SRS version 5.1.0

Thure Etzold etzold at ebi.ac.uk
Mon Dec 22 20:35:22 EST 1997


Dear all,

happy Christmas and lots of new features. Have fun!
The file is at ftp://ftp.ebi.ac.uk/pub/software/unix/srs/srs5.1.0.tar.gz

Release notes:

SRS version 5.1.0
=================

-- new features
1)  New hierarchical link index allows taxonomic queries and in general
    queries on hierarchical entry relations.
2)  New named indexes group several index files with the same meaning
    into a single "virtual" index.
3)  Created databanks of databanks which allows to search which servers
    provide specified databanks.


-- changes in the www interface

1)  New databank selection page, which uses JavaScript and compatible
    with Netscape 4.0 and Microsoft Internet Explorer 4.0 (and the
    following minor releases of the programs). Allows working with
    large sets of databanks.
2)  Following user demands, we added new Query form, similar to the
    one present in srs 4.0. Allows simple views to be directly specified

    in the query form. The srs5 query form is still available as
    "alternate query form".
3)  In the query result page the user can now select if the operation to

    be performed is on the "selected" entries or on "all but selected".
    The second option allows to link or save a set of entries without
    need to go to the query manager.
4)  The View Manager has been simplified by inserting a new front page
    showing the different options from view management. In the list for
    selecting the linked databanks, the new named links have been
included
    to allow linking to entire databank groups (i.e. searchDB=all
sequence
    databanks) with one click.
5)  The databank information page now shows if a databank is currently
    being reindexed and it can show the progress of indexing.

-- changes in the Icarus language

1)  Added objects as a new basic type that can be assigned to variables.

    Object have methods. Predefined classes Strv (a string class),
Sequence,
    Job.
2)  Token tables now accept objects as tokens (using $Wrt:[o:$blabla]).
    Very useful for streaming and reorganizing large chunks of text.
3)  Added the new parsing concept of TINs (Token INdices). The lazy
parsing
    model has beed modified to allow token tables to be dependent from
TINs.

-- changes in the server maintanance

1)  Completely changed the way subentries are described, now using TINs.

    This modification is NOT backward compatible with the previos
version
    of subentries, but because we don't know of anybody specifying
subentries
    yet, we hope not to give too much trouble :O)
2)  New way of adding applications, makes interfacing applications
    even using remote shells (rsh) a breeze.
3)  Now it is possible to limit access to internal resources
    (databanks, applications or even single fields within a databank)
    depending from the internet domain which requests access.
4)  The way sequences are treated is changed, and it writes the sequence

    in the token table as a "sequence" object. This object has various
methods
    which allow sequence conversion in all major formats.
5)  All existing parsers have been modified to take advantage of TINs
and of
    sequence objects.
6)  Inserted the indexing log file as a databank, this allows
    to quickly spot indexing problems by querying the log file.
7)  SRSCHECK now generates calls to SRSBUILD using the new -nn option
    which causes SRSBUILD to be completely silent (no numbers written
    during indexing)
8)  GETZ has a new option -stat <db_name> which displays the status of
the
    indexing process for the specified databank.

The version has been compiled and tested on IRIX5.3, IRIX6.2,
OSF versions 2 and 4, Solaris, Linux. Almost all compiler warnings have
been removed. The ones left are inconsequential.


Thure Etzold,   etzold at ebi.ac.uk
Giorgio Verde, verde at ebi.ac.uk
22 Dec, 1997






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