diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..6b468b62a9884e67ca19b673f8e14e1931d65036
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1 @@
+*.class
diff --git a/Makefile b/Makefile
index 3db90a76666d3178ea9a37f730980909b9de770f..8dc99b0bb2a7e42b5d43bea05d46c8bde2f5a72e 100644
--- a/Makefile
+++ b/Makefile
@@ -10,207 +10,232 @@ 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:.
-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
+# 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
-CLASSES := $(NAMES:%=%.class)
-SOURCES := $(NAMES:%=%.java)
+ARTEMIS_DIRS = uk/ac/sanger/artemis \
+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
+# Utils needs to be built before controller
+uk/ac/sanger/artemis/circular/digest/CircularGenomeController.class:uk/ac/sanger/artemis/circular/digest/Utils.class
+ $(REAL_CLASSPATH) $(JAVAC) $(@:%.class=%.java)
+
code: $(CLASSES)
topdown: idl
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index eed41cb46836a87023c7d1cd94b62dbd08c17318..59e4aea56a93eefb5f6be591ef60f36e5df0738c 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -52,40 +52,40 @@ import uk.ac.sanger.artemis.util.StringVector;
* @author Kim Rutherford
**/
public class GFFStreamFeature extends SimpleDocumentFeature
- implements DocumentFeature, StreamFeature, ComparableFeature
+ implements DocumentFeature, StreamFeature, ComparableFeature
{
- private static org.apache.log4j.Logger logger4j =
+ private static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(GFFStreamFeature.class);
/** store for spliced features containing id and range of each segment */
private Hashtable<String, Range> id_range_store;
-
+
/** store a record of the new and old uniquenames that have been changed */
private Hashtable<String, String> newIdMapToOldId;
/** store the Timestamp for the feature */
private Timestamp timelastmodified;
-
+
private ChadoCanonicalGene chadoGene;
-
+
private boolean visible = true;
-
+
/** combined feature_relationship.rank store for exons */
private Hashtable<String, Integer> feature_relationship_rank_store;
-
+
/** first tabbed parameter */
private String gffSeqName;
/** second tabbed parameter */
private String gffSource;
/** duplication count */
private short duplicate = 0;
-
+
protected static Hashtable<String, Range> contig_ranges;
private boolean lazyLoaded = false;
private org.gmod.schema.sequence.Feature chadoLazyFeature;
private boolean readOnlyFeature = false;
-
+
private static String MAP_DECODE[][] = {
{ " ", "%20" }, // white space
@@ -99,10 +99,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{ ")", "%29" }, // right bracket
{ "'", "\"" }
};
-
+
private static String MAP_ENCODE[][] = {
// { " ", "%20" }, // white space
- { ",", "%2C" }, // comma
+ { ",", "%2C" }, // comma
{ ";", "%3B" }, // semi-colon
{ "=", "%3D" }, // equals
{ "\t", "%09" }, // tab
@@ -110,9 +110,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{ " ", "+" }, // white space
{ "(", "%28" }, // left bracket
{ ")", "%29" }, // right bracket
- { "\n", "%5C" } // new-line
+ { "\n", "%5C" } // new-line
};
-
+
/**
* Create a new GFFStreamFeature object. The feature should be added
* to an Entry (with Entry.add()).
@@ -121,11 +121,11 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* @param qualifiers The qualifiers for the new feature
**/
public GFFStreamFeature(final Key key, final Location location,
- final QualifierVector qualifiers)
+ final QualifierVector qualifiers)
{
super(null);
-
- try
+
+ try
{
setKey(key);
setLocation(location);
@@ -149,19 +149,19 @@ public class GFFStreamFeature extends SimpleDocumentFeature
idStr = key.getKeyString()+":"+location.toString();
setQualifier(new Qualifier("ID", idStr));
}
-
- }
- catch(EntryInformationException e)
+
+ }
+ catch(EntryInformationException e)
{
// this should never happen because the feature will not be in an Entry
throw new Error("internal error - unexpected exception: " + e);
}
- catch(ReadOnlyException e)
+ catch(ReadOnlyException e)
{
// this should never happen because the feature will not be in an Entry
throw new Error("internal error - unexpected exception: " + e);
- }
- catch(OutOfRangeException e)
+ }
+ catch(OutOfRangeException e)
{
// this should never happen because the feature will not be in an Entry
throw new Error("internal error - unexpected exception: " + e);
@@ -172,37 +172,37 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
this(feature, false);
}
-
+
/**
* Create a new GFFStreamFeature with the same key, location and
* qualifiers as the given feature. The feature should be added to an
* Entry (with Entry.add()).
