# This is a GNU Makefile for agct

# $Header: /nfs/disk222/yeastpub/Repository/agctimpl/Makefile,v 1.16 2000/09/18 18:11:55 kmr Exp $

SHELL=/bin/sh

OPT_FLAGS = -g

JAVAC := javac $(OPT_FLAGS) -deprecation -J-mx150m $(EXTRA_FLAGS)

NAMES:= \
	uk/ac/sanger/pathogens/ReadOnlyException \
	uk/ac/sanger/pathogens/Document \
	uk/ac/sanger/pathogens/FileDocument \
	uk/ac/sanger/pathogens/OutOfRangeException \
	uk/ac/sanger/pathogens/StringVector \
	uk/ac/sanger/pathogens/embl/Key \
	uk/ac/sanger/pathogens/embl/OutOfDateException \
	uk/ac/sanger/pathogens/embl/KeyVector \
	uk/ac/sanger/pathogens/embl/EMBLObject \
	uk/ac/sanger/pathogens/embl/EntryInformation \
	uk/ac/sanger/pathogens/embl/QualifierParseException \
	uk/ac/sanger/pathogens/embl/ReadFormatException \
	uk/ac/sanger/pathogens/embl/UpperInteger \
	uk/ac/sanger/pathogens/embl/LowerInteger \
	uk/ac/sanger/pathogens/embl/Location \
	uk/ac/sanger/pathogens/embl/LocationLexer \
	uk/ac/sanger/pathogens/embl/LocationParseException \
	uk/ac/sanger/pathogens/embl/LocationParseNode \
	uk/ac/sanger/pathogens/embl/LocationParseNodeVector \
	uk/ac/sanger/pathogens/embl/LineGroup \
	uk/ac/sanger/pathogens/embl/LineGroupVector \
	uk/ac/sanger/pathogens/embl/LinePushBackReader \
	uk/ac/sanger/pathogens/embl/Range \
	uk/ac/sanger/pathogens/embl/FuzzyRange \
	uk/ac/sanger/pathogens/embl/BetweenRange \
	uk/ac/sanger/pathogens/embl/RangeVector \
	uk/ac/sanger/pathogens/embl/Sequence \
	uk/ac/sanger/pathogens/embl/StreamSequence \
	uk/ac/sanger/pathogens/embl/EmblStreamSequence \
	uk/ac/sanger/pathogens/embl/GenbankStreamSequence \
	uk/ac/sanger/pathogens/embl/RawStreamSequence \
	uk/ac/sanger/pathogens/embl/FastaStreamSequence \
	uk/ac/sanger/pathogens/embl/StreamSequenceFactory \
	uk/ac/sanger/pathogens/embl/Feature \
	uk/ac/sanger/pathogens/embl/StreamFeature \
	uk/ac/sanger/pathogens/embl/FeatureTable \
	uk/ac/sanger/pathogens/embl/FeatureTree \
	uk/ac/sanger/pathogens/embl/FeatureVector \
	uk/ac/sanger/pathogens/embl/Qualifier \
	uk/ac/sanger/pathogens/embl/InvalidRelationException \
	uk/ac/sanger/pathogens/embl/StreamQualifier \
	uk/ac/sanger/pathogens/embl/QualifierVector \
	uk/ac/sanger/pathogens/embl/QualifierInfoVector \
	uk/ac/sanger/pathogens/embl/QualifierInfo \
	uk/ac/sanger/pathogens/embl/QualifierInfoException \
	uk/ac/sanger/pathogens/embl/PushBackException \
	uk/ac/sanger/pathogens/embl/Entry \
	uk/ac/sanger/pathogens/embl/DocumentEntry \
	uk/ac/sanger/pathogens/embl/DateStampFeature \
	diana/sequence/SequenceChangeEvent \
	diana/sequence/SequenceChangeListener \
	diana/sequence/AminoAcidSequence \
	diana/sequence/Bases \
	diana/sequence/BasePattern \
	diana/sequence/BasePatternFormatException \
	diana/sequence/Strand \
	diana/sequence/Marker \
	diana/sequence/MarkerChangeEvent \
	diana/sequence/MarkerChangeListener \
	diana/sequence/MarkerRange \
	diana/sequence/MarkerRangeVector \
	diana/Selectable \
	diana/SelectionChangeEvent \
	diana/SelectionChangeListener \
	diana/GotoEvent \
	diana/GotoEventSource \
