This details how the various filters in Gatherer work, their impact on the interface and some of the controls not strictly part of filters that affect the display of items.
Global Filters (Minimap, World Map):
Location: command line, quick menu, filter dropdowns (Filter tab in configuration dialog and world map)
Effect: Hide mininote or world map notes (recording still works).
Side effect: World Map global filter also control display of the Show/Hide button and filters dropdown on the World Map screen.
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Basic Filters (Herbs, Ore, Treasure):
Location: command line, quick menu, filter dropdowns (Filter tab in configuration dialog and world map)
Effect: Controls display on minimap and world map of the 3 basic gather types. The "auto" setting will check if the character has the required gathering skill (always true for treasure type) to decide if the gather type should be displayed or not.
Side effect: While checking what gather skills the character has the skill tree is completely expanded, this happens every few seconds. Hidden items on the minimap are not considered for display, and thus do not count toward the maximum displayable number of mininotes.
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Elaborate filters (filter dropdown menus):
Location: Filter tab in configuration dialog and World Map
Effect: This works by gather types (one dropdown menu for each) and once something is checked in the list restrict the display both on minimap and world map to the items checked in the list (for that list's gather type only).
Side effect: No item checked is the same as having all items checked for a given gather type. Hidden items on the minimap are not considered for display, and thus do not count toward the maximum displayable number of mininotes.
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Minimum skill filters:
Location: Filter tab in configuration dialog, min skill editboxes above filter dropdowns.
Effect: Setting a minimum for one of the 2 gather skills will restrict display to item that have an equal or higher minimum required skill for gatherering (this doesn't take character skill level into account) on both minimap and world map.
Side effect: hidden items on the minimap are not considered for display, and thus do not count toward the maximum displayable number of mininotes.
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Rare Ore:
Location: Globals tab in configuration dialog
Effect: Extend item display to parent type if specific filters are set.
For example, if "Tin" is specified in the Ore filter dropdown menu and Silver is not, without the Rare Ore option only Tin nodes will display. with the Rare Ore option checked both Tin and Silver will display.
This works slightly differently for herbs, in that case the Rare Ore option is used to display secondary items that can be gathered in a main node. For example, having swiftthistle selected will result in displaying both Mage Royal and Briarthorn.
Side effect: If both type have been gathered in a given node ( for example, Tin and Silver from the same node) both will then be displayed, the visible one will depend on internal display order.
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Theme:
Location: Globals tab in configuration dialog
Effect: Change the icons displayed for nodes on the minimap according the the selected theme. Original: small hollowed circle with a basic color corresponding to gather type. Iconic: display the icon corresponding to the item in inventory. Shaded (default): A mix of both, above a minimum distance iconic will display, under it hollowed colored circle are displayed (slightly larger than in the Original theme).
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Minimap distance control: There are multiple controls involved, each is described separately below.
Location: Globals tab in configuration dialog
Maximum number of mininotes: Affect the number of notes that will be considered in the minimap.
Maximum distance: The maximum distance (in Gatherer units, the one shown in the mininote tooltip) at which a node can be considered for inclusion in the closest maximum number of displayable mininotes list.
A setting of 0 means infinite (including other zones and continents).
Minimum icon distance and Hide under minimum icon distance: The minimum icon distance determine the distance (in pixels) under which the icons is changed to a hollowed circle (in shaded theme mode). If the "Hide under min distance option" is checked then the hollowed circles will not be displayed at all.
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Link Record:
Location: Filter tab in configuration dialog
Effect: This restrict actual recording of items to the ones checked in the filters dropdown menus. In other words, if it's not checked it won't be recorded into the database.