* @param feature The feature to copy.
**/
- public GFFStreamFeature(final Feature feature, final boolean isDuplicatedInChado)
+ public GFFStreamFeature(final Feature feature, final boolean isDuplicatedInChado)
{
this(feature.getKey(), feature.getLocation(), feature.getQualifiers());
-
+
if(feature instanceof GFFStreamFeature)
{
if(((GFFStreamFeature)feature).id_range_store != null)
- this.id_range_store =
+ this.id_range_store =
(Hashtable)(((GFFStreamFeature)feature).id_range_store).clone();
-
+
if(((GFFStreamFeature)feature).feature_relationship_rank_store != null)
- this.feature_relationship_rank_store =
+ this.feature_relationship_rank_store =
(Hashtable)(((GFFStreamFeature)feature).feature_relationship_rank_store).clone();
-
+
this.setGffSeqName(((GFFStreamFeature)feature).getGffSeqName());
this.setGffSource(((GFFStreamFeature)feature).getGffSource());
-
+
if(isDuplicatedInChado)
{
try
{
final String uniquename;
final String duplicatePrefix;
-
+
if(feature instanceof GFFStreamFeature)
{
((GFFStreamFeature)feature).duplicate++;
@@ -222,7 +222,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
id_range_store.clear();
this.id_range_store = (Hashtable) new_id_range_store.clone();
-
+
if(getLocation().getRanges().size() > 1)
uniquename = getSegmentID(getLocation().getRanges());
@@ -237,26 +237,26 @@ public class GFFStreamFeature extends SimpleDocumentFeature
else
uniquename = duplicatePrefix+ (String)getQualifierByName("ID").getValues().get(0);
setQualifier(new Qualifier("ID", uniquename));
-
+
if(getQualifierByName("Parent") != null)
{
final String parent =
(String) getQualifierByName("Parent").getValues().get(0);
setQualifier(new Qualifier("Parent", duplicatePrefix+parent));
}
-
+
if(getQualifierByName("Derives_from") != null)
{
final String derives_from =
(String) getQualifierByName("Derives_from").getValues().get(0);
setQualifier(new Qualifier("Derives_from", duplicatePrefix+derives_from));
}
-
+
// remove qualifiers that don't get transferred to duplicate
- final String removeQualifierNames[] =
- { "feature_id",
- "timelastmodified",
- "feature_relationship_rank",
+ final String removeQualifierNames[] =
+ { "feature_id",
+ "timelastmodified",
+ "feature_relationship_rank",
ProteinMapPanel.POLYPEPTIDE_DOMAIN,
ProteinMapPanel.TMHMM[0],
ProteinMapPanel.TMHMM[1],
@@ -265,7 +265,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
MatchPanel.ORTHOLOG,
MatchPanel.ORTHOLOG
};
-
+
for(int i=0;i<removeQualifierNames.length; i++)
removeQualifierByName(removeQualifierNames[i]);
}
@@ -284,12 +284,12 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* in gene finder format.
