CHANGES

; -*- mode: Text; eval: (set-fill-column 75); -*-

Version 1.68 2024-09-08

Changes:
- Allow non-terminal asterisks in input Pearson/FASTA format
- Allow non-terminal asterisks in input PIR format

Input formats:

- Tested with BLAST 2.16.0+


Version 1.68-beta 2020-10-01

Changes:
- Remove copyright from output.

Input formats:

- Tested with BLAST 2.10.1+
- Tested with FASTA 36.3.8h [2020-05 build]

Bug fix:
- MSF output on Windows would hang waiting for input - fixed.


Version 1.67 2020-02-14

Changes:

- Added PHIBLAST parser for BLAST+
- Added cross-platform installer script 'install.pl'.
- Added 'Makefile.PL' as alternative installer.

Input formats:

- Tested with BLAST 2.10.0+
- Tested with FASTA 36.3.8h [2020-02 build]

Bug fix:

- MS Windows gave parse error and lost initial alignment lines when reading
  from stdin.


Version 1.66 2019-09-01

Changes:

- Added '-sort cov | pid | cov:pid | pid:cov' option to resort sequences by
  (1) coverage, (2) percent identity, (3) coverage then percent identity,
  (4) percent identity then coverage, with respect to the reference
  sequence.

Input formats:

- Tested with BLAST 2.9.0+
- Tested with FASTA 36.3.8h [2019-08 build]

Bug fix:

- FASTA 36 parser omitted database hits with very short identifiers.


Version 1.65  2019-04-22

Changes:

- Speed improvement.
- MAF format now outputs all blocks instead of just the first.
- Format conversions add newline between separate alignment blocks.

Input formats:

- Tested with BLAST 2.8.1+
- Tested with FASTA 36.3.8g [2018-10-23 build]

Bug fixes:

- Replaced option range processing 1..N, lost in version 1.63.

Other:
- Refactoring of parsers.


Version 1.64  2018-05-14

Input formats:

- Tested with BLAST 2.8.0+ [alpha]

New features:

- Speed improvement.

- Added '-sequences on|off' option to disable processing and output of
  sequences for faster analysis (issue #13).

- Added pass-through of extra 'blast -outfmt 7' sbjct fields (staxid,
  ssciname, scomname, sblastname, sskingdom, staxids, sscinames, scomnames,
  sblastnames, sskingdoms). These can be switched off using new label
  control option '-label8' (issue #14).

Bug fixes:

- Fixed regression in output format conversion since v1.62, whereby
  unaligned input sequences were truncated instead of being passed through
  unchanged.

Other:

- Complete rewrite of display mechanism.
- Ongoing refactoring.


Version: 1.63  2018-03-25

Input formats:

- Tested with BLAST 2.7.1+
- Tested with FASTA 36.3.8f, 36.3.8g [2018-01-01 build]

Changes:

- Changed option '-width flat' to '-width full'.
  WARNING! BACKWARDS INCOMPATIBILITY: the default setting, so probably not
  an issue.
- Changed name of output format '-outfmt new' to '-outfmt mview'.
  WARNING! BACKWARDS INCOMPATIBILITY: the default setting, so probably not
  an issue.

New features:

- Added "comment" mode for rows starting with hash, '#'.
- Added "comment" row colouring mode that reads a colormap name embedded in
  the row comment identifier, like '#DSSP:id'
- Added 'DSSP' colormap for protein secondary structure rows.
- Added GNU-style '--' end of command line options flag.

Bug fixes:

- Fixed undefined variable warnings when using '-groupfile' option.
- Fixed JNETZ parser warnings.
- Fixed JNETZ reporting colours even when no colouring set.
- Fixed clustal conservation line bug losing some '.' symbols.

Other:

- Complete rewrite of option parsing mechanism.
- Ongoing refactoring.


Version 1.62  2017-08-06

Changes:

- Added new column reporting percent coverage of hits with respect to
  reference sequence.
  WARNING! BACKWARDS INCOMPATIBILITY: the additional data column is
  inserted as label4 before the percent identity column, so label numbers 4
  through 6 are now 5 through 7.

- Added new '-keepinserts on|off' option for BLAST to preserve hit
  insertions relative to the query. This is useful when dumping a search to
  an unaligned output format (fasta, pir) and the full length HSPs are
  needed. Note: the default behaviour is to cut hit insertions to make the
  query contiguous.

- Added/moved column header information to ruler line in default and html
  output modes; changed default behaviour to display ruler (-ruler on is
  now the default).

- Changed percent identity filtering from all pairwise comparisons to
  simple pairwise comparison with reference row. WARNING! BACKWARDS
  INCOMPATIBILITY: changes meaning of '-minident' and '-maxident' options.

Colouring:

- Changed to allow 'find' colouring independently of 'alignment' colouring,
  so both can be applied (formerly 'find' colouring overrode any
  other).

- Added single colour colormap capability to consensus line colouring.

Input formats:

- Updated to handle BLAST 2.6.0+ '-outfmt 7' changes.

Output formats (clustal, fasta, msf, pir, plain, rdb):

- Added percent coverage, percent identity to output format converters.

- Added search row number to output format converters as a prefix to the
  sequence identifier:

     0:test                     (query row)
     8:emb|AL021726|DMC171E4    (search hit 8)
     8.2:emb|AL021726|DMC171E4  (search hit 8, discrete HSP 2).

- rdb output mode now reports search query as row 0 (was empty before).

Bugs fixed:

- Fixed bug in output format converters that replaced unknown 'X' residues
  in blast query with gaps.

- Fixed bug in propagation of symcolor and gapcolor options in the absence
  of an explicit coloring scheme.

- Fixed bug in minident/maxident truncating search listings.


