Search
-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. -
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 | -
| . | -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 | -
+ 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