# Tcl autoload index file, version 2.0
# This file was generated by the "auto_mkindex" command and then hand
# edited to remove unrequired items.
#
# Remember to set your auto_path variable correctly to use this file.
#
set auto_index(acd2tag::parse) [list source [file join $dir acd2tag.tcl]]

set auto_index(AlterRelationships) [list source [file join $dir alter_rel.tcl]]

set auto_index(DirectAssembly) [list source [file join $dir assemble_direct.tcl]]

set auto_index(AssemblySingle) [list source [file join $dir assemble_single.tcl]]
set auto_index(AssemblySinglePostLoad) [list source [file join $dir assemble_single.tcl]]

set auto_index(NormalShotgun) [list source [file join $dir auto_assemble.tcl]]
set auto_index(Screen) [list source [file join $dir auto_assemble.tcl]]
set auto_index(OneContig) [list source [file join $dir auto_assemble.tcl]]
set auto_index(NewContig) [list source [file join $dir auto_assemble.tcl]]
set auto_index(SSAssemble) [list source [file join $dir auto_assemble.tcl]]
set auto_index(IgnorePrev) [list source [file join $dir auto_assemble.tcl]]
set auto_index(expand_hash_archives) [list source [file join $dir auto_assemble.tcl]]

set auto_index(BreakContig) [list source [file join $dir break_contig.tcl]]

set auto_index(CheckAssembly) [list source [file join $dir check_assembly.tcl]]

set auto_index(QualityClip) [list source [file join $dir clip.tcl]]
set auto_index(NClip) [list source [file join $dir clip.tcl]]
set auto_index(QClipEnds) [list source [file join $dir clip.tcl]]
set auto_index(DifferenceClip) [list source [file join $dir clip.tcl]]

set auto_index(ComplementContig) [list source [file join $dir complement.tcl]]
set auto_index(ContigRenameBulk) [list source [file join $dir complement.tcl]]

set auto_index(ConfigureCutoffs) [list source [file join $dir configure.tcl]]
set auto_index(SetMaxseq) [list source [file join $dir configure.tcl]]
set auto_index(ConfigureMenus) [list source [file join $dir configure.tcl]]
set auto_index(SetGeneticCode) [list source [file join $dir configure.tcl]]
set auto_index(SetAlignmentScores) [list source [file join $dir configure.tcl]]
set auto_index(SetRawData) [list source [file join $dir configure.tcl]]
set auto_index(FindRawDataNote) [list source [file join $dir configure.tcl]]
set auto_index(SetTemplateStatusConfig) [list source [file join $dir configure.tcl]]

set auto_index(NormalDialog) [list source [file join $dir consen.tcl]]
set auto_index(ExtendedDialog) [list source [file join $dir consen.tcl]]
set auto_index(UnfinishedDialog) [list source [file join $dir consen.tcl]]
set auto_index(QualityDialog) [list source [file join $dir consen.tcl]]
set auto_index(get_consensus) [list source [file join $dir consen.tcl]]

set auto_index(ConfidenceGraph) [list source [file join $dir confidence_graph.tcl]]
set auto_index(CreateConfidenceGraph) [list source [file join $dir confidence_graph.tcl]]
set auto_index(DeleteConfidenceGraph) [list source [file join $dir confidence_graph.tcl]]

set auto_index(PopUpSingleContigMenu) [list source [file join $dir consistency_display.tcl]]
set auto_index(CreateConsistencyDisplay) [list source [file join $dir consistency_display.tcl]]
set auto_index(AddConsistencyCrossHair) [list source [file join $dir consistency_display.tcl]]
set auto_index(consistency_zoom) [list source [file join $dir consistency_display.tcl]]
set auto_index(update_geom) [list source [file join $dir consistency_display.tcl]]

set auto_index(edit_contig) [list source [file join $dir contig_editor.tcl]]
set auto_index(join_contig) [list source [file join $dir contig_editor.tcl]]
set auto_index(create_editor) [list source [file join $dir contig_editor.tcl]]
set auto_index(EditContig) [list source [file join $dir contig_editor.tcl]]
set auto_index(JoinContig) [list source [file join $dir contig_editor.tcl]]
set auto_index(create_or_move_editor) [list source [file join $dir contig_editor.tcl]]
set auto_index(editor_olist_populate) [list source [file join $dir contig_editor.tcl]]

