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Commit b4f91404 authored by Sascha Steinbiss's avatar Sascha Steinbiss
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make Makefile process all .java files

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...@@ -10,205 +10,225 @@ JAVAC := javac -source 1.5 -target 1.5 $(OPT_FLAGS) $(EXTRA_FLAGS) ...@@ -10,205 +10,225 @@ 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:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:. 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:lib/batik/batik-awt-util.jar:lib/batik/batik-dom.jar:lib/batik/batik-ext.jar:lib/batik/batik-svggen.jar:lib/batik/batik-util.jar:lib/batik/batik-xml.jar:.
NAMES:= \ # NAMES:= \
uk/ac/sanger/artemis/OptionChangeListener \ # uk/ac/sanger/artemis/OptionChangeListener \
uk/ac/sanger/artemis/OptionChangeEvent \ # uk/ac/sanger/artemis/OptionChangeEvent \
uk/ac/sanger/artemis/Options \ # uk/ac/sanger/artemis/Options \
uk/ac/sanger/artemis/Selection \ # uk/ac/sanger/artemis/Selection \
uk/ac/sanger/artemis/components/ArtemisMain \ # uk/ac/sanger/artemis/components/ArtemisMain \
uk/ac/sanger/artemis/components/ActMain \ # uk/ac/sanger/artemis/components/ActMain \
uk/ac/sanger/artemis/components/Splash \ # uk/ac/sanger/artemis/components/Splash \
uk/ac/sanger/artemis/components/ListDialog \ # uk/ac/sanger/artemis/components/ListDialog \
uk/ac/sanger/artemis/components/FeatureListFrame \ # uk/ac/sanger/artemis/components/FeatureListFrame \
uk/ac/sanger/artemis/components/FeatureList \ # uk/ac/sanger/artemis/components/FeatureList \
uk/ac/sanger/artemis/components/FeatureDisplay \ # uk/ac/sanger/artemis/components/FeatureDisplay \
uk/ac/sanger/artemis/components/CanvasPanel \ # uk/ac/sanger/artemis/components/CanvasPanel \
uk/ac/sanger/artemis/components/EntryGroupDisplay \ # uk/ac/sanger/artemis/components/EntryGroupDisplay \
uk/ac/sanger/artemis/components/EntryHeaderEdit \ # uk/ac/sanger/artemis/components/EntryHeaderEdit \
uk/ac/sanger/artemis/components/BasePlotGroup \ # uk/ac/sanger/artemis/components/BasePlotGroup \
uk/ac/sanger/artemis/components/EntryEditVector \ # uk/ac/sanger/artemis/components/EntryEditVector \
uk/ac/sanger/artemis/components/EntryEdit \ # uk/ac/sanger/artemis/components/EntryEdit \
uk/ac/sanger/artemis/components/WritableEMBLCorbaEntrySource \ # uk/ac/sanger/artemis/components/WritableEMBLCorbaEntrySource \
uk/ac/sanger/artemis/components/DbfetchEntrySource \ # uk/ac/sanger/artemis/components/DbfetchEntrySource \
uk/ac/sanger/artemis/components/EMBLCorbaEntrySource \ # uk/ac/sanger/artemis/components/EMBLCorbaEntrySource \
uk/ac/sanger/artemis/components/CorbaEntrySource \ # uk/ac/sanger/artemis/components/CorbaEntrySource \
uk/ac/sanger/artemis/components/BioJavaEntrySource \ # uk/ac/sanger/artemis/components/BioJavaEntrySource \
