlinSigAlgorithm \
uk/ac/sanger/artemis/plot/UserDataAlgorithm \
uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm \
uk/ac/sanger/artemis/plot/ATDeviationAlgorithm \
uk/ac/sanger/artemis/plot/GCDeviationAlgorithm \
uk/ac/sanger/artemis/plot/GCFrameAlgorithm \
uk/ac/sanger/artemis/plot/CodonUsageAlgorithm \
uk/ac/sanger/artemis/plot/CodonUsageFormatException \
uk/ac/sanger/artemis/plot/CodonUsageWeight \
uk/ac/sanger/artemis/plot/CodonWeight \
uk/ac/sanger/artemis/plot/AGWindowAlgorithm \
uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm \
uk/ac/sanger/artemis/plot/GCWindowAlgorithm \
uk/ac/sanger/artemis/plot/HydrophilicityAlgorithm \
uk/ac/sanger/artemis/plot/HydroAlgorithm \
uk/ac/sanger/artemis/plot/HydrophobicityAlgorithm \
uk/ac/sanger/artemis/plot/CoilFeatureAlgorithm \
uk/ac/sanger/artemis/plot/FeatureAlgorithm \
uk/ac/sanger/artemis/plot/BaseAlgorithm \
uk/ac/sanger/artemis/plot/Algorithm \
uk/ac/sanger/artemis/Logger \
uk/ac/sanger/artemis/ExternalProgramListener \
uk/ac/sanger/artemis/ExternalProgramException \
uk/ac/sanger/artemis/ExternalProgramVector \
uk/ac/sanger/artemis/SimpleExternalProgramMonitor \
uk/ac/sanger/artemis/ProcessMonitor \
uk/ac/sanger/artemis/ProcessMonitor \
uk/ac/sanger/artemis/ExternalProgramMonitor \
uk/ac/sanger/artemis/ExternalProgram \
uk/ac/sanger/artemis/EntryGroupChangeListener \
uk/ac/sanger/artemis/EntryGroupChangeEvent \
uk/ac/sanger/artemis/EntryChangeListener \
uk/ac/sanger/artemis/EntryChangeEvent \
uk/ac/sanger/artemis/FilteredEntryGroup \
uk/ac/sanger/artemis/SimpleEntryGroup \
uk/ac/sanger/artemis/EntryGroup \
uk/ac/sanger/artemis/EntryVector \
uk/ac/sanger/artemis/EntrySourceVector \
uk/ac/sanger/artemis/EntrySource \
uk/ac/sanger/artemis/Entry \
uk/ac/sanger/artemis/LastSegmentException \
uk/ac/sanger/artemis/FeatureFromVectorPredicate \
uk/ac/sanger/artemis/FeatureKeyQualifierPredicate \
uk/ac/sanger/artemis/FeatureKeyPredicate \
uk/ac/sanger/artemis/FeaturePatternPredicate \
uk/ac/sanger/artemis/FeaturePredicateConjunction \
uk/ac/sanger/artemis/FeaturePredicate \
uk/ac/sanger/artemis/FeaturePredicateVector \
uk/ac/sanger/artemis/FeatureEnumeration \
uk/ac/sanger/artemis/FeatureSegmentVector \
uk/ac/sanger/artemis/FeatureChangeListener \
uk/ac/sanger/artemis/FeatureChangeEvent \
uk/ac/sanger/artemis/FeatureVector \
uk/ac/sanger/artemis/Feature \
uk/ac/sanger/artemis/FeatureSegment \
uk/ac/sanger/artemis/ActionController \
uk/ac/sanger/artemis/ActionVector \
uk/ac/sanger/artemis/Action \
uk/ac/sanger/artemis/ChangeListener \
uk/ac/sanger/artemis/ChangeEventVector \
uk/ac/sanger/artemis/ChangeEvent \
uk/ac/sanger/artemis/GotoListener \
uk/ac/sanger/artemis/GotoEvent \
uk/ac/sanger/artemis/GotoEventSource \
uk/ac/sanger/artemis/SimpleGotoEventSource \
uk/ac/sanger/artemis/SelectionChangeListener \
uk/ac/sanger/artemis/SelectionChangeEvent \
uk/ac/sanger/artemis/Selectable \
uk/ac/sanger/artemis/sequence/NoSequenceException \
uk/ac/sanger/artemis/sequence/MarkerRangeVector \
uk/ac/sanger/artemis/sequence/MarkerRange \
uk/ac/sanger/artemis/sequence/MarkerChangeListener \
uk/ac/sanger/artemis/sequence/MarkerChangeEvent \
uk/ac/sanger/artemis/sequence/Marker \
uk/ac/sanger/artemis/sequence/Strand \
uk/ac/sanger/artemis/sequence/BasePatternFormatException \
uk/ac/sanger/artemis/sequence/BasePattern \
uk/ac/sanger/artemis/sequence/Bases \
uk/ac/sanger/artemis/sequence/AminoAcidSequence \
uk/ac/sanger/artemis/sequence/SequenceChangeListener \
uk/ac/sanger/artemis/sequence/SequenceChangeEvent \
uk/ac/sanger/artemis/io/BioJavaFeature \
uk/ac/sanger/artemis/io/BioJavaSequence \
uk/ac/sanger/artemis/io/BioJavaEntry \
uk/ac/sanger/artemis/io/GenbankStreamSequence \
uk/ac/sanger/artemis/io/RWCorbaEntry \
uk/ac/sanger/artemis/io/CorbaEntry \
uk/ac/sanger/artemis/io/DocumentEntryFactory \
uk/ac/sanger/artemis/io/BlastDocumentEntry \
uk/ac/sanger/artemis/io/MSPcrunchDocumentEntry \
uk/ac/sanger/artemis/io/GFFDocumentEntry \
uk/ac/sanger/artemis/io/GenbankDocumentEntry \