**/
public GFFStreamFeature(final String line)
- throws ReadFormatException
+ throws ReadFormatException
{
super(null);
final StringVector line_bits = StringVector.getStrings(line, "\t", true);
- if(line_bits.size() < 8)
+ if(line_bits.size() < 8)
throw new ReadFormatException("invalid GFF line: 8 fields needed " +
"(got " + line_bits.size () +
" fields) from: " + line);
@@ -299,33 +299,33 @@ public class GFFStreamFeature extends SimpleDocumentFeature
final int start_base;
final int end_base;
- try
+ try
{
start_base = Integer.parseInt(start_base_str);
end_base = Integer.parseInt(end_base_str);
- }
+ }
catch(NumberFormatException e)
{
throw new ReadFormatException("Could not understand the start or end base " +
- "of a GFF feature: " + start_base_str +
+ "of a GFF feature: " + start_base_str +
" " + end_base_str);
}
// start of qualifier parsing and setting
- try
+ try
{
final boolean complement_flag;
- if(line_bits.elementAt(6).equals("+"))
+ if(line_bits.elementAt(6).equals("+"))
complement_flag = false;
else if(line_bits.elementAt(6).equals("-"))
complement_flag = true;
- else
+ else
{
// must be unstranded
complement_flag = false;
}
- if(line_bits.size() == 9)
+ if(line_bits.size() == 9)
{
final String rest_of_line = line_bits.elementAt(8);
final Hashtable<String, StringVector> attributes = parseAttributes(rest_of_line);
@@ -356,29 +356,29 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if( !line_bits.elementAt(0).equals("null") )
setGffSeqName( decode(line_bits.elementAt(0)) );
-
+
setKey(new Key(line_bits.elementAt(2)));
setGffSource(line_bits.elementAt(1));
-
+
if( !line_bits.elementAt(5).equals(".") )
{
final Qualifier score_qualifier =
new Qualifier("score", line_bits.elementAt(5));
setQualifier(score_qualifier);
}
-
+
String frame = line_bits.elementAt(7);
if(frame.equals ("0"))
frame = "1";
else if(frame.equals("1"))
frame = "2";
- else if(frame.equals("2"))
+ else if(frame.equals("2"))
frame = "3";
else
frame = ".";
- if(!frame.equals("."))
+ if(!frame.equals("."))
{
final Qualifier codon_start_qualifier =
new Qualifier("codon_start", frame);
@@ -386,28 +386,28 @@ public class GFFStreamFeature extends SimpleDocumentFeature
setQualifier(codon_start_qualifier);
}
- if(start_base > end_base)
+ if(start_base > end_base)
throw new ReadFormatException("start position is greater than end " +
"position: " + start_base + " > " +
end_base+"\n"+line);
if(start_base < 0)
throw new ReadFormatException("start position must be positive: " +
- start_base);
-
+ start_base);
+
final Range location_range = new Range(start_base, end_base);
final RangeVector location_ranges = new RangeVector(location_range);
setLocation(new Location(location_ranges, complement_flag));
}
- catch(ReadOnlyException e)
+ catch(ReadOnlyException e)
{
throw new Error("internal error - unexpected exception: " + e);
- }
- catch(EntryInformationException e)
+ }
+ catch(EntryInformationException e)
{
throw new Error("internal error - unexpected exception: " + e);
- }
- catch(OutOfRangeException e)
+ }
+ catch(OutOfRangeException e)
{
throw new Error("internal error - unexpected exception: " + e);
}
@@ -430,17 +430,17 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if(id_range_store == null)
{
id_range_store = new Hashtable<String, Range>();
- id_range_store.put((String)this.getQualifierByName("ID").getValues().get(0),
+ id_range_store.put((String)this.getQualifierByName("ID").getValues().get(0),
this.getLocation().getTotalRange());
}
return id_range_store;
}
-
+
public Hashtable<String, String> getNewIdMapToOldId()
{
return newIdMapToOldId;
}
-
+
/**
* Used when changing spliced feature uniquenames
* @param newIdMapToOldId
@@ -449,7 +449,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
this.newIdMapToOldId = newIdMapToOldId;
}
-
+
/**
* Store for ID's and CHADO feature_relationship.rank
* @param feature_relationship_rank_store
@@ -459,7 +459,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
this.feature_relationship_rank_store = feature_relationship_rank_store;
}
-
+
/**
* Store for ID's and CHADO feature_relationship.rank
* @return
@@ -468,10 +468,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
return feature_relationship_rank_store;
}
-
-
+
+
/**
- * Get the chado uniquename
+ * Get the chado uniquename
* @param r
* @return
*/
@@ -487,7 +487,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
Range offset_range = contig_ranges.get(getGffSeqName());
offset = offset_range.getStart()-1;
}
-
+
Enumeration<String> enum_ranges = id_range_store.keys();
while(enum_ranges.hasMoreElements())
{
@@ -509,7 +509,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
/**
- * Get the feature ID based on the segments chado
+ * Get the feature ID based on the segments chado
* uniquename's.
