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Commit 875897a1 authored by tjc's avatar tjc
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J2 version 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1643 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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Makefile 0 → 100644
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# This is a GNU Makefile for Artemis
# $Header: //tmp/pathsoft/artemis/Makefile,v 1.1 2004-06-09 12:51:51 tjc Exp $
SHELL=/bin/sh
OPT_FLAGS = -g
JAVAC := javac $(OPT_FLAGS) -target 1.1 -deprecation -J-mx150m $(EXTRA_FLAGS)
#REAL_CLASSPATH := CLASSPATH=.:lib/biojava.jar:lib/jobcontrol.jar:/nfs/team81/kmr/psu/jobcontrol/ant-build/src/main:/nfs/pathsoft/prod/javalibs/psu_all.jar:/nfs/pathsoft/external/javalib/velocity-dep-1.2.jar:/nfs/pathsoft/external/javalib/log4j-1.1.3.jar:$(CLASSPATH)
REAL_CLASSPATH := CLASSPATH=.:lib/biojava.jar:lib/jobcontrol.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/TaskMonitor \
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 \
CLASSES := $(NAMES:%=%.class)
SOURCES := $(NAMES:%=%.java)
all: idl code
code: $(CLASSES)
topdown: idl
$(REAL_CLASSPATH) $(JAVAC) Diana.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/icon.gif META-INF/MANIFEST.MF images/helix.gif images/sanger-centre.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
if [ ! -d org ]; then unzip lib/minimal_biojava.jar; fi
tar cf - $(OTHER_FILES) art etc | (cd tar_build/artemis; tar xf -)
tar cf - $(CLASS_FILES) | (cd tar_build/artemis; tar xf -)
(cd tar_build; tar czvf ../artemis_compiled.tar.gz artemis)
jar : all powmap.jar
powmap.jar : $(CLASSES)
rm -f powmap.jar
if [ ! -d org ]; then unzip lib/minimal_biojava.jar; fi
(echo $(CLASS_FILES) ; echo $(OTHER_FILES) ; \
echo etc/options; echo etc/feature_keys; echo etc/qualifier_types) | \
perl -pne 's/ /\n/g' | \
zip -u9@ powmap.jar
clean :
-rm -rf *.html powmap.jar seqdb nsdb type org
-rm -rf TAGS* *.o
-find . -name '*.class' -print | xargs rm -f
lib/biojava.jar 0 → 100644
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lib/jobcontrol.jar 0 → 100644
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View file @ 875897a1
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