uk/ac/sanger/artemis/io/EmblDocumentEntry \
uk/ac/sanger/artemis/io/PublicDBDocumentEntry \
uk/ac/sanger/artemis/io/SimpleDocumentEntry \
uk/ac/sanger/artemis/io/DocumentEntry \
uk/ac/sanger/artemis/io/Entry \
uk/ac/sanger/artemis/io/ReadOnlyEntry \
uk/ac/sanger/artemis/io/QualifierInfoException \
uk/ac/sanger/artemis/io/QualifierInfo \
uk/ac/sanger/artemis/io/QualifierInfoVector \
uk/ac/sanger/artemis/io/QualifierInfoHash \
uk/ac/sanger/artemis/chado/DbSqlConfig \
uk/ac/sanger/artemis/circular/DNADraw \
uk/ac/sanger/artemis/circular/digest/Utils \
uk/ac/sanger/artemis/circular/digest/CircularGenomeController
CLASSES := $(NAMES:%=%.class)
SOURCES := $(NAMES:%=%.java)
all: idl code
code: $(CLASSES)
topdown: idl
$(REAL_CLASSPATH) $(JAVAC) uk/ac/sanger/artemis/components/ArtemisMain.java
%.class : %.java
$(REAL_CLASSPATH) $(JAVAC) $<
idl : type/*.java nsdb/*.java seqdb/*.java
IDL = idlj
IDLCMD = $(IDL) -Icorba
type/*.java : corba/types.idl
$(IDLCMD) corba/types.idl
nsdb/*.java : corba/nsdb.idl corba/nsdb_write.idl
$(IDLCMD) corba/nsdb.idl
$(IDLCMD) corba/nsdb_write.idl
seqdb/*.java : corba/seqdb.idl
$(IDLCMD) corba/seqdb.idl
doc :
$(REAL_CLASSPATH) javadoc -J-mx200m -version \
AppGlobal.java \
uk.ac.sanger.artemis uk.ac.sanger.artemis.components \
uk.ac.sanger.artemis.sequence uk.ac.sanger.artemis.plot \
uk.ac.sanger.artemis.util uk.ac.sanger.artemis.io
manual :
(cd docs; make)
CLASS_FILES := `find org uk nsdb type seqdb -name '*.class' -print`
OTHER_FILES := `find images/PSUlogo.gif images/icon.gif COPYING README`
dist :
rm -rf artemis_compiled.tar.gz tar_build
mkdir tar_build
mkdir tar_build/artemis
rm -f artemis_compiled_latest.tar.gz
tar cf - $(OTHER_FILES) act art etc | (cd tar_build/artemis; tar xf -)
tar cf - artemis_sqlmap dnaplotter uk org nsdb type seqdb lib | (cd tar_build/artemis; tar xf -)
(cd tar_build; find . -name 'CVS' -print | xargs rm -rf; find . -name '.svn' -print | xargs rm -rf; tar cvf ../artemis_compiled.tar artemis)
jar : all artemis.jar
artemis.jar : $(CLASSES)
mkdir jar_build
rm -f artemis.jar
cd jar_build; \
if [ ! -d org ]; then \
for fileJar in ../lib/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../lib/j2ssh/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../lib/ibatis/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
for fileJar in ../lib/picard/*.jar; do \
jar xvf $$fileJar; \
rm -rf META-INF/MANIFEST.MF; \
done; \
fi; \
cp -R ../lib/LICENSE.Apache ../uk ../org ../nsdb ../type ../seqdb ../etc ../images ../lib/j2ssh/j2ssh.properties \
../images/PSUlogo.gif ../images/icon.gif ../README ../artemis_sqlmap .
find jar_build -name '*.java' -print | xargs rm -f
find jar_build -name '.svn' -print | xargs rm -rf
cd jar_build; \
rm -rf META-INF/MANIFEST.MF; \
echo "Main-Class: uk.ac.sanger.artemis.components.ArtemisMain" > manifest-art; \
jar cmf manifest-art artemis.jar images/PSUlogo.gif images/icon.gif README etc \
artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
echo "Main-Class: uk.ac.sanger.artemis.circular.DNADraw" > manifest-circular; \
jar cmf manifest-circular DNAPlotter.jar images/PSUlogo.gif README etc \
uk org/gmod org/apache org/biojava/bio/ com/ibatis/common/jdbc/ LICENSE.Apache j2ssh.properties; \
echo "Main-Class: uk.ac.sanger.artemis.components.alignment.BamView" > manifest-bamview; \
jar cmf manifest-bamview BamView.jar etc uk org net/sf com/ibatis; \
echo "Main-Class: uk.ac.sanger.artemis.components.ActMain" > manifest-act; \
jar cmf manifest-act act.jar images/PSUlogo.gif images/icon.gif README etc \
artemis_sqlmap org uk com net nsdb type seqdb LICENSE.Apache j2ssh.properties; \
rm -f etc/log4j.properties; \
jar cmf manifest-art artemis_mac.jar images/PSUlogo.gif images/icon.gif README \
uk org/gmod nsdb type seqdb LICENSE.Apache artemis_sqlmap
clean :
-rm -rf *.html artemis.jar seqdb nsdb type resources uk/ac/sanger/jcon/ jar_build tar_build artemis_compiled.tar
-rm -rf TAGS* *.o
-find . -name '*.class' -print | xargs rm -f