Version 1.61  2016-11-14

- Added '-coloring mismatch' mode, which behaves like '-coloring identity',
  but highlights the mismatches instead of the identities. Using this you
  can see blocks of misalignment and individuate particular misaligned
  residue types by colour.

- Changed colormap and consensus group 'mismatch' pattern from '*' to '.':
  (1) if you use your own colormaps or consensus maps, the wildcard
  effect in a colormap map is now obtained with . instead of *, and (2)
  the * character now explicitly matches * in the input sequences
  (typically a translated stop codon) so these can now be coloured
  independently like a normal residue.

- Added colouring by single named colour; added X11 and Web 4.0 colours:
  list them with 'mview -listcolors'.

- Updated to handle BLAST 2.5.0+ change in '-outfmt 7' standard field
  names: 'query /sbjct id' became 'query/sbjct acc.'

- Tested with BLAST 2.4.0+, 2.5.0+, FASTA 36.3.8e.


Version 1.60.1  2015-10-13

- Fixed error in get_hsp_groups calling keys(); affects BLAST, but only
  triggered under older versions of perl (seen with 5.10, fine with 5.18).


Version 1.60  2015-10-09

- Changed HTML output to HTML5: added DOCTYPE html, removed FONT tags.

- Added BLAST+ PSIBLAST parser.

- Added BLAST+ '-outfmt 7' support.

- Changed BLAST '-hsp discrete' mode to always set HSP count, N = 1.

- Fixed 'plain' output format to not truncate long identifiers.


Version 1.59  2015-07-17 (GitHub)

- This is a re-release with only documentation changes.

- Code base moved to GitHub.


Version 1.59  2015-07-06 (SourceForge)

- Improved algorithm for assembly of alternative search alignment fragments
  with stricter constraints on selection of fragments that maintain query
  and hit sequence orderings; affects all BLAST and FASTA searches when
  the number of search result fragments is greater than 1.

- Changed BLAST scoring information to report number of HSPs, best score
  and significance for the HSPs used in the assembly, rather than those
  stated in the parsed BLAST ranking; affects all BLAST searches.

- Updated FASTA parsers to recognise '>--' alternative alignments.

- Added FASTA family support for TFASTM, TFASTF, TFASTS (experimental).

- Modified code to work on Windows: fixed problems with filepaths
  containing backslashes; added low-level handling of line endings to
  allow UNIX (LF) and Windows/DOS (CRLF) data files to be read on either
  system. Tested with Strawberry Perl 5.22.0.1 64bit under Wine.

- Fixed bug in CLUSTAL conservation line that sometimes miscalculated
  column positions; affects BLAST and FASTA searches.

- Fixed bug in PIR output that inserted wrong terminal gap character.

- Fixed bug in percent identity calculation: now case-insensitive and
  treats unknown 'X' characters as mismatches.

- Fixed bug in FASTA/Pearson parser that could skip description field.

- Major refactoring of components and discontinued CVS on SourceForge.


Version 1.58  2015-06-14
  Added CLUSTAL/aln output mode.
  Added new '-conservation' option to produce CLUSTAL-style '*:.' line for
    any alignment.
  Added new molecule type option: -moltype { aa | na | dna | rna } and
    removed old '-dna' option.
  Tidied output conversion formatters: now use molecule type.
  Extended MAF parser and added column header text to Ruler, currently
    used by MAF output.
  Extended bin/mview check_format() to better guess input format from
    filename.
  Fixed bug in Sequence.pm to recognise '~' gap characters; affects MSF.
  Fixed bug in UV FASTA handling of peptide tuple matches: each query tuple
    now processed and output separately; affects FASTM, FASTF, FASTS.
  Fixed bugs in UV FASTA translated nucleotide sequence numbering;
    frameshift symbols '/' and '\' now elided and treated like gaps;
    affects FASTX, FASTY, TFASTX, TFASTY, TFASTXY.
  Switched from CVS to git version control.


Version 1.57.1  2015-05-21
  Fixed bug in bin/mview which always set 'find' colour scheme, reported on
  SourceForge.


Version 1.57  2015-01-24
  WARNING! BACKWARDS INCOMPATIBILITY: Changed FASTA-related input format
  names to avoid long-standing confusion, as follows:
    1. FASTA multiple alignment file format:
         old name "pearson"
         new name "fasta".
    2. FASTA family of sequence database search tools from Uni. Virginia:
         old name "fasta"
         new name "uvfasta"
  Added MAF parser (experimental).
  Extended the pattern search mechanism to assign a different colour to
    each input sub-pattern; see command line option '-find' in the manual.
  Added small change to Pearson/Fasta parser to strip description fields
    comprising a single '.' from GeneDoc output.
  Fixed CLUSTAL parser failure when input file uses CRLF line terminators.
  Fixed bug in MSF parser so that sequence identifies can contain spaces.


Version 1.56  2013-10-20
  Updated FASTA suite GGSEARCH, GLSEARCH, SSEARCH, FASTM parsers and added
    support for FASTF, FASTS.


Version 1.55  2013-09-27
  Converted documentation to Sphinx and rewrote and extended the manual.
  Changed HTML output to place the header text within the alignment table.
  Reading from stdin via scratch file on /tmp fixed.
  Added -listcss option; removed -html css; changed CSS layout.
  Added R and Y to D1 consensus for nucleotide alignments.
  Pattern search mechanism now sets own colormap.
  Consensus lines missing '.' characters in partial gaps fixed.


Version 1.54  2013-08-27
  New FASTA parser; old parser retained in legacy FASTA versions.
  Added FASTA family SSEARCH, GGSEARCH, GLSEARCH support.
  Added FASTA family FASTM support (experimental).


Version 1.53  2013-08-21
  BLAST parsers modified to remove trailing junk from identifiers.
  BLAST parsers modified to handle score summaries with empty description
    field.
  