Module:ImportProtein/doc - Revision history

Warudo: Added the page to :Category:Module documentation pages

2024-08-29T21:50:20Z

Added the page to Category:Module documentation pages

← Previous revision		Revision as of 21:50, 29 August 2024
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	==Usage==		==Usage==
	This module requires a very large text input that would usually overwhelm a page if #invoked in it directly. The output is generally large masses of styled HTML that would overwhelm the page if substed. So it is usually best #invoked from a subpage. (Another option for compactness might be to use a screencap) The recommended policy in this area hasn't been queried yet.		This module requires a very large text input that would usually overwhelm a page if #invoked in it directly. The output is generally large masses of styled HTML that would overwhelm the page if substed. So it is usually best #invoked from a subpage. (Another option for compactness might be to use a screencap) The recommended policy in this area hasn't been queried yet.
			<noinclude>
			[[Category:Module documentation pages]]
			</noinclude>

KolbertBot: Bot: HTTP→HTTPS (v485)

2018-03-23T08:52:59Z

Bot: HTTP→HTTPS (v485)

← Previous revision		Revision as of 08:52, 23 March 2018
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	The parameters are:		The parameters are:

	*The ''file'' is an unnamed parameter. It should be a standard [[GenPept]] format file cut and pasted from a site like [https://www.ncbi.nlm.nih.gov/protein/P12931] or [~~http~~://www.uniprot.org/uniprot/P12931].		*The ''file'' is an unnamed parameter. It should be a standard [[GenPept]] format file cut and pasted from a site like [https://www.ncbi.nlm.nih.gov/protein/P12931] or [https://www.uniprot.org/uniprot/P12931].
	* ''tableoutput'' -- determines if/how the long table of protein features is displayed. ''collapsed'', the default value, begins by displaying the table in closed form. ''collapsible'' leaves it open at the beginning. ''no'' means no table output. Anything else leaves a non-collapsible table.		* ''tableoutput'' -- determines if/how the long table of protein features is displayed. ''collapsed'', the default value, begins by displaying the table in closed form. ''collapsible'' leaves it open at the beginning. ''no'' means no table output. Anything else leaves a non-collapsible table.
	* ''height'' (default 50) -- the height of the protein bar itself in pixels not counting any surrounding content		* ''height'' (default 50) -- the height of the protein bar itself in pixels not counting any surrounding content

Wnt: /* Usage */

2013-04-28T02:21:39Z

Usage

← Previous revision		Revision as of 02:21, 28 April 2013
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	==Usage==		==Usage==
	This module ~~can~~ ~~generate~~ large ~~masses~~ of ~~styled~~ ~~HTML~~ ~~that can~~ overwhelm a page, so it is ~~usually~~ ~~best~~ ~~left~~ to a ~~subpage.~~ ~~For~~ ~~some~~ ~~proteins~~ ~~for~~ ~~which~~ ~~only~~ a ~~few~~ ~~large~~ ~~regions~~ ~~(using~~ ~~''include'')~~ ~~are~~ ~~to be shown,~~ it ~~may~~ be ~~practical~~ to ~~subst:~~ ~~the~~ ~~template~~. Another option for compactness might be to use a screencap. The recommended policy in this area hasn't been queried yet.		This module requires a very large text input that would usually overwhelm a page if #invoked in it directly. The output is generally large masses of styled HTML that would overwhelm the page if substed. So it is usually best #invoked from a subpage. (Another option for compactness might be to use a screencap) The recommended policy in this area hasn't been queried yet.

Wnt at 14:34, 17 April 2013

2013-04-17T14:34:02Z

← Previous revision		Revision as of 14:34, 17 April 2013
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			{{Module rating\|alpha}}
	==Purpose==		==Purpose==

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	==Usage==		==Usage==
	This module can generate large masses of styled HTML that can overwhelm a page, so it is usually best left to a subpage. For some proteins for which only a few large regions (using ''include'') are to be shown, it may be practical to subst: the template. Another option for compactness might be to use a screencap. The recommended policy in this area hasn't been queried yet.		This module can generate large masses of styled HTML that can overwhelm a page, so it is usually best left to a subpage. For some proteins for which only a few large regions (using ''include'') are to be shown, it may be practical to subst: the template. Another option for compactness might be to use a screencap. The recommended policy in this area hasn't been queried yet.

