Filter Columns by Annotation

From dee7812a050818dc8cd626edca3422e71f39403e Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Wed, 15 Jul 2015 14:26:26 +0100 Subject: [PATCH] JAL-1553 reviewed & updated docs --- .../calculations/columnFilterByAnnotation.html | 31 ++++++++++---------- 1 file changed, 15 insertions(+), 16 deletions(-) diff --git a/help/html/calculations/columnFilterByAnnotation.html b/help/html/calculations/columnFilterByAnnotation.html index c5f42df..a69e234 100644 --- a/help/html/calculations/columnFilterByAnnotation.html +++ b/help/html/calculations/columnFilterByAnnotation.html @@ -20,21 +20,21 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. --> -Filter Columns by Annotation +Select/Hide Columns by Annotation

- Filter Columns by Annotation + Select/Hide Columns by Annotation

Jalview allows the columns of an alignment to be filtered using +

From Jalview-2.9 columns of an alignment can be filtered using any annotation rows added to that alignment.

- From "Select" menu - → "Select by Annotation..." to bring - up the Select by Annotation window. The filter options vary depending + To carry out this operation, navigate to "Select" menu + → "Select/Hide Columns by Annotation..." to bring + up the Select/Hide by Annotation window. The filter options vary depending on the type of annotation selected. If an annotation that has a numeric values is selected, the threshold filter option is activated as seen in the - figure on the right below. + figure on the right below, otherwise the dialog will exclude the threshold filter option as seen in the figure on the left.

@@ -47,15 +47,14 @@

Select which annotation to base the filtering on using the - top-most selection box.
The target annotation row can be selected using the drop-down option menu in the top-most part of the window.
Search Filter
- When a text is entered in the textfield on the search - filter section, the "Display Label" and "Description" - checkboxes becomes selectable.
- On selecting any of the checkboxes, a regular expresion +
- When a text is entered in the text box within the Search + Filter section, the "Display Label" and "Description" + options becomes enabled for selection.
- On selecting any of the options, a regular expression search (RegEx) is executed on the specified field of the current annotation row selected, and the matching columns will be highlighted in the alignment.
- Structure Filter
  - Alignment columns can also be filtered by the type of - secondary structure present in a choosen annotation row.
  - This can be achieved by ticking the type of structure you wish to filter by under the structures filter section.
  @@ -71,7 +70,7 @@
  - This filter is only activated for annotation which contain numeric values
  - Select whether to Filter the alignment above or below an +
  - Select whether to filter the alignment above or below an adjustable threshold with the selection box within the threshold filter section.
  - Change the threshold value with the slider, or enter the @@ -87,7 +86,7 @@
  - While the "Hide" option enables the matching columns to be hidden automatically during the filtering process.
  - The "Ok" button applies the filter when clicked.
  - And finally, The "Cancel" button restores the alignment to its previous state before the filtering when clicked. +
  - And finally, the "Cancel" button restores the alignment to its previous state before any filtering was applied.
-- 1.7.10.2