set auto_index(contig_id) [list source [file join $dir contig_id.tcl]]
set auto_index(contig_id_configure) [list source [file join $dir contig_id.tcl]]
set auto_index(contig_id_gel) [list source [file join $dir contig_id.tcl]]
set auto_index(contig_id_lreg) [list source [file join $dir contig_id.tcl]]
set auto_index(contig_id_rreg) [list source [file join $dir contig_id.tcl]]
set auto_index(contig_id_focus) [list source [file join $dir contig_id.tcl]]

set auto_index(init_contig_order_list) [list source [file join $dir contig_order.tcl]]
set auto_index(create_contig_order_list) [list source [file join $dir contig_order.tcl]]

set auto_index(popup_cs_contig_1) [list source [file join $dir contig_selector.tcl]]
set auto_index(popup_cs_contig_3) [list source [file join $dir contig_selector.tcl]]
set auto_index(popup_cs_contig_cnotes) [list source [file join $dir contig_selector.tcl]]
set auto_index(ContigSelector) [list source [file join $dir contig_selector.tcl]]
set auto_index(ContigComparator) [list source [file join $dir contig_selector.tcl]]
set auto_index(ContigInitReg) [list source [file join $dir contig_selector.tcl]]
set auto_index(ContigParams) [list source [file join $dir contig_selector.tcl]]
set auto_index(UpdateListContigs) [list source [file join $dir contig_selector.tcl]]

set auto_index(DisReadings) [list source [file join $dir dis_readings.tcl]]
set auto_index(DisContigs) [list source [file join $dir dis_readings.tcl]]
set auto_index(DisEditorReadingsDialog) [list source [file join $dir dis_readings.tcl]]
set auto_index(RemoveContigHoles) [list source [file join $dir dis_readings.tcl]]

set auto_index(DoubleStrand) [list source [file join $dir dstrand.tcl]]

set auto_index(create_search_win) [list source [file join $dir editor_search.tcl]]

set auto_index(EnterTags) [list source [file join $dir enter_tags.tcl]]
set auto_index(reformat_tag_file) [list source [file join $dir enter_tags.tcl]]

set auto_index(ExtractReadingsDialog) [list source [file join $dir extract.tcl]]

set auto_index(FIJDialog) [list source [file join $dir fij.tcl]]
set auto_index(HiddenParametersDialogInit) [list source [file join $dir fij.tcl]]

set auto_index(FindOligos) [list source [file join $dir find_oligo.tcl]]

set auto_index(FindRepeatsDialog) [list source [file join $dir find_repeats.tcl]]

set auto_index(gap_zoom) [list source [file join $dir gap_canvas_box.tcl]]
set auto_index(canvas_cursor_move) [list source [file join $dir gap_canvas_box.tcl]]
set auto_index(canvas_cursor_editor) [list source [file join $dir gap_canvas_box.tcl]]
set auto_index(gc_scroll_x) [list source [file join $dir gap_canvas_box.tcl]]
set auto_index(gc_scroll_y) [list source [file join $dir gap_canvas_box.tcl]]

set auto_index(GapRestrictionEnzymeDialogue) [list source [file join $dir gap_restriction_enzymes.tcl]]
set auto_index(next_template_renz_display) [list source [file join $dir gap_restriction_enzymes.tcl]]
set auto_index(unset_next_template_renz_display) [list source [file join $dir gap_restriction_enzymes.tcl]]
set auto_index(TemplateREnzPlot) [list source [file join $dir gap_restriction_enzymes.tcl]]
set auto_index(TemplateREnzDisplay) [list source [file join $dir gap_restriction_enzymes.tcl]]

set auto_index(InitListContigs) [list source [file join $dir list_contigs.tcl]]
set auto_index(ListContigsScaffoldSort) [list source [file join $dir list_contigs.tcl]]
set auto_index(ListContigsScaffoldFormat) [list source [file join $dir list_contigs.tcl]]