	[[Category:Modules in alpha]]

Wnt: New ratings scheme - going ahead with my own to prime things

2013-04-16T23:03:04Z

New ratings scheme - going ahead with my own to prime things

← Previous revision		Revision as of 23:03, 16 April 2013
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	==Usage==		==Usage==
	This module can generate large masses of styled HTML that can overwhelm a page, so it is usually best left to a subpage. For some proteins for which only a few large regions (using ''include'') are to be shown, it may be practical to subst: the template. Another option for compactness might be to use a screencap. The recommended policy in this area hasn't been queried yet.		This module can generate large masses of styled HTML that can overwhelm a page, so it is usually best left to a subpage. For some proteins for which only a few large regions (using ''include'') are to be shown, it may be practical to subst: the template. Another option for compactness might be to use a screencap. The recommended policy in this area hasn't been queried yet.

			[[Category:Modules in alpha]]

Wnt: /* Purpose */

2013-03-19T18:20:16Z

Purpose

← Previous revision		Revision as of 18:20, 19 March 2013
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	==Purpose==		==Purpose==

	This module is meant to allow you to take a plaintext protein file and paste it in as a template parameter to get an annotated figure and legend. See [[Module talk:ImportProtein/Src (gene)]] for an example.		This module is meant to allow you to take a plaintext protein file and paste it in as a template parameter to get an annotated figure and legend. See [[Module talk:ImportProtein/Src (gene)]] for an example in trial use at [[Src (gene)]]

	Usually, the figure should be placed on a separate page and transcluded. Until people advise to the contrary, the space [[Module talk:ImportProtein/(Article name)]] is being used for this (note Wikipedia article space doesn't have subpages set AFAIK).		Usually, the figure should be placed on a separate page and transcluded. Until people advise to the contrary, the space [[Module talk:ImportProtein/(Article name)]] is being used for this (note Wikipedia article space doesn't have subpages set AFAIK).

Wnt: /* Parameters */

2013-03-19T18:19:34Z

Parameters

← Previous revision		Revision as of 18:19, 19 March 2013
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	Many parameters exist to try to make it easier to customize the output. Overlapping features marked vertically are randomly not displayed, so these features may be necessary to adequately describe all the known sites. Others improve the labels used.		Many parameters exist to try to make it easier to customize the output. Overlapping features marked vertically are randomly not displayed, so these features may be necessary to adequately describe all the known sites. Others improve the labels used.


	* ''usenotes'' -- a list of "region_name" or "site_type" names that aren't very informative. The entry under "notes" will be used as the feature name for all other operations.		* ''usenotes'' -- a list of "region_name" or "site_type" names that aren't very informative. The entry under "notes" will be used as the feature name for all other operations.
	* ''include'' -- defaults to ''all'', in which case labels to be excluded must be mentioned individually with ''exclude''. If another value is given, it should be a list of names in quotes - ''only'' those names will be shown in the figure or in the table.		* ''include'' -- defaults to ''all'', in which case labels to be excluded must be mentioned individually with ''exclude''. If another value is given, it should be a list of names in quotes - ''only'' those names will be shown in the figure or in the table.
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	* ''replaceregion'' -- a list of numeric ranges xx..yy followed by a colon and a quoted phrase. Use this when a lump of different features requires a single summary. So 77..85:"PS/PT/PY" can annotate a group of several phosphorylated amino acids with this short text. Note that placement of the text is at the center of the region you select; this feature therefore can be used to add extra markings if you like. Replaceregion does ''not'' affect the table of motifs.		* ''replaceregion'' -- a list of numeric ranges xx..yy followed by a colon and a quoted phrase. Use this when a lump of different features requires a single summary. So 77..85:"PS/PT/PY" can annotate a group of several phosphorylated amino acids with this short text. Note that placement of the text is at the center of the region you select; this feature therefore can be used to add extra markings if you like. Replaceregion does ''not'' affect the table of motifs.
	* ''toprow'' - a list of motifs (for example secondary structure - helices, sheets, and turns) that are to be displayed as colored markings at the top of the protein graphics box. No vertical annotation is given. A legend beneath the vertical annotation will list them by color.		* ''toprow'' - a list of motifs (for example secondary structure - helices, sheets, and turns) that are to be displayed as colored markings at the top of the protein graphics box. No vertical annotation is given. A legend beneath the vertical annotation will list them by color.

