Merge pull request #196 from tcarver/master

misc

Makefile

 # 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)
 

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"