set auto_index(ListGet) [list source [file join $dir list_proc.tcl]]
set auto_index(ListType) [list source [file join $dir list_proc.tcl]]
set auto_index(ListLoad) [list source [file join $dir list_proc.tcl]]
set auto_index(ListSave) [list source [file join $dir list_proc.tcl]]
set auto_index(ListCreate) [list source [file join $dir list_proc.tcl]]
set auto_index(ListCreate2) [list source [file join $dir list_proc.tcl]]
set auto_index(ListAppend) [list source [file join $dir list_proc.tcl]]
set auto_index(ListDelete) [list source [file join $dir list_proc.tcl]]
set auto_index(ListClear) [list source [file join $dir list_proc.tcl]]
set auto_index(ListCopy) [list source [file join $dir list_proc.tcl]]
set auto_index(ListExists2) [list source [file join $dir list_proc.tcl]]
set auto_index(ListExists) [list source [file join $dir list_proc.tcl]]
set auto_index(ListWritable) [list source [file join $dir list_proc.tcl]]
set auto_index(ListEdit) [list source [file join $dir list_proc.tcl]]
set auto_index(ListToItems) [list source [file join $dir list_proc.tcl]]
set auto_index(StringToList) [list source [file join $dir list_proc.tcl]]
set auto_index(ListBrowse) [list source [file join $dir list_proc.tcl]]
set auto_index(LoadListDialog) [list source [file join $dir list_proc.tcl]]
set auto_index(SaveListDialog) [list source [file join $dir list_proc.tcl]]
set auto_index(DeleteListDialog) [list source [file join $dir list_proc.tcl]]
set auto_index(ListListsDialog) [list source [file join $dir list_proc.tcl]]
set auto_index(EditListDialog) [list source [file join $dir list_proc.tcl]]
set auto_index(PrintListDialog) [list source [file join $dir list_proc.tcl]]
set auto_index(CreateListDialog) [list source [file join $dir list_proc.tcl]]
set auto_index(CopyListDialog) [list source [file join $dir list_proc.tcl]]
set auto_index(NameToNum) [list source [file join $dir list_proc.tcl]]
set auto_index(InitLists) [list source [file join $dir list_proc.tcl]]
set auto_index(CreateAllContigList) [list source [file join $dir list_proc.tcl]]
set auto_index(CreateAllContigListNumbers) [list source [file join $dir list_proc.tcl]]
set auto_index(CreateAllContigList=Numbers) [list source [file join $dir list_proc.tcl]]
set auto_index(MinimalCoverage) [list source [file join $dir list_proc.tcl]]
set auto_index(UnattachedReadings) [list source [file join $dir list_proc.tcl]]
set auto_index(CheckOutList) [list source [file join $dir list_proc.tcl]]
set auto_index(UpdateReadingList) [list source [file join $dir list_proc.tcl]]
set auto_index(UpdateReadingDisplays) [list source [file join $dir list_proc.tcl]]
set auto_index(UpdateReadingDisplays_enable) [list source [file join $dir list_proc.tcl]]
set auto_index(UpdateReadingDisplays_disable) [list source [file join $dir list_proc.tcl]]
set auto_index(GetReadingList) [list source [file join $dir list_proc.tcl]]
set auto_index(InitListTrace) [list source [file join $dir list_proc.tcl]]

set auto_index(message_box) [list source [file join $dir message_box.tcl]]

set auto_index(NewFile) [list source [file join $dir ng_fb_cmds.tcl]]
set auto_index(NewFileBrowser_invoke) [list source [file join $dir ng_fb_cmds.tcl]]
set auto_index(New_Open_Database) [list source [file join $dir ng_fb_cmds.tcl]]
set auto_index(DB_Load) [list source [file join $dir ng_fb_cmds.tcl]]
set auto_index(PostLoadSetup) [list source [file join $dir ng_fb_cmds.tcl]]
set auto_index(InitOpenAnotherDB) [list source [file join $dir ng_fb_cmds.tcl]]
set auto_index(viewer_mode) [list source [file join $dir ng_fb_cmds.tcl]]

set auto_index(NoteSelector) [list source [file join $dir notes.tcl]]

set auto_index(get_primer_defs) [list source [file join $dir oligo_param.tcl]] 
set auto_index(select_oligos) [list source [file join $dir oligo_param.tcl]]
set auto_index(select_oligo_params) [list source [file join $dir oligo_param.tcl]]
set auto_index(SuggestPrimers) [list source [file join $dir oligo_param.tcl]]