* @param rv
* @return
@@ -526,7 +526,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
range = (Range)rv.get(i);
id_new = getSegmentID(range);
-
+
String prefix[] = getPrefix(id_new, ':');
if(prefix[0] != null)
{
@@ -538,9 +538,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature
id = id+prefix[0] + "{" + prefix[1] + "}";
continue;
}
-
+
index = id.indexOf('}', index);
- id = id.substring(0,index) + "," +
+ id = id.substring(0,index) + "," +
prefix[1] + id.substring(index);
}
else if(id_new != null)
@@ -551,10 +551,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
}
}
-
+
return id;
}
-
+
/**
* Get the ID prefix, e.g. for SPAC1556.06.1:exon:2
* returns SPAC1556.06.1:exon as the prefix and 2 as the
@@ -575,7 +575,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
return prefix;
}
-
+
/**
* Used to automatically generate
* @param prefix
@@ -593,7 +593,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
return auto;
}
-
+
/**
* For gff-version 3:
@@ -616,7 +616,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
return s;
}
-
+
/**
* For gff-version 3:
* http://www.sequenceontology.org/gff3.shtml
@@ -642,7 +642,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
/**
* Return the reference of a new copy of this Feature.
**/
- public Feature copy()
+ public Feature copy()
{
final Feature return_value = new GFFStreamFeature(this);
return return_value;
@@ -660,17 +660,17 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* called
*/
protected static GFFStreamFeature readFromStream(LinePushBackReader stream)
- throws IOException, InvalidRelationException
+ throws IOException, InvalidRelationException
{
final String line = stream.readLine();
- if(line == null)
+ if(line == null)
return null;
try
{
return new GFFStreamFeature(line);
- }
- catch(ReadFormatException exception)
+ }
+ catch(ReadFormatException exception)
{
// re-throw the exception with the line number added
final String new_error_string = exception.getMessage();
@@ -692,7 +692,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
**/
public void setFromStream(final EntryInformation entry_information,
final LinePushBackReader in_stream)
- throws IOException, InvalidRelationException, ReadOnlyException
+ throws IOException, InvalidRelationException, ReadOnlyException
{
throw new ReadOnlyException();
}
@@ -704,13 +704,13 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* the Feature.
**/
public void writeToStream(final Writer writer)
- throws IOException
+ throws IOException
{
final RangeVector ranges = getLocation().getRanges();
final int ranges_size = ranges.size();
// final Hashtable contig_ranges = SimpleDocumentEntry.getContigRanges();
- for(int i = 0; i < ranges_size; ++i)
+ for(int i = 0; i < ranges_size; ++i)
{
Range this_range = (Range)ranges.elementAt(i);
@@ -725,19 +725,19 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
source_str = getDbxrefGFFSource(getQualifierByName("Dbxref"));
}
-
+
int start = this_range.getStart();
int end = this_range.getEnd();
-
- if(seqname == null && ((GFFDocumentEntry)getEntry()).getDocument() != null)
+
+ if(seqname == null && ((GFFDocumentEntry)getEntry()).getDocument() != null)
seqname = ((GFFDocumentEntry)getEntry()).getDocument().getName();
if(seqname == null)
seqname = deriveSeqName(start);
-
- if(source == null)
+
+ if(source == null)
source = "artemis";
- if(score == null)
+ if(score == null)
score = new Qualifier("score", ".");
if(seqname != null && contig_ranges != null &&
@@ -753,20 +753,20 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
final Qualifier gene = getQualifierByName("gene");
- if(gene == null)
+ if(gene == null)
group = new Qualifier("group", "");
- else
+ else
group = gene;
}
String frame = ".";
final Qualifier codon_start = getQualifierByName("codon_start");
- if(codon_start != null)
+ if(codon_start != null)
{
frame = (String)(codon_start.getValues()).elementAt(0);
- if(frame.equals ("1"))
+ if(frame.equals ("1"))
frame = "0";
else if(frame.equals("2"))
frame = "1";
@@ -775,7 +775,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
else
frame = ".";
}
-
+
// phase is REQUIRED for all CDS features
if(getKey().equals("CDS") && frame.equals("."))
