X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fsearch.html;h=72e5bdf2d4aa05b440162721233cbf4ecd93da6f;hb=72cf0003490f887c3bc8fe0dfea8ac9d48c53eed;hp=2c1ed0f0b592beede2cb7807ec4c97d30920750d;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/help/html/features/search.html b/help/html/features/search.html index 2c1ed0f..72e5bdf 100755 --- a/help/html/features/search.html +++ b/help/html/features/search.html @@ -1,7 +1,7 @@ @@ -36,8 +36,8 @@ td {
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
+
+
"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 @@ -48,7 +48,10 @@ td { of posix and perl style regex - see below for a summary)
Creating Features from Search Results @@ -65,6 +71,19 @@ td { 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 @@ -73,7 +92,7 @@ td { 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 + "[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:
@@ -129,5 +148,26 @@ td {
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