uk/ac/sanger/artemis/components/FileDialogEntrySource \ # uk/ac/sanger/artemis/components/FileDialogEntrySource \
uk/ac/sanger/artemis/components/EntryActionListener \ # uk/ac/sanger/artemis/components/EntryActionListener \
uk/ac/sanger/artemis/components/DisplayComponent \ # uk/ac/sanger/artemis/components/DisplayComponent \
uk/ac/sanger/artemis/components/EntryFileDialog \ # uk/ac/sanger/artemis/components/EntryFileDialog \
uk/ac/sanger/artemis/components/StickyFileChooser \ # uk/ac/sanger/artemis/components/StickyFileChooser \
uk/ac/sanger/artemis/components/LogReadListener \ # uk/ac/sanger/artemis/components/LogReadListener \
uk/ac/sanger/artemis/components/Selector \ # uk/ac/sanger/artemis/components/Selector \
uk/ac/sanger/artemis/components/Navigator \ # uk/ac/sanger/artemis/components/Navigator \
uk/ac/sanger/artemis/components/EntryGroupPanel \ # uk/ac/sanger/artemis/components/EntryGroupPanel \
uk/ac/sanger/artemis/components/FeaturePopup \ # uk/ac/sanger/artemis/components/FeaturePopup \
uk/ac/sanger/artemis/components/WriteMenu \ # uk/ac/sanger/artemis/components/WriteMenu \
uk/ac/sanger/artemis/components/SelectMenu \ # uk/ac/sanger/artemis/components/SelectMenu \
uk/ac/sanger/artemis/components/GraphMenu \ # uk/ac/sanger/artemis/components/GraphMenu \
uk/ac/sanger/artemis/components/RunMenu \ # uk/ac/sanger/artemis/components/RunMenu \
uk/ac/sanger/artemis/components/AddMenu \ # uk/ac/sanger/artemis/components/AddMenu \
uk/ac/sanger/artemis/components/ViewMenu \ # uk/ac/sanger/artemis/components/ViewMenu \
uk/ac/sanger/artemis/components/GotoMenu \ # uk/ac/sanger/artemis/components/GotoMenu \
uk/ac/sanger/artemis/components/EditMenu \ # uk/ac/sanger/artemis/components/EditMenu \
uk/ac/sanger/artemis/components/SelectionMenu \ # uk/ac/sanger/artemis/components/SelectionMenu \
uk/ac/sanger/artemis/components/SelectionViewer \ # uk/ac/sanger/artemis/components/SelectionViewer \
uk/ac/sanger/artemis/components/FeaturePlotGroup \ # uk/ac/sanger/artemis/components/FeaturePlotGroup \
uk/ac/sanger/artemis/components/FeaturePlot \ # uk/ac/sanger/artemis/components/FeaturePlot \
uk/ac/sanger/artemis/components/FeatureEdit \ # uk/ac/sanger/artemis/components/FeatureEdit \
uk/ac/sanger/artemis/components/FeatureViewer \ # uk/ac/sanger/artemis/components/FeatureViewer \
uk/ac/sanger/artemis/components/SearchResultViewer \ # uk/ac/sanger/artemis/components/SearchResultViewer \
uk/ac/sanger/artemis/components/LogViewer \ # uk/ac/sanger/artemis/components/LogViewer \
uk/ac/sanger/artemis/components/FileViewer \ # uk/ac/sanger/artemis/components/FileViewer \
uk/ac/sanger/artemis/components/MessageFrame \ # uk/ac/sanger/artemis/components/MessageFrame \
uk/ac/sanger/artemis/components/MessageDialog \ # uk/ac/sanger/artemis/components/MessageDialog \
uk/ac/sanger/artemis/components/YesNoDialog \ # uk/ac/sanger/artemis/components/YesNoDialog \