frame = "0";
@@ -831,12 +831,12 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
catch(Exception e) {}
}
-
+
if(seqname == null)
seqname = "gff_seqname";
return seqname;
}
-
+
/**
* Return a String containing the qualifiers of this feature in a form
* suitable for using as the last field of a GFF line. The codon_start
@@ -844,15 +844,15 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* gff_source and score aren't included since they have corresponding
* fields.
**/
- private String unParseAttributes(final String myId)
+ private String unParseAttributes(final String myId)
{
final StringBuffer buffer = new StringBuffer();
final QualifierVector qualifiers = getQualifiers();
final String names[] = { "ID", "Name", "Alias", "Parent",
"Derives_from",
- "Target", "Gap", "Note",
- "Dbxref", "Ontology_term",
+ "Target", "Gap", "Note",
+ "Dbxref", "Ontology_term",
"Start_range", "End_range",
"Is_circular"};
int count = 0;
@@ -864,12 +864,12 @@ public class GFFStreamFeature extends SimpleDocumentFeature
buffer.append(encode(myId));
count++;
}
-
+
for(int i=1; i<names_length; i++)
{
Qualifier this_qualifier = qualifiers.getQualifierByName(names[i]);
-
- if(this_qualifier == null)
+
+ if(this_qualifier == null)
continue;
final String this_qualifier_str = getQualifierString(this_qualifier, true);
@@ -881,9 +881,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature
buffer.append(this_qualifier_str);
count++;
}
-
+
boolean lname;
- for(Qualifier this_qualifier: qualifiers)
+ for(Qualifier this_qualifier: qualifiers)
{
lname = false;
for(int j=0; j<names_length; j++)
@@ -892,16 +892,16 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if(lname)
continue;
-
+
if( (this_qualifier.getName().equals("private") && System.getProperty("noprivate") != null) ||
(this_qualifier.getName().equals("history") && System.getProperty("nohistory") != null) )
continue;
final String this_qualifier_str = getQualifierString(this_qualifier, false);
-
+
if(this_qualifier_str == null)
continue;
-
+
if(count != 0)
buffer.append(";");
buffer.append(this_qualifier_str);
@@ -910,11 +910,11 @@ public class GFFStreamFeature extends SimpleDocumentFeature
return buffer.toString();
}
-
+
/**
* Get the translation qualifier string for polypeptide features.
*/
- private String getTranslation()
+ private String getTranslation()
{
if (! getKey().getKeyString().equals("polypeptide"))
return null;
@@ -922,15 +922,15 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
if(getUserData() == null)
new uk.ac.sanger.artemis.Feature(this);
- // the above line constructs the appropriate userData within this current GFFStreamFeature object,
- // which is required by the following GeneUtils.deriveResidues()
+ // the above line constructs the appropriate userData within this current GFFStreamFeature object,
+ // which is required by the following GeneUtils.deriveResidues()
String residues = GeneUtils.deriveResidues(this);
if (residues != null)
return "translation="+residues;
- }
+ }
return null;
}
-
+
/**
* Used to write out the GFF attributes.
* @param q the qualifier to represent as a <code>String</code>
@@ -947,24 +947,32 @@ public class GFFStreamFeature extends SimpleDocumentFeature
return null;
final StringVector values = q.getValues();
-
- /*
+
+ /* ignore qualifiers with just one empty value, will mess up GFF3 output */
+ if(values != null && values.size() == 1)
+ {
+ if (values.elementAt(0).replaceAll("\\s+","").equals(""))
+ return null;
+ }
+
+ /*
* GSV :
- * The Bio::FeatureIO perl module falls over if there are Uppercased
- * attribute names for tags which aren't part of the standard reserved
+ * The Bio::FeatureIO perl module falls over if there are Uppercased
+ * attribute names for tags which aren't part of the standard reserved
* set. So we lowercase these, since in the specification it says :
- *
+ *
* "All attributes that begin with an uppercase letter are reserved for
* later use. Attributes that begin with a lowercase letter can be used
* freely by applications."
