X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fsearch.html;h=72e5bdf2d4aa05b440162721233cbf4ecd93da6f;hb=b1e2aea95b3839a1a53f809c579666075cd3d348;hp=531816259b6893f4f055638dda18a8e152d4c665;hpb=1693646e78fb0dddebcd94f8bef7e2acd3bdaae0;p=jalview.git diff --git a/help/html/features/search.html b/help/html/features/search.html index 5318162..72e5bdf 100755 --- a/help/html/features/search.html +++ b/help/html/features/search.html @@ -1,71 +1,173 @@ - -
- - - - -Search
-The search box can be displayed by pressing the keys Control and F or selecting - "Search"
-Note: -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.
--
. | -Any single character. | -
[] | -Any one of the characters in the brackets | -
^ | -The start of a line (column 1). | -
$ | -The end of a line | -
* | -Matches zero or more of the preceding characters or expressions. | -
? | -Matches zero or one of the preceding characters or expressions. | -
+ | -Matches one or more of the preceding characters or expressions. | -
{count} | -Matches the specified number of the preceding characters or expressions. - | -
{min,} | -Matches at least the specified number of the preceding characters or - expressions. | -
{min,max} | -Matches between min and max of the preceding characters or expressions. | -
+ Search +
+The search box is displayed by pressing Control and F or + selecting "Find..." from the "Search" menu.
+ +"Find next" will find the next occurrence 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. +
+ 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.
++
+ Selecting regions from Search Results +
++ Press 'B' or use the Select Highlighted Columns option from + the alignment window's select menu to add columns containing + highlighted search results to the alignment window's column + selection. Alt-'B' will add all but the highlighted columns, and + Ctrl (or Cmd) -B will toggle the column selection for the + highlighted region. +
++ + 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 + "[GVATC]{;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 | +
. | +Matches any single character | +
[] | +Matches any one of the characters in the brackets | +
^ | +Matches at the start of an ID or sequence | +
$ | +Matches at the end of an ID or sequence | +
* | +Matches if the preceding element matches zero or more + times | +
? | +Matches if the preceding element matched once or not at + all | +
+ | +Matches if the preceding element matched at least once | +
{count} | +Matches if the preceding element matches a specified + number of times | +
{min,} | +Matches of the preceding element matched at least the + specified number of times | +
{min,max} | +Matches if the preceding element matches min or at most + max number of times | +
A record of all the recent queries made via the Find dialog are + stored along with your Jalview user preferences. To open the search + history, click on the button to the right of the query field, or + press the down arrow key.
+ +The search history keeps up to 99 queries by default. To clear + the history, or modify the size of the history, right-click the text + box.
+ ++ Other dialogs that provide a query history +
++ Jalview's Uniprot and PDB free text database search + dialogs also provide a query history. +
+ The query histories were introduced in Jalview 2.10.2 + +