uk/ac/sanger/artemis/components/KeyChooser \ # uk/ac/sanger/artemis/components/KeyChooser \
uk/ac/sanger/artemis/components/KeyChoice \ # uk/ac/sanger/artemis/components/KeyChoice \
uk/ac/sanger/artemis/components/QualifierEditor \ # uk/ac/sanger/artemis/components/QualifierEditor \
uk/ac/sanger/artemis/components/QualifierTextArea \ # uk/ac/sanger/artemis/components/QualifierTextArea \
uk/ac/sanger/artemis/components/QualifierChoice \ # uk/ac/sanger/artemis/components/QualifierChoice \
uk/ac/sanger/artemis/components/ChoiceFrame \ # uk/ac/sanger/artemis/components/ChoiceFrame \
uk/ac/sanger/artemis/components/SelectionInfoDisplay \ # uk/ac/sanger/artemis/components/SelectionInfoDisplay \
uk/ac/sanger/artemis/components/EntryGroupMenu \ # uk/ac/sanger/artemis/components/EntryGroupMenu \
uk/ac/sanger/artemis/components/EntryGroupInfoDisplay \ # uk/ac/sanger/artemis/components/EntryGroupInfoDisplay \
uk/ac/sanger/artemis/components/Utilities \ # uk/ac/sanger/artemis/components/Utilities \
uk/ac/sanger/artemis/components/MarkerRangeRequester \ # uk/ac/sanger/artemis/components/MarkerRangeRequester \
uk/ac/sanger/artemis/components/MarkerRangeRequesterListener \ # uk/ac/sanger/artemis/components/MarkerRangeRequesterListener \
uk/ac/sanger/artemis/components/MarkerRangeRequesterEvent \ # uk/ac/sanger/artemis/components/MarkerRangeRequesterEvent \
uk/ac/sanger/artemis/components/TextRequester \ # uk/ac/sanger/artemis/components/TextRequester \
uk/ac/sanger/artemis/components/TextRequesterListener \ # uk/ac/sanger/artemis/components/TextRequesterListener \
uk/ac/sanger/artemis/components/TextRequesterEvent \ # uk/ac/sanger/artemis/components/TextRequesterEvent \
uk/ac/sanger/artemis/components/TextDialog \ # uk/ac/sanger/artemis/components/TextDialog \
uk/ac/sanger/artemis/components/BasePlot \ # uk/ac/sanger/artemis/components/BasePlot \
uk/ac/sanger/artemis/components/ProcessWatcher \ # uk/ac/sanger/artemis/components/ProcessWatcher \
uk/ac/sanger/artemis/components/ProcessWatcherEvent \ # uk/ac/sanger/artemis/components/ProcessWatcherEvent \
uk/ac/sanger/artemis/components/ProcessWatcherListener \ # uk/ac/sanger/artemis/components/ProcessWatcherListener \
uk/ac/sanger/artemis/components/ExternalProgramOptions \ # uk/ac/sanger/artemis/components/ExternalProgramOptions \
uk/ac/sanger/artemis/components/Plot \ # uk/ac/sanger/artemis/components/Plot \
uk/ac/sanger/artemis/components/PlotMouseListener \ # uk/ac/sanger/artemis/components/PlotMouseListener \
uk/ac/sanger/artemis/components/FeatureAminoAcidViewer \ # uk/ac/sanger/artemis/components/FeatureAminoAcidViewer \
uk/ac/sanger/artemis/components/FeatureBaseViewer \ # uk/ac/sanger/artemis/components/FeatureBaseViewer \
uk/ac/sanger/artemis/components/SequenceViewer \ # uk/ac/sanger/artemis/components/SequenceViewer \
