X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fsearch.html;h=3d608589608b4de33dde3838a6171c50ab5cfbb0;hb=442b6bc246ee877d5e977baf80fd96299e0e05c4;hp=ca63dc7ca837aaafcb48b328d4c1d1a0028b18aa;hpb=3396e9f33cf3a16a7f38f5163cd057df4b859e7e;p=jalview.git diff --git a/help/html/features/search.html b/help/html/features/search.html index ca63dc7..3d60858 100755 --- a/help/html/features/search.html +++ b/help/html/features/search.html @@ -11,60 +11,89 @@ td {

Search

The search box can be displayed by pressing the keys Control and F or selecting - "Search"

-Note: +

The search box is displayed by pressing Control and F or + selecting "Find..." from the "Search" menu.

"Find next" will find the next occurence of the specified and adjust + the alignment window view to show it, and "Find all" highlights all + matches for a pattern. The "New Feature" is a quick way to highlight + and group residues matching the specified search pattern throughout the alignment.

The search will be performed on the selected region. If no region is selected, - the search will operate on the full alignment.
To clear any selection, press the "Escape" key.
The search uses regular expressions. (understands a mixture of posix and + perl style regex - see below for a summary)
Gaps are ignored when matching the query to the sequences in the alignment.
The search is applied to both sequences and their IDs but the "Find + next" and "Find all" buttons only count the sequence matches.
If a region is selected, then search will only be performed + on that region.
To quickly clear the current selection, press the "Escape" key.
Tick the "Match Case" box to perform a case sensitive search.

Using the "Create new group" is a quick way to group and highlight - residues with the specified search pattern throughout the alignment.

The search allows regular expression matching.

Creating Features from Search Results

+ If "New Feature" is selected, the feature can be given a name from + a popup input box. Use the "Feature Settings" under the "View" + menu to change the visibility and colour of the new sequence feature.

A quick Regular Expression Guide

A regular expression is not just a simple text query - although it +can be used like one, the query is not parsed literally, but +interpreted like a series of instructions defining the features of the +match. For example, a simple query like "ACDED" would +match all occurences of that string, but "ACD+ED" matches +both 'ACDDED' and 'ACDDDDDDDDED'. More usefully, the query +"[ILGVMA]{;5,}" would find stretches of small, +hydrophobic amino acids of at least five residues in length. +

The table +below describes some of the regular expression syntax:

+ + + + - + - + - + - + - + - + - + - - + - +

Regular Expression Element	Effect
.	Any single character.	Matches any single character
[]	Any one of the characters in the brackets	Matches any one of the characters in the brackets
^	The start of a line (column 1).	Matches at the start of an ID or sequence
$	The end of a line	Matches at the end of an ID or sequence
*	Matches zero or more of the preceding characters or expressions.	Matches if the preceding element matches zero or more times
?	Matches zero or one of the preceding characters or expressions.	Matches if the preceding element matched once or not at all
+	Matches one or more of the preceding characters or expressions.	Matches if the preceding element matched at least once
{count}	Matches the specified number of the preceding characters or expressions. +	Matches if the preceding element matches a specified number of + times
{min,}	Matches at least the specified number of the preceding characters or - expressions.	Matches of the preceding element matched at least the + specified number of times
{min,max}	Matches between min and max of the preceding characters or expressions.	Matches if the preceding element matches min or at most max + number of times