* see http://www.sequenceontology.org/gff3.shtml
*/
String nameToBuffer = encode(name);
+
if (! reserved)
nameToBuffer = Character.toLowerCase(nameToBuffer.charAt(0)) + nameToBuffer.substring(1);
buffer.append(nameToBuffer);
-
- if(values != null)
+
+ if(values != null && values.size() > 0)
{
buffer.append('=');
for(int value_index = 0; value_index < values.size();
@@ -981,10 +989,10 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
else
this_value = encode(values.elementAt(value_index));
-
+
if(value_index>0)
buffer.append("%2C");
-
+
if(name.equals("Parent"))
buffer.append(this_value);
else
@@ -1009,6 +1017,8 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
}
}
+ if (buffer.toString().charAt(buffer.toString().length()-1) == '=')
+ System.out.println(buffer.toString() + " ----- values length was " + values.size() + ": '" + values.elementAt(0) + "'");
return buffer.toString();
}
@@ -1022,13 +1032,13 @@ public class GFFStreamFeature extends SimpleDocumentFeature
* If the attribute has no value then the Hashtable value will be a zero
* length vector.
**/
- private Hashtable<String, StringVector> parseAttributes(final String att_val_list)
+ private Hashtable<String, StringVector> parseAttributes(final String att_val_list)
{
final Hashtable<String, StringVector> attr = new Hashtable<String, StringVector>();
int ind_start = 0;
int ind_end;
- while( (ind_end = att_val_list.indexOf(";",ind_start)) > -1 ||
+ while( (ind_end = att_val_list.indexOf(";",ind_start)) > -1 ||
ind_start < att_val_list.length() )
{
if(ind_end < 0)
@@ -1038,7 +1048,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
ind_start = ind_end+1;
int index_of_first_space = this_token.indexOf(" ");
-
+
final String att_name;
StringVector att_values = new StringVector();
@@ -1050,28 +1060,28 @@ public class GFFStreamFeature extends SimpleDocumentFeature
att_name = this_token.substring(0, index_of_first_space);
att_values.add(this_token.substring(index_of_first_space+1).trim());
}
- else if(index_of_first_space == -1)
+ else if(index_of_first_space == -1)
att_name = this_token;
- else
+ else
{
att_name = this_token.substring(0, index_of_first_space);
String rest_of_token =
this_token.substring(index_of_first_space+1).trim();
- while(rest_of_token.length() > 0)
+ while(rest_of_token.length() > 0)
{
if(rest_of_token.startsWith("\""))
{
int quote_index = 0;
- do
+ do
{
quote_index++;
quote_index = rest_of_token.indexOf("\"", quote_index);
} while(quote_index > -1 &&
rest_of_token.charAt(quote_index - 1) == '\\');
- if(quote_index < 0)
+ if(quote_index < 0)
{
// no closing quote - panic
final Hashtable<String, StringVector> panic_attributes =
@@ -1086,17 +1096,17 @@ public class GFFStreamFeature extends SimpleDocumentFeature
final String next_bit = rest_of_token.substring(1, quote_index);
att_values.add(next_bit);
rest_of_token = rest_of_token.substring(quote_index + 1).trim();
- }
+ }
else
{
final int index_of_next_space = rest_of_token.indexOf(" ");
- if(index_of_next_space == -1)
+ if(index_of_next_space == -1)
{
att_values.add(rest_of_token);
rest_of_token = "";
- }
- else
+ }
+ else
{
final String next_bit =
rest_of_token.substring(0, index_of_next_space);
@@ -1114,7 +1124,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
if(att_name.equals("Dbxref") || att_name.equals("Alias")) // convert to multi-line
{
- StringTokenizer stok =
+ StringTokenizer stok =
new StringTokenizer((String)att_values.get(0), ",");
StringVector str_values = new StringVector();
while(stok.hasMoreTokens())
@@ -1122,14 +1132,14 @@ public class GFFStreamFeature extends SimpleDocumentFeature
att_values = str_values;
}
-
+
if(att_name.equals("timelastmodified"))
{
try
{
- this.timelastmodified =
+ this.timelastmodified =
new Timestamp( Long.parseLong((String)att_values.get(0)) );
- SimpleDateFormat date_format =
+ SimpleDateFormat date_format =
new SimpleDateFormat("dd.MM.yyyy hh:mm:ss z");
att_values.set(0,date_format.format(timelastmodified));
}
@@ -1139,9 +1149,9 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
}
- if(attr.get(att_name) != null)
+ if(attr.get(att_name) != null)
attr.get(att_name).add(att_values);
- else
+ else
attr.put(att_name, att_values);
}
@@ -1156,7 +1166,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
return timelastmodified;
}
-
+
/**
* Get the GFF_source value of a Dbxref qualifier.