uk/ac/sanger/artemis/components/FeatureInfo \ # uk/ac/sanger/artemis/components/FeatureInfo \
uk/ac/sanger/artemis/components/DisplayAdjustmentListener \ # uk/ac/sanger/artemis/components/DisplayAdjustmentListener \
uk/ac/sanger/artemis/components/DisplayAdjustmentEvent \ # uk/ac/sanger/artemis/components/DisplayAdjustmentEvent \
uk/ac/sanger/artemis/components/ScoreChanger \ # uk/ac/sanger/artemis/components/ScoreChanger \
uk/ac/sanger/artemis/components/ScoreScrollbar \ # uk/ac/sanger/artemis/components/ScoreScrollbar \
uk/ac/sanger/artemis/components/ScoreChangeListener \ # uk/ac/sanger/artemis/components/ScoreChangeListener \
uk/ac/sanger/artemis/components/ScoreChangeEvent \ # uk/ac/sanger/artemis/components/ScoreChangeEvent \
uk/ac/sanger/artemis/components/InputStreamProgressDialog \ # uk/ac/sanger/artemis/components/InputStreamProgressDialog \
uk/ac/sanger/artemis/plot/KarlinSigAlgorithm \ # uk/ac/sanger/artemis/plot/KarlinSigAlgorithm \
uk/ac/sanger/artemis/plot/UserDataAlgorithm \ # uk/ac/sanger/artemis/plot/UserDataAlgorithm \
uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm \ # uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm \
uk/ac/sanger/artemis/plot/ATDeviationAlgorithm \ # uk/ac/sanger/artemis/plot/ATDeviationAlgorithm \
uk/ac/sanger/artemis/plot/GCDeviationAlgorithm \ # uk/ac/sanger/artemis/plot/GCDeviationAlgorithm \
uk/ac/sanger/artemis/plot/GCFrameAlgorithm \ # uk/ac/sanger/artemis/plot/GCFrameAlgorithm \
uk/ac/sanger/artemis/plot/CodonUsageAlgorithm \ # uk/ac/sanger/artemis/plot/CodonUsageAlgorithm \
uk/ac/sanger/artemis/plot/CodonUsageFormatException \ # uk/ac/sanger/artemis/plot/CodonUsageFormatException \
uk/ac/sanger/artemis/plot/CodonUsageWeight \ # uk/ac/sanger/artemis/plot/CodonUsageWeight \
uk/ac/sanger/artemis/plot/CodonWeight \ # uk/ac/sanger/artemis/plot/CodonWeight \
uk/ac/sanger/artemis/plot/AGWindowAlgorithm \ # uk/ac/sanger/artemis/plot/AGWindowAlgorithm \
uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm \ # uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm \
uk/ac/sanger/artemis/plot/GCWindowAlgorithm \ # uk/ac/sanger/artemis/plot/GCWindowAlgorithm \
uk/ac/sanger/artemis/plot/HydrophilicityAlgorithm \ # uk/ac/sanger/artemis/plot/HydrophilicityAlgorithm \
uk/ac/sanger/artemis/plot/HydroAlgorithm \ # uk/ac/sanger/artemis/plot/HydroAlgorithm \
uk/ac/sanger/artemis/plot/HydrophobicityAlgorithm \ # uk/ac/sanger/artemis/plot/HydrophobicityAlgorithm \
uk/ac/sanger/artemis/plot/CoilFeatureAlgorithm \ # uk/ac/sanger/artemis/plot/CoilFeatureAlgorithm \
uk/ac/sanger/artemis/plot/FeatureAlgorithm \ # uk/ac/sanger/artemis/plot/FeatureAlgorithm \
uk/ac/sanger/artemis/plot/BaseAlgorithm \ # uk/ac/sanger/artemis/plot/BaseAlgorithm \
uk/ac/sanger/artemis/plot/Algorithm \ # uk/ac/sanger/artemis/plot/Algorithm \
uk/ac/sanger/artemis/Logger \ # uk/ac/sanger/artemis/Logger \
