GenDBWiki/WebDocumentation/ContextMenus: Difference between revisions

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= The GenDB [[ContextMenu]] =
= The GenDB [[ContextMenu]] =


The context menu is located in the bottom right corner of the GenDB [[MainView]]. It displays buttons for all actions that can be performed on the selected region in the [[ContigView]].
The context menu is located in the bottom right corner of the GenDB [[MainView]]. It displays buttons for all actions that can be performed on the selected region in the [[GenDBWiki/WebDocumentation/MainViews/ContigView|Contig View]].


[[Image:GenDBWiki$$WebDocumentation$$ContextMenus$GenDBContextMenuContig.png]]
[[Image:GenDBWiki$$WebDocumentation$$ContextMenus$GenDBContextMenuContig_08082005.png]]


The screenshot above shows possible actions for a contig.
The screenshot above shows possible actions for a contig.
* '''Export CDS''': Exports all coding seqeunces in EMBL format
* '''Export fasta''': Exports the sequence of the contig in fasta format
* '''Create Region manually''': A [[GenDBWiki/WebDocumentation/DialogWindows/CreateRegionDialog|new dialog window]] lets you enter start, stop and region type for a new region.
* '''Create a new Mutation''': A [[GenDBWiki/WebDocumentation/DialogWindows/CreateMutationDialog|dialog window]] lets you create a new mutation.
* '''Show virtual 2D gel''': A virtual 2D gel pops up in a new window
* '''Set genetic code''': A [[GenDBWiki/WebDocumentation/DialogWindows/SetGeneticCode|dialog window]] lets you know what types of genetic codes are currently supported and lets you specify the genetic code for that contig.
* '''Set organism and strain''': A [[GenDBWiki/WebDocumentation/DialogWindows/SetOrganismAndStrain|dialog window]] lets you specify or edit settings like organism, strain and taxonomy ID for that contig.


[[Image:GenDBWiki$$WebDocumentation$$ContextMenus$GenDBContextMenu.png]]
[[Image:GenDBWiki$$WebDocumentation$$ContextMenus$GenDBContextMenu.png]]
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The screenshot above shows possible actions for a CDS region.
The screenshot above shows possible actions for a CDS region.


* '''Annotate region''': Displays the [[AnnotationDialog]] in a new browser window that lets you add, view and edit existing annotations  
* '''Annotate region''': Displays the [[GenDBWiki/WebDocumentation/DialogWindows/AnnotationDialog|Annotation Dialog]] in a new browser window that lets you add, view and edit existing annotations  
* '''Show observations''': Displays the [[ObservationDialog]] in a new browser window. This dialog enables you to sort and browse existing functionals observations (e.g. Blast vs NT) .
* '''Show observations''': Displays the [[GenDBWiki/WebDocumentation/DialogWindows/ObservationDialog|Observation Dialog]] in a new browser window. This dialog enables you to sort and browse existing functionals observations (e.g. Blast vs NT) .
* '''Add Alias''': Creates a new alias name for the selected region and adds it to the list of alternative names.
* '''Add Alias''': Creates a new alias name for the selected region and adds it to the list of alternative names.
* '''Show region report''': Pops up a new browserwindow that displays condensed information for the selected region.
* '''Show region report''': Pops up a new browser window that displays condensed information for the selected region.
* '''Edit region''': The [[RegionEditor]] dialog enables you to adjust the genestart for an existing CDS region.
* '''Edit region''': The [[GenDBWiki/WebDocumentation/DialogWindows/RegionEditor|Region Editor]] dialog enables you to adjust the gene start for an existing CDS region.
* '''Create region''': A new browser window lets you enter start, stop and regiontype for a new region. After the region is created a list of tools can be selected to produce observations.
* '''Create region''': The [[GenDBWiki/WebDocumentation/DialogWindows/CreateRegionDialog|CreateRegion]] dialog window lets you enter start, stop and region type for a new region. After the region is created a list of tools can be selected to produce observations.
* '''Show sequence''': Shows the six frame AA and nucleotide sequence for the selected region including 30 up- and downstream aminoacids.
* '''(Re)start tools''': A [[GenDBWiki/WebDocumentation/DialogWindows/CreateRegionDialog|new dialog window]] lets you restart existing jobs for this region. If new tools have been created jobs can be submitted for them as well.
* '''DNA sequence''': Displays the nucleotides for the selected region in a tabular way.
* '''Region status''': The [[GenDBWiki/WebDocumentation/DialogWindows/CreateRegionDialog|region status]] shows the current state of tools that have been submitted for this region.  
* '''AA sequence''': Displays the amino acids for the selected region in a tabular way.
* '''Show sequence''': Shows the [[GenDBWiki/WebDocumentation/DialogWindows/ShowSequenceDialog|six frame AA and nucleotide sequence dialog]] for the selected region including 30 up- and downstream amino acids.
* '''DNA sequence''': Displays the [[GenDBWiki/WebDocumentation/DialogWindows/DNASequenceDialog|Nucleotides dialog]] for the selected region in a tabular way.
* '''AA sequence''': Displays the [[GenDBWiki/WebDocumentation/DialogWindows/AASequenceDialog|AminoAcids dialog]] for the selected region in a tabular way.

Latest revision as of 07:15, 26 October 2011

The GenDB ContextMenu

The context menu is located in the bottom right corner of the GenDB MainView. It displays buttons for all actions that can be performed on the selected region in the Contig View.

File:GenDBWiki$$WebDocumentation$$ContextMenus$GenDBContextMenuContig 08082005.png

The screenshot above shows possible actions for a contig.

  • Export CDS: Exports all coding seqeunces in EMBL format
  • Export fasta: Exports the sequence of the contig in fasta format
  • Create Region manually: A new dialog window lets you enter start, stop and region type for a new region.
  • Create a new Mutation: A dialog window lets you create a new mutation.
  • Show virtual 2D gel: A virtual 2D gel pops up in a new window
  • Set genetic code: A dialog window lets you know what types of genetic codes are currently supported and lets you specify the genetic code for that contig.
  • Set organism and strain: A dialog window lets you specify or edit settings like organism, strain and taxonomy ID for that contig.

File:GenDBWiki$$WebDocumentation$$ContextMenus$GenDBContextMenu.png

The screenshot above shows possible actions for a CDS region.

  • Annotate region: Displays the Annotation Dialog in a new browser window that lets you add, view and edit existing annotations
  • Show observations: Displays the Observation Dialog in a new browser window. This dialog enables you to sort and browse existing functionals observations (e.g. Blast vs NT) .
  • Add Alias: Creates a new alias name for the selected region and adds it to the list of alternative names.
  • Show region report: Pops up a new browser window that displays condensed information for the selected region.
  • Edit region: The Region Editor dialog enables you to adjust the gene start for an existing CDS region.
  • Create region: The CreateRegion dialog window lets you enter start, stop and region type for a new region. After the region is created a list of tools can be selected to produce observations.
  • (Re)start tools: A new dialog window lets you restart existing jobs for this region. If new tools have been created jobs can be submitted for them as well.
  • Region status: The region status shows the current state of tools that have been submitted for this region.
  • Show sequence: Shows the six frame AA and nucleotide sequence dialog for the selected region including 30 up- and downstream amino acids.
  • DNA sequence: Displays the Nucleotides dialog for the selected region in a tabular way.
  • AA sequence: Displays the AminoAcids dialog for the selected region in a tabular way.
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