	diana/SimpleGotoEventSource \
	diana/ChangeEvent \
	diana/ChangeListener \
	diana/FeatureSegment \
	diana/Feature \
	diana/FeatureVector \
	diana/FeatureChangeEvent \
	diana/FeatureChangeListener \
	diana/FeatureSegment \
	diana/FeatureSegmentVector \
	diana/FeatureEnumeration \
	diana/FeaturePredicate \
	diana/FeatureKeyPredicate \
	diana/FeatureKeyQualifierPredicate \
	diana/Entry \
	diana/EntryVector \
	diana/SimpleEntryGroup \
	diana/FilteredEntryGroup \
	diana/EntryGroup \
	diana/EntryChangeEvent \
	diana/EntryChangeListener \
	diana/EntryGroupChangeEvent \
	diana/EntryGroupChangeListener \
	diana/AlignMatch \
	diana/AlignMatchVector \
	diana/ComparisonData \
	diana/ComparisonDataParseException \
	diana/MUMmerComparisonData \
	diana/MSPcrunchComparisonData \
	diana/SimpleComparisonData \
	diana/ComparisonDataFactory \
	diana/components/DisplayAdjustmentEvent \
	diana/components/DisplayAdjustmentListener \
	diana/components/FeatureInfo \
	diana/components/SequenceViewer \
	diana/components/FeatureBaseViewer \
	diana/components/FeatureAminoAcidViewer \
	diana/components/Plot \
	diana/components/PlotMouseListener \
	diana/components/TextRequester \
	diana/components/TextRequesterListener \
	diana/components/TextRequesterEvent \
	diana/components/EditMenu \
	diana/components/GotoMenu \
	diana/components/ViewMenu \
	diana/components/AddMenu \
	diana/components/RunMenu \
	diana/components/SelectMenu \
	diana/components/WriteMenu \
	diana/components/Navigator \
	diana/components/EntryGroupInfoDisplay \
	diana/components/YesNoDialog \
	diana/components/MessageDialog \
	diana/components/MessageFrame \
	diana/components/FileViewer \
	diana/components/FeatureViewer \
	diana/components/FeatureEdit \
	diana/components/FeaturePlot \
	diana/components/FeaturePlotGroup \
	diana/components/FeaturePopup \
	diana/components/BasePlotGroup \
	diana/components/BasePlot \
	diana/components/SelectionViewer \
	diana/components/SelectionMenu \
	diana/components/EntryFileDialog \
	diana/components/DisplayComponent \
	diana/components/EntryHeaderEdit \
	diana/components/CanvasPanel \
	diana/components/FeatureDisplay \
        diana/components/FeatureList \
	diana/components/Comparator \
	diana/components/AlignmentViewer \
	diana/components/ComparatorDialog \
	diana/components/Splash \
	diana/components/ActMain \
	diana/Selection \
	diana/Options \
	AppGlobal \
	Dad

CLASSES := $(NAMES:%=%.class)
SOURCES := $(NAMES:%=%.java)

all: $(CLASSES)

topdown:
	CLASSPATH=.:$(CLASSPATH) $(JAVAC) -depend Dad.java

%.class : %.java
	CLASSPATH=. $(JAVAC) $<

manual :
	(cd docs; \
	jade -t sgml -d /usr/lib/dsssl/stylesheets/docbook/html/docbook.dsl manual.sgml)

jar : all act.jar

act.jar : $(CLASSES)
	rm -f act.jar
	(find * -name '*.class' -print;  \
	echo etc/options; echo etc/feature_keys; echo etc/qualifier_types; \
	echo META-INF/MANIFEST.MF; \
	echo diana/helix.gif; echo diana/sanger-centre.gif) | \
	zip -u9@ act.jar

clean :
	-rm -rf *.html act.jar
	-find . -name '*.class' -print | xargs rm -f