uk/ac/sanger/artemis/ExternalProgramListener \ # uk/ac/sanger/artemis/ExternalProgramListener \
uk/ac/sanger/artemis/ExternalProgramException \ # uk/ac/sanger/artemis/ExternalProgramException \
uk/ac/sanger/artemis/ExternalProgramVector \ # uk/ac/sanger/artemis/ExternalProgramVector \
uk/ac/sanger/artemis/SimpleExternalProgramMonitor \ # uk/ac/sanger/artemis/SimpleExternalProgramMonitor \
uk/ac/sanger/artemis/ProcessMonitor \ # uk/ac/sanger/artemis/ProcessMonitor \
uk/ac/sanger/artemis/ProcessMonitor \ # uk/ac/sanger/artemis/ProcessMonitor \
uk/ac/sanger/artemis/ExternalProgramMonitor \ # uk/ac/sanger/artemis/ExternalProgramMonitor \
uk/ac/sanger/artemis/ExternalProgram \ # uk/ac/sanger/artemis/ExternalProgram \
uk/ac/sanger/artemis/EntryGroupChangeListener \ # uk/ac/sanger/artemis/EntryGroupChangeListener \
uk/ac/sanger/artemis/EntryGroupChangeEvent \ # uk/ac/sanger/artemis/EntryGroupChangeEvent \
uk/ac/sanger/artemis/EntryChangeListener \ # uk/ac/sanger/artemis/EntryChangeListener \
uk/ac/sanger/artemis/EntryChangeEvent \ # uk/ac/sanger/artemis/EntryChangeEvent \
uk/ac/sanger/artemis/FilteredEntryGroup \ # uk/ac/sanger/artemis/FilteredEntryGroup \
uk/ac/sanger/artemis/SimpleEntryGroup \ # uk/ac/sanger/artemis/SimpleEntryGroup \
uk/ac/sanger/artemis/EntryGroup \ # uk/ac/sanger/artemis/EntryGroup \
uk/ac/sanger/artemis/EntryVector \ # uk/ac/sanger/artemis/EntryVector \
uk/ac/sanger/artemis/EntrySourceVector \ # uk/ac/sanger/artemis/EntrySourceVector \
uk/ac/sanger/artemis/EntrySource \ # uk/ac/sanger/artemis/EntrySource \
uk/ac/sanger/artemis/Entry \ # uk/ac/sanger/artemis/Entry \
uk/ac/sanger/artemis/LastSegmentException \ # uk/ac/sanger/artemis/LastSegmentException \
uk/ac/sanger/artemis/FeatureFromVectorPredicate \ # uk/ac/sanger/artemis/FeatureFromVectorPredicate \
uk/ac/sanger/artemis/FeatureKeyQualifierPredicate \ # uk/ac/sanger/artemis/FeatureKeyQualifierPredicate \
uk/ac/sanger/artemis/FeatureKeyPredicate \ # uk/ac/sanger/artemis/FeatureKeyPredicate \
uk/ac/sanger/artemis/FeaturePatternPredicate \ # uk/ac/sanger/artemis/FeaturePatternPredicate \
uk/ac/sanger/artemis/FeaturePredicateConjunction \ # uk/ac/sanger/artemis/FeaturePredicateConjunction \
uk/ac/sanger/artemis/FeaturePredicate \ # uk/ac/sanger/artemis/FeaturePredicate \
uk/ac/sanger/artemis/FeaturePredicateVector \ # uk/ac/sanger/artemis/FeaturePredicateVector \
uk/ac/sanger/artemis/FeatureEnumeration \ # uk/ac/sanger/artemis/FeatureEnumeration \
uk/ac/sanger/artemis/FeatureSegmentVector \ # uk/ac/sanger/artemis/FeatureSegmentVector \
uk/ac/sanger/artemis/FeatureChangeListener \ # uk/ac/sanger/artemis/FeatureChangeListener \
uk/ac/sanger/artemis/FeatureChangeEvent \ # uk/ac/sanger/artemis/FeatureChangeEvent \
uk/ac/sanger/artemis/FeatureVector \ # uk/ac/sanger/artemis/FeatureVector \
uk/ac/sanger/artemis/Feature \ # uk/ac/sanger/artemis/Feature \