			It is also, of course, possible to edit the original protein sequence annotations directly to remedy any problems, though the module flexibility is provided in the hope that for many proteins an undamaged copy of the original can be kept for versatility

			==Usage==
			This module can generate large masses of styled HTML that can overwhelm a page, so it is usually best left to a subpage. For some proteins for which only a few large regions (using ''include'') are to be shown, it may be practical to subst: the template. Another option for compactness might be to use a screencap. The recommended policy in this area hasn't been queried yet.

Wnt: parameters

2013-03-19T18:14:38Z

parameters

New page

==Purpose==

This module is meant to allow you to take a plaintext protein file and paste it in as a template parameter to get an annotated figure and legend. See [[Module talk:ImportProtein/Src (gene)]] for an example.

Usually, the figure should be placed on a separate page and transcluded. Until people advise to the contrary, the space [[Module talk:ImportProtein/(Article name)]] is being used for this (note Wikipedia article space doesn't have subpages set AFAIK).

==Parameters==
The parameters are:

*The ''file'' is an unnamed parameter. It should be a standard [[GenPept]] format file cut and pasted from a site like [https://www.ncbi.nlm.nih.gov/protein/P12931] or [http://www.uniprot.org/uniprot/P12931].
* ''tableoutput'' -- determines if/how the long table of protein features is displayed. ''collapsed'', the default value, begins by displaying the table in closed form. ''collapsible'' leaves it open at the beginning. ''no'' means no table output. Anything else leaves a non-collapsible table.
* ''height'' (default 50) -- the height of the protein bar itself in pixels not counting any surrounding content
* ''width'' (default 500) -- the width of the protein bar and all other table and legend material in pixels
* ''background'' (default #333333) -- the color of the unadorned protein bar (such as in disordered N- and C-terminal regions)
* ''vtext'' (default 25) -- the number of characters of annotation written vertically beneath each site
* ''vwidth'' (default 4) -- determines how close the vertical labels can be to one another. Labels that don't fit are not shown, but the numeric position of the missing labels is mentioned further down. Typically the user should look them up in the table and use the parameters at the end to process them to be able to fit.
* ''largeonlyregion'' (default 20) -- the number of vertical pixels set aside only for the large domains that are labelled horizontally in bold within themselves.

Many parameters exist to try to make it easier to customize the output. Overlapping features marked vertically are randomly not displayed, so these features may be necessary to adequately describe all the known sites. Others improve the labels used.

* ''usenotes'' -- a list of "region_name" or "site_type" names that aren't very informative. The entry under "notes" will be used as the feature name for all other operations.
* ''include'' -- defaults to ''all'', in which case labels to be excluded must be mentioned individually with ''exclude''. If another value is given, it should be a list of names in quotes - ''only'' those names will be shown in the figure or in the table.
* ''exclude'' -- omit for default no effect. A list of features by name, in quotes, not to be mentioned. These are also omitted from the table.
* ''substitute'' -- a list of feature names and replacements, each in quotes, separated by a colon. "binding":"ATP binding site" will convert a feature labelled "binding" to display the second name instead. This affects all annotations. Note that substituting a name with "" will suppress the text, but not the marking on the protein diagram.
* ''replaceregion'' -- a list of numeric ranges xx..yy followed by a colon and a quoted phrase. Use this when a lump of different features requires a single summary. So 77..85:"PS/PT/PY" can annotate a group of several phosphorylated amino acids with this short text. Note that placement of the text is at the center of the region you select; this feature therefore can be used to add extra markings if you like. Replaceregion does ''not'' affect the table of motifs.
* ''toprow'' - a list of motifs (for example secondary structure - helices, sheets, and turns) that are to be displayed as colored markings at the top of the protein graphics box. No vertical annotation is given. A legend beneath the vertical annotation will list them by color.