set auto_index(Preassemble) [list source [file join $dir preass.tcl]]

set auto_index(SuggestProbes) [list source [file join $dir probe.tcl]]

set auto_index(next_template_quality_display) [list source [file join $dir quality_plot.tcl]]
set auto_index(unset_next_template_quality_display) [list source [file join $dir quality_plot.tcl]]
set auto_index(QualityPlotDisplay) [list source [file join $dir quality_plot.tcl]]
set auto_index(TemplateQualityPlot) [list source [file join $dir quality_plot.tcl]]

set auto_index(LongGelsDialog) [list source [file join $dir reactions.tcl]]
set auto_index(TaqTerminatorDialog) [list source [file join $dir reactions.tcl]]

set auto_index(ReadingCoverage) [list source [file join $dir reading_coverage.tcl]]
set auto_index(ConsistencyReadingCoverage) [list source [file join $dir reading_coverage.tcl]]

set auto_index(ReadPairDialog) [list source [file join $dir readpair.tcl]]

set auto_index(ReadPairCoverage) [list source [file join $dir readpair_coverage.tcl]]
set auto_index(CreateReadPairCoverage) [list source [file join $dir readpair_coverage.tcl]]

set auto_index(gap4_text_init) [list source [file join $dir search.tcl]]
set auto_index(searchSeqDialog) [list source [file join $dir search.tcl]]
set auto_index(searchTemplateDialog) [list source [file join $dir search.tcl]]
set auto_index(searchAnnoDialog) [list source [file join $dir search.tcl]]

set auto_index(CheckGelName) [list source [file join $dir select_contig.tcl]]
set auto_index(CheckDBFilename) [list source [file join $dir select_contig.tcl]]
set auto_index(CheckEntry) [list source [file join $dir select_contig.tcl]]
set auto_index(UpdateContigLimits) [list source [file join $dir select_contig.tcl]]

set auto_index(ShowRelationshipsDialog) [list source [file join $dir show_relationships.tcl]]

set auto_index(ShufflePads) [list source [file join $dir shuffle_pads.tcl]]
set auto_index(RemovePadColumns) [list source [file join $dir shuffle_pads.tcl]]

set auto_index(StopCodonDisplay) [list source [file join $dir stop_codon.tcl]]
set auto_index(CodonReplot) [list source [file join $dir stop_codon.tcl]]

set auto_index(StrandCoverage) [list source [file join $dir strand_coverage.tcl]]
set auto_index(ConsistencyStrandCoverage) [list source [file join $dir strand_coverage.tcl]]

set auto_index(create_tag_editor) [list source [file join $dir tag_editor.tcl]]
set auto_index(tag_editor_select_type) [list source [file join $dir tag_editor.tcl]]
set auto_index(tag_macro_create) [list source [file join $dir tag_editor.tcl]]
set auto_index(tag_macro_callback) [list source [file join $dir tag_editor.tcl]]
set auto_index(tag_macro_invoke) [list source [file join $dir tag_editor.tcl]]
set auto_index(tag_macro_load) [list source [file join $dir tag_editor.tcl]]
set auto_index(tag_macro_save) [list source [file join $dir tag_editor.tcl]]
set auto_index(on_screen) [list source [file join $dir tag_editor.tcl]]

set auto_index(tag_checklist) [list source [file join $dir tag_checklist.tcl]]
set auto_index(TagDialog) [list source [file join $dir tag_checklist.tcl]]
set auto_index(SetDefaultTags) [list source [file join $dir tag_checklist.tcl]]
set auto_index(GetDefaultTags) [list source [file join $dir tag_checklist.tcl]]
set auto_index(tag_checklist) [list source [file join $dir tag_checklist.tcl]]
set auto_index(tag_checklist_list) [list source [file join $dir tag_checklist.tcl]]
set auto_index(tag_checklist_tidy) [list source [file join $dir tag_checklist.tcl]]
set auto_index(InitTagVar) [list source [file join $dir tag_checklist.tcl]]
set auto_index(InitTagArray) [list source [file join $dir tag_checklist.tcl]]

set auto_index(::pcr_primers::GUI) [list source [file join $dir pcr_primers.tcl]]