uk/ac/sanger/artemis/FeatureSegment \ # uk/ac/sanger/artemis/FeatureSegment \
uk/ac/sanger/artemis/ActionController \ # uk/ac/sanger/artemis/ActionController \
uk/ac/sanger/artemis/ActionVector \ # uk/ac/sanger/artemis/ActionVector \
uk/ac/sanger/artemis/Action \ # uk/ac/sanger/artemis/Action \
uk/ac/sanger/artemis/ChangeListener \ # uk/ac/sanger/artemis/ChangeListener \
uk/ac/sanger/artemis/ChangeEventVector \ # uk/ac/sanger/artemis/ChangeEventVector \
uk/ac/sanger/artemis/ChangeEvent \ # uk/ac/sanger/artemis/ChangeEvent \
uk/ac/sanger/artemis/GotoListener \ # uk/ac/sanger/artemis/GotoListener \
uk/ac/sanger/artemis/GotoEvent \ # uk/ac/sanger/artemis/GotoEvent \
uk/ac/sanger/artemis/GotoEventSource \ # uk/ac/sanger/artemis/GotoEventSource \
uk/ac/sanger/artemis/SimpleGotoEventSource \ # uk/ac/sanger/artemis/SimpleGotoEventSource \
uk/ac/sanger/artemis/SelectionChangeListener \ # uk/ac/sanger/artemis/SelectionChangeListener \
uk/ac/sanger/artemis/SelectionChangeEvent \ # uk/ac/sanger/artemis/SelectionChangeEvent \
uk/ac/sanger/artemis/Selectable \ # uk/ac/sanger/artemis/Selectable \
uk/ac/sanger/artemis/sequence/NoSequenceException \ # uk/ac/sanger/artemis/sequence/NoSequenceException \
uk/ac/sanger/artemis/sequence/MarkerRangeVector \ # uk/ac/sanger/artemis/sequence/MarkerRangeVector \
uk/ac/sanger/artemis/sequence/MarkerRange \ # uk/ac/sanger/artemis/sequence/MarkerRange \
uk/ac/sanger/artemis/sequence/MarkerChangeListener \ # uk/ac/sanger/artemis/sequence/MarkerChangeListener \
uk/ac/sanger/artemis/sequence/MarkerChangeEvent \ # uk/ac/sanger/artemis/sequence/MarkerChangeEvent \
uk/ac/sanger/artemis/sequence/Marker \ # uk/ac/sanger/artemis/sequence/Marker \
uk/ac/sanger/artemis/sequence/Strand \ # uk/ac/sanger/artemis/sequence/Strand \
uk/ac/sanger/artemis/sequence/BasePatternFormatException \ # uk/ac/sanger/artemis/sequence/BasePatternFormatException \
uk/ac/sanger/artemis/sequence/BasePattern \ # uk/ac/sanger/artemis/sequence/BasePattern \
uk/ac/sanger/artemis/sequence/Bases \ # uk/ac/sanger/artemis/sequence/Bases \
uk/ac/sanger/artemis/sequence/AminoAcidSequence \ # uk/ac/sanger/artemis/sequence/AminoAcidSequence \
uk/ac/sanger/artemis/sequence/SequenceChangeListener \ # uk/ac/sanger/artemis/sequence/SequenceChangeListener \
uk/ac/sanger/artemis/sequence/SequenceChangeEvent \ # uk/ac/sanger/artemis/sequence/SequenceChangeEvent \
uk/ac/sanger/artemis/io/BioJavaFeature \ # uk/ac/sanger/artemis/io/BioJavaFeature \
uk/ac/sanger/artemis/io/BioJavaSequence \ # uk/ac/sanger/artemis/io/BioJavaSequence \
uk/ac/sanger/artemis/io/BioJavaEntry \ # uk/ac/sanger/artemis/io/BioJavaEntry \
uk/ac/sanger/artemis/io/GenbankStreamSequence \ # uk/ac/sanger/artemis/io/GenbankStreamSequence \
uk/ac/sanger/artemis/io/RWCorbaEntry \ # uk/ac/sanger/artemis/io/RWCorbaEntry \
uk/ac/sanger/artemis/io/CorbaEntry \ # uk/ac/sanger/artemis/io/CorbaEntry \