* @param qualifier
@@ -1166,11 +1176,11 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
StringVector qualifier_strings =
StreamQualifier.toStringVector(null, qualifier);
-
+
for(int i=0; i<qualifier_strings.size(); i++)
{
String qualifier_string = (String)qualifier_strings.elementAt(i);
-
+
if(qualifier_string.indexOf("GFF_source:") >-1)
{
int index = qualifier_string.indexOf(":")+1;
@@ -1182,7 +1192,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
}
return null;
}
-
+
/**
* Set the feature time last modified timestamp.
* @param timelastmodified
@@ -1190,20 +1200,20 @@ public class GFFStreamFeature extends SimpleDocumentFeature
public void setLastModified(final Timestamp timelastmodified)
{
this.timelastmodified = timelastmodified;
-
+
// now update the qualifier value itself
QualifierVector qualifiers = getQualifiers();
Qualifier qualifier = qualifiers.getQualifierByName("timelastmodified");
- SimpleDateFormat date_format =
+ SimpleDateFormat date_format =
new SimpleDateFormat("dd.MM.yyyy hh:mm:ss z");
-
+
if(qualifier != null)
qualifier.removeValue((String)qualifier.getValues().get(0));
else
{
try
{
- qualifier = new Qualifier("timelastmodified",
+ qualifier = new Qualifier("timelastmodified",
date_format.format(timelastmodified));
setQualifier(qualifier);
return;
@@ -1213,15 +1223,15 @@ public class GFFStreamFeature extends SimpleDocumentFeature
catch(ReadOnlyException roe)
{}
}
-
+
qualifier.addValue(date_format.format(timelastmodified));
}
-
+
/**
* Returns true if and only if this Feature can't be changed or can't be
* removed from it's entry.
**/
- public boolean isReadOnly ()
+ public boolean isReadOnly ()
{
if(readOnlyFeature)
return true;
@@ -1232,7 +1242,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
this.readOnlyFeature = readOnlyFeature;
}
-
+
public ChadoCanonicalGene getChadoGene()
{
return chadoGene;
@@ -1242,7 +1252,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
this.chadoGene = chadoGene;
}
-
+
public boolean isVisible()
{
return visible;
@@ -1293,24 +1303,24 @@ public class GFFStreamFeature extends SimpleDocumentFeature
{
this.chadoLazyFeature = chadoLazyFeature;
}
-
+
protected static boolean isGTF(Feature feature)
{
if(!(feature instanceof GFFStreamFeature))
return false;
-
+
final String names[] = { "ID", "Name", "Alias", "Parent",
"Derives_from",
- "Target", "Gap", "Note",
+ "Target", "Gap", "Note",
"Dbxref", "Ontology_term" };
-
+
for(String name: names)
{
if(feature.getQualifiers().getQualifierByName(name) != null)
return false;
}
-
- if(feature.getQualifiers().getQualifierByName("gene_id") != null &&
+
+ if(feature.getQualifiers().getQualifierByName("gene_id") != null &&
feature.getQualifiers().getQualifierByName("transcript_id") != null)
{
if(feature.getEntry() != null)