From 244a1460b0d7ae9a7a8c57d3a767b327788e8bd3 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 12 Aug 2008 14:19:03 +0000 Subject: [PATCH] URL help update --- help/html/features/preferences.html | 21 ++++++++++++++++++++- help/html/menus/popupMenu.html | 5 ++++- help/html/releases.html | 2 ++ help/html/whatsNew.html | 4 +++- 4 files changed, 29 insertions(+), 3 deletions(-) diff --git a/help/html/features/preferences.html b/help/html/features/preferences.html index 08e210e..c173212 100755 --- a/help/html/features/preferences.html +++ b/help/html/features/preferences.html @@ -71,7 +71,26 @@ vbersion of the font to sequence labels.

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/$SEQUENCE_ID$

+ 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 parentheseses can be used to specify which regions of the regular expression will be used to generate the URL: + +

Default Browser (Unix)
Its difficult in Java to detect the default web browser for Unix users. If Jalview can't find your default web browser, enter the name or full path to your web diff --git a/help/html/menus/popupMenu.html b/help/html/menus/popupMenu.html index 9393570..a836c9f 100755 --- a/help/html/menus/popupMenu.html +++ b/help/html/menus/popupMenu.html @@ -86,7 +86,10 @@ not be accessible when in 'Cursor Mode' (toggled with the F2 key).

sequence will be propagated to the hidden sequences.
  • Link
    This menu item lists all links which have been set up in the Preferences - Connections tab.
    + Connections tab.
    + Since Jalview 2.4, links will also be made for database cross + references (where the database name exactly matches the link name set up in Preferences). +
    • diff --git a/help/html/releases.html b/help/html/releases.html index c9265f0..2f340ff 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -45,6 +45,8 @@
  • Fetch sequences from DAS sources supporting the sequence command
  • Fetch either seed alignment or full alignment from PFAM
  • Sequence Fetcher GUI provides example accession numbers and 'clear' button
    • +
  • URL Links created for matching database cross references as well as sequence ID
    • +
  • URL Links can be created using regular-expressions
  • Application command line
    • -tree parameter to open trees (introduced for passing from diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html index 7bad5c0..98f01dc 100755 --- a/help/html/whatsNew.html +++ b/help/html/whatsNew.html @@ -10,7 +10,9 @@ DAS Sequence Fetching
      PFAM full alignment retrieval
      DNA/Protein Product traversal (Experimental)
      - .. (more to come) + .. (more to come)
      + URL links can be generated using regular + expressions and created for sequence database cross references

    Issues Resolved

      -- 1.7.10.2