uk/ac/sanger/artemis/io/DocumentEntryFactory \ # uk/ac/sanger/artemis/io/DocumentEntryFactory \
uk/ac/sanger/artemis/io/BlastDocumentEntry \ # uk/ac/sanger/artemis/io/BlastDocumentEntry \
uk/ac/sanger/artemis/io/MSPcrunchDocumentEntry \ # uk/ac/sanger/artemis/io/MSPcrunchDocumentEntry \
uk/ac/sanger/artemis/io/GFFDocumentEntry \ # uk/ac/sanger/artemis/io/GFFDocumentEntry \
uk/ac/sanger/artemis/io/GenbankDocumentEntry \ # uk/ac/sanger/artemis/io/GenbankDocumentEntry \
uk/ac/sanger/artemis/io/EmblDocumentEntry \ # uk/ac/sanger/artemis/io/EmblDocumentEntry \
uk/ac/sanger/artemis/io/PublicDBDocumentEntry \ # uk/ac/sanger/artemis/io/PublicDBDocumentEntry \
uk/ac/sanger/artemis/io/SimpleDocumentEntry \ # uk/ac/sanger/artemis/io/SimpleDocumentEntry \
uk/ac/sanger/artemis/io/DocumentEntry \ # uk/ac/sanger/artemis/io/DocumentEntry \
uk/ac/sanger/artemis/io/Entry \ # uk/ac/sanger/artemis/io/Entry \
uk/ac/sanger/artemis/io/ReadOnlyEntry \ # uk/ac/sanger/artemis/io/ReadOnlyEntry \
uk/ac/sanger/artemis/io/QualifierInfoException \ # uk/ac/sanger/artemis/io/QualifierInfoException \
uk/ac/sanger/artemis/io/QualifierInfo \ # uk/ac/sanger/artemis/io/QualifierInfo \
uk/ac/sanger/artemis/io/QualifierInfoVector \ # uk/ac/sanger/artemis/io/QualifierInfoVector \
uk/ac/sanger/artemis/io/QualifierInfoHash \ # uk/ac/sanger/artemis/io/QualifierInfoHash \
uk/ac/sanger/artemis/chado/DbSqlConfig \ # uk/ac/sanger/artemis/chado/DbSqlConfig \
uk/ac/sanger/artemis/circular/DNADraw \ # uk/ac/sanger/artemis/circular/DNADraw \
uk/ac/sanger/artemis/circular/digest/Utils \ # uk/ac/sanger/artemis/circular/digest/Utils \
uk/ac/sanger/artemis/circular/digest/CircularGenomeController \ # uk/ac/sanger/artemis/circular/digest/CircularGenomeController \
uk/ac/sanger/artemis/io/GffToEMBL # uk/ac/sanger/artemis/io/GffToEMBL
CLASSES := $(NAMES:%=%.class) ARTEMIS_DIRS = uk/ac/sanger/artemis \
SOURCES := $(NAMES:%=%.java) uk/ac/sanger/artemis/chado \
uk/ac/sanger/artemis/circular \
uk/ac/sanger/artemis/circular/digest \
uk/ac/sanger/artemis/components \
uk/ac/sanger/artemis/components/alignment \
uk/ac/sanger/artemis/components/database \
uk/ac/sanger/artemis/components/filetree \
uk/ac/sanger/artemis/components/genebuilder \
uk/ac/sanger/artemis/components/genebuilder/cv \
uk/ac/sanger/artemis/components/genebuilder/gff \
uk/ac/sanger/artemis/components/genebuilder/ortholog \
uk/ac/sanger/artemis/components/variant \
uk/ac/sanger/artemis/editor \
uk/ac/sanger/artemis/io \
uk/ac/sanger/artemis/j2ssh \
uk/ac/sanger/artemis/plot \
uk/ac/sanger/artemis/sequence \
uk/ac/sanger/artemis/util
#CLASSES := $(NAMES:%=%.class)
SOURCES := $(foreach DIR,$(ARTEMIS_DIRS),$(wildcard $(DIR)/*.java))
CLASSES := $(SOURCES:%.java=%.class)
all: idl code all: idl code
code: $(CLASSES) code: $(CLASSES)
......
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