diff --git a/Makefile b/Makefile index 8d27e27af0755be37cea8ca51ba6bceb2d6957bb..5d72710cbad59dcc60475dd0dc170c1de7f28c86 100644 --- a/Makefile +++ b/Makefile @@ -1,7 +1,5 @@ # 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 @@ -10,202 +8,6 @@ JAVAC := javac -source 1.5 -target 1.5 $(OPT_FLAGS) $(EXTRA_FLAGS) REAL_CLASSPATH := CLASSPATH=lib/commons-lang-2.6.jar: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:= \ -# 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 \ -# uk/ac/sanger/artemis/io/GffToEMBL - ARTEMIS_DIRS = uk/ac/sanger/artemis \ uk/ac/sanger/artemis/chado \ uk/ac/sanger/artemis/circular \ @@ -226,7 +28,6 @@ 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) diff --git a/etc/qualifier_types b/etc/qualifier_types index 7dfd32a0df52e1b7fd5065068ddb82e48499cecc..763de70dcb1d018e9bb5bb99181f44511853f0da 100644 --- a/etc/qualifier_types +++ b/etc/qualifier_types @@ -73,8 +73,8 @@ map no "text" mating_type yes "text" mobile_element_type no "text" mod_base yes list OTHER ac4c chm5u cm cmnm5s2u cmnm5u d fm gal q gm i i6a m1a m1f m1g m1i m22g m2a m2g m3c m5c m6a m7g mam5s2u mam5u man q mcm5s2u mcm5u mo5u ms2i6a ms2t6a mt6a mv o5u osyw p q s2c s2t s2u s4u t t6a tm um x yw -mol_type yes "list" "unassigned DNA" "unassigned RNA" "genomic DNA" "genomic RNA" "mRNA" "tRNA" "rRNA" "transcribed RNA" "other RNA" "other DNA" "protein" "viral cRNA" -ncRNA_class yes list "antisense_RNA" "autocatalytically_spliced_intron" "hammerhead_ribozyme" "RNase_P_RNA" "RNase_MRP_RNA" "telomerase_RNA" "guide_RNA" "rasiRNA" "scRNA" "siRNA" "miRNA" "piRNA" "snoRNA" "snRNA" "SRP_RNA" "vault_RNA" "Y_RNA" "other" "ribozyme" +mol_type yes "list" "unassigned DNA" "unassigned RNA" "genomic DNA" "genomic RNA" "mRNA" "tRNA" "rRNA" "transcribed RNA" "other RNA" "other DNA" "protein" "viral cRNA" +ncRNA_class yes "list" "antisense_RNA" "autocatalytically_spliced_intron" "hammerhead_ribozyme" "RNase_P_RNA" "RNase_MRP_RNA" "telomerase_RNA" "guide_RNA" "rasiRNA" "scRNA" "siRNA" "miRNA" "piRNA" "snoRNA" "snRNA" "SRP_RNA" "vault_RNA" "Y_RNA" "other" "ribozyme" note no "text" number yes number 1 99999999 old_locus_tag no "text"