// Style for paramecium data, based on game.style
ImportStyle "game.style" 

GeneticCode "6"

// The name of the types file (a file--expected to be in the user's ~/.apollo directory
// or in the APOLLO_ROOT/conf directory)
Types		        "paramecium.tiers"

//HELP WHAT IS NEXT LINE?
NameAdapterInstall "apollo.config.ParameciumNameAdapter"

// Whether to enable the navigation manager, default false.
EnableNavigationManager "false"

// List of chromosomes for pulldown menu in navigation bar and load-by-location 
// data adapter. data adapter gets this from chado-adapter.xml config. navigation
// is not yet enabled. rice chado only chrom 1 at this point.
// Chromosomes             "1, 2, 3, 4"

// Whether to show the genes ID field in the annot info editor. default true.
ShowIdField  "false"

// Whether the transcript symbol should be editable in annotinfo. default true
TranscriptSymbolEditable "false"

// Whether to show the "Is Dicsitronic?" checkbox in annot info
ShowIsDicistronicAnnotInfoCheckbox "false"

// Whether to show the "Evauluation of Peptide" drop down list. This is more or less
// a flybase specific dropdown list, where a peptide analysis program was run and the
// curator could pick from the results (or something like that)       
// also whether to show associated menu item in annotation menu
//ShowEvaluationOfPeptideAnnotInfoList "false"
ShowEvaluationOfPeptide "false"

// Whether to display/use the isProblematic checkbox in annot info editor
ShowIsProblematicAnnotInfoCheckbox "true"

// Whether to display/use the "Finished?" checkbox in annot info
// transcript panel. Indicates work on that transcript is done I think.
ShowFinishedAnnotInfoCheckbox "true"

// Show table in annot info that displays database cross references
// for the annotation, that can potentially bring up web pages
ShowDBCrossRefAnnotInfoTable "true"

// Show "Replace stop codon with selenocysteine" checkbox in annot info
ShowReplaceStopAnnotInfoCheckbox "false"

// allow for translational frame shift editing in the exon detail editor
// which also get displayed in the annot info editor. default is "true"
EnableTranslationalFrameShiftEditing "true"

// Allow for sequence error editing in exon detail editor, which also displays in
// annot info editor. Default is "true".
EnableSequenceErrorEditing "true"

// Whether to show/use ownership menu item in annot menu for disowning
// & owning annots. default is true.
ShowOwnershipAnnotMenuItem "false"

// Whether to show/use annot menu item for setting transcript
// finished/unfinished - default is true
ShowTranscriptFinishedAnnotMenuItem "false"

// Display preferences LINDA
DisplayPreferences "apollo.config.ParameciumDisplayPrefs"


// This will add a menu item to the result popup menu that will bring
// the link up as the other species (in synteny of course)
// Presently this is specific to game synteny.
AddSyntenyResultMenuItem "true"

// Whether to show feature rectangles in 3D (default false).  Generally, programmers think
// the 3D effect is cool and biologists find it annoying.
Draw3D                  "true"


// Canned comments for use by annotators
AnnotationComment "Only one EST supports this alternative transcript"
AnnotationComment "EST data support existence of multiple transcripts"
AnnotationComment "Unconventional splice site postulated"
AnnotationComment "GC splice donor site postulated"
AnnotationComment "Gene prediction data only"
AnnotationComment "5' terminus extended to first start codon; no experimental data confirming this prediction"
AnnotationComment "3' terminus extended to first stop codon; no experimental data confirming this prediction"
AnnotationComment "EST data suggest additional 3' exon(s)"
AnnotationComment "EST data suggest additional 5' exon(s)"
AnnotationComment "Flag Cambridge: gene merge (internal view only)" 
AnnotationComment "Flag Cambridge: gene split (internal view only)"
AnnotationComment "Evidence indicates that 3' UTR overlaps 5' UTR of downstream gene; extends to coordinate AE00 :  (based upon 3' extent of  )"
AnnotationComment "Although this gene model is supported by multiple pieces of evidence, the computed ORF is questionable because it is much smaller than the predicted transcript"
AnnotationComment "tRNA type: putative tRNA-___ <fill aminoac.> implied by tRNAScan-SE analysis. (internal view only)"
AnnotationComment "Multiple ESTs homologous to non-coding strand of this gene"
AnnotationComment "DGC clone appears problematic:  incomplete CDS"
AnnotationComment "DGC clone appears problematic:  unspliced intron"
AnnotationComment "DGC clone appears problematic:  chimeric"
AnnotationComment "DGC clone appears problematic:  contains transposon sequences"
AnnotationComment "First Priority for Reannotation (internal view only)"
AnnotationComment "Transposon inserted in intron" 
AnnotationComment "Gene split based on BLASTX data"
AnnotationComment "Gene split based on EST data"
AnnotationComment "Gene merge based on BLASTX data; no experimental evidence for splice sites"
AnnotationComment "Gene merge based on EST data"
AnnotationComment "Flag Cambridge: new annotation == existing FB gene FBgn (internal view only)"
AnnotationComment "Flag Cambridge: discistronic gene (internal view only)"
AnnotationComment "Flag Cambridge: DGC clone not consistent with gene report (internal view only)"
AnnotationComment "Flag Cambridge: DGC clone not consistent with gene report (internal view only)"
AnnotationComment "EST data support existence of multiple transcripts due to variable use of mini-exons"
AnnotationComment "EST data support existence of multiple transcripts due to variable use of 5' exons"
AnnotationComment "EST data support existence of multiple transcripts due to variable use of poly-A sites"
AnnotationComment "5' exon not determined (no ATG translation start identified)"
AnnotationComment "Unconventional translation start"
AnnotationComment "Translation start as per FBrf"
AnnotationComment "EST data support dicistronic gene model"
AnnotationComment "May be component of a dicistronic gene; available data inconclusive"
AnnotationComment "Hand editing required (internal view only)"
AnnotationComment "Probable mutation in sequenced strain: premature stop"
AnnotationComment "Probable mutation in sequenced strain:  [other]"
AnnotationComment "Known mutation in sequenced strain"
AnnotationComment "EST <fill clone name> from opposite strand used to extend gene model"
AnnotationComment "Although multiple ESTs support this model, read-through of predicted intron results in shorter CDS"
AnnotationComment "Putative repetitive region: the region matches several EST and P insertions that map to various locations in the genome"
AnnotationComment "CDS edit:  sequencing error (internal view only)"
AnnotationComment "CDS edit:  possible [] stop codon suppression could cause production of [] residue protein (internal view only)"
AnnotationComment "CDS edit:  mutation in sequenced strain (internal view only)"
AnnotationComment "CDS edit:  [other]"
AnnotationComment "Short CDS OK (internal view only)"
AnnotationComment "Shares UTR: 5' UTR shared with downstream gene"
AnnotationComment "Shares UTR: 3' UTR shared with downstream gene"
AnnotationComment"Transposon overlap OK (internal view only)"


// Be sure that the last line of this file ends with a newline.