Removing Redundancy

2.4
diff --git a/help/html/vamsas/index.html b/help/html/vamsas/index.html index 7cc841a..3bcdc9f 100644 --- a/help/html/vamsas/index.html +++ b/help/html/vamsas/index.html @@ -4,8 +4,9 @@

VAMSAS Interoperation

Please Note: VAMSAS is not fully operational in Jalview 2.4.0b2 - it is more reliable in later versions.

Jalview can interact with other applications using - "the VAMSAS Interoperaton framework" + "the VAMSAS Interoperation framework" which is an experimental model for interoperation between bioinformatics applications (Visualization and Analysis of Molecular diff --git a/help/html/webServices/dbreffetcher.html b/help/html/webServices/dbreffetcher.html index 98300aa..5cd44ac 100644 --- a/help/html/webServices/dbreffetcher.html +++ b/help/html/webServices/dbreffetcher.html @@ -14,7 +14,7 @@ retrieving sequence cross-references such as the protein products of a DNA sequence.

Jalview discovers references for a sequence by generating a set of ID queries from the ID string of each sequence in the alignment. It -then tries to query all the databases it can access in order to match +then tries to query a subset of all the databases it can access in order to match the alignment sequence to any records retrieved from the database. If a match is found, then the sequence is annotated with that database's reference, and any cross-references that it's records contain.

@@ -23,7 +23,7 @@ The method of accession id discovery is derived from the method which earlier Jalview versions used for Uniprot sequence feature retrieval, and was originally restricted to the identifaction of valid Uniprot accessions.
-Essentially, Jalview will try to retrieve records from all the databases +Essentially, Jalview will try to retrieve records from a subset of the databases accessible by the sequence fetcher using each sequence's ID string (or each string in the ID separated by the '∣' symbol).

diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html new file mode 100644 index 0000000..32111e4 --- /dev/null +++ b/help/html/webServices/urllinks.html @@ -0,0 +1,72 @@ + + +Opening URLs from Jalview + + +

Opening URLs from Jalview
+Both the applet and the desktop application are able to open URLs as +'popups' in your web browser.
+Double-clicking on the ID of a sequence will open the first URL that can +be generated from its sequence ID. This is often the SRS site, but you +can easily configure your own Configuring URL Links +
URL links are defined in the "Connections" tab of the Jalview desktop preferences, or +specified as applet +parameters.
+By default the item "SRS" is added to this link menu. This +link will show a web page in your default browser with the selected +sequence id as part of the URL.
+In the preferences dialog box, click new to add a new +link, and edit to modify an existing link, or delete +to remove it.
+You can name the link, this will be displayed on a new menu item under +the "Link" menu when you right click on a sequence id.
+The URL string must contain a token that can be replaced with a sequence +ID. The simplest token is "$SEQUENCE_ID$", which will be +replaced by the chosen sequence id when you click on it.

eg.
+UniRef100 = +http://www.ebi.uniprot.org/uniprot-srv/uniRefView.do?proteinAc=$SEQUENCE_ID$&library=uniref100
+Swissprot = http://www.expasy.org/uniprot/$SEQUENCE_ID$
+
+Links will also be made for any database cross references associated +with the sequence where the database name exactly matches a URL link +name. In this case, the $SEQUENCE_ID$ string will be replaced with the +accession string for the database cross-reference, rather than the +sequence ID for the sequence (since Jalview 2.4).

Regular Expression Substitution
+A url may contain a string of the form $SEQUENCE_ID=/regular +expression/=$. In this case, the regular expression will be applied to +the full sequence ID string and the resulting match will be inserted +into the URL. Groups of parentheses can be used to specify which regions +of the regular expression will be used to generate the URL: +

Each top level parenthesis will yield a URL containing the + text matched within that parenthesis.
Regions matching sub-parentheses within a top-level + parenthesis will be concatenated to form the text inserted into the URL + for the top-level parenthesis.

Please Note: +
+
The regular expressions supported by Jalview are those + provided by the Stevesoft javaregex + package.
+
Some characters must be escaped when specifying them as a + match within a regular expression.
+
+
+ Many Thanks to Bernd Brandt of the Free University of Amsterdam for + testing this new regular-expression expansion feature!

+
+
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