set auto_index(trace_add) [list source [file join $dir trace_display.tcl]]
set auto_index(trace_create) [list source [file join $dir trace_display.tcl]]
set auto_index(trace_diff_specific) [list source [file join $dir trace_display.tcl]]
set auto_index(trace_display_diff) [list source [file join $dir trace_display.tcl]]
set auto_index(trace_small_add) [list source [file join $dir trace_display.tcl]]

set auto_index(c_length) [list source [file join $dir gap_utils.tcl]]
set auto_index(r_length) [list source [file join $dir gap_utils.tcl]]
set auto_index(r_name) [list source [file join $dir gap_utils.tcl]]
set auto_index(left_gel) [list source [file join $dir gap_utils.tcl]]
set auto_index(InitContigGlobals) [list source [file join $dir gap_utils.tcl]]
set auto_index(SetContigGlobals) [list source [file join $dir gap_utils.tcl]]
set auto_index(complement_tag_list) [list source [file join $dir gap_utils.tcl]]
set auto_index(contig_rename) [list source [file join $dir gap_utils.tcl]]
set auto_index(contig_add_to_scaffold) [list source [file join $dir gap_utils.tcl]]

set auto_index(ListResults) [list source [file join $dir result_manager.tcl]]
set auto_index(result_list_update) [list source [file join $dir result_manager.tcl]]
set auto_index(consistency_result_list_update) [list source [file join $dir result_manager.tcl]]
set auto_index(result_list_popup_single) [list source [file join $dir result_manager.tcl]]

set auto_index(SendTo) [list source [file join $dir sendto.tcl]]
set auto_index(EventHandler) [list source [file join $dir sendto.tcl]]

set auto_index(ListConfidence) [list source [file join $dir qual.tcl]]
set auto_index(ListBaseConfidence) [list source [file join $dir qual.tcl]]

set auto_index(prefinish) [list source [file join $dir gap_prefinish.tcl]] 

set auto_index(ViewNavigationData) [list source [file join $dir gap_nav.tcl]] 

set auto_index(check_database) [list source [file join $dir gap4_compat.tcl]]
set auto_index(io_read_contig) [list source [file join $dir gap4_compat.tcl]]
set auto_index(cname2crec) [list source [file join $dir gap4_compat.tcl]]

set auto_index(jog) [list source [file join $dir jog.tcl]]

set auto_index(ReadingCoverage) [list source [file join $dir depth.tcl]]
set auto_index(TemplateDisplay) [list source [file join $dir depth.tcl]]
set auto_index(CreateTemplateDisplay) [list source [file join $dir depth.tcl]]
set auto_index(nice_num) [list source [file join $dir depth.tcl]]

set auto_index(ListResults) [list source [file join $dir result_manager.tcl]]
set auto_index(result_list_update) [list source [file join $dir result_manager.tcl]]
set auto_index(consistency_result_list_update) [list source [file join $dir result_manager.tcl]]

set auto_index(ImportSequences) [list source [file join $dir import_contigs.tcl]]

set auto_index(ExportSequences) [list source [file join $dir export_contigs.tcl]]
set auto_index(ExportTags) [list source [file join $dir export_contigs.tcl]]

set auto_index(ListLibraries) [list source [file join $dir libraries.tcl]]
set auto_index(ListLibrariesPopulate) [list source [file join $dir libraries.tcl]]

set auto_index(MapReads_bwa_aln) [list source [file join $dir map_reads.tcl]]
set auto_index(MapReads_bwa_bwasw) [list source [file join $dir map_reads.tcl]]
set auto_index(generate_fastq) [list source [file join $dir map_reads.tcl]]

set auto_index(ImportGFF) [list source [file join $dir import_gff.tcl]]

set auto_index(ImportAGP) [list source [file join $dir scaffold.tcl]]
set auto_index(ExportAGP) [list source [file join $dir scaffold.tcl]]

set auto_index(CheckDatabase) [list source [file join $dir check_database.tcl]]

set auto_index(CheckAssembly) [list source [file join $dir check_assembly.tcl]]

set auto_index(ContigExtend) [list source [file join $dir contig_extend.tcl]]

set auto_index(set_global_defaults) [list source [file join $dir gap_globals.tcl]]
set auto_index(set_database_defaults) [list source [file join $dir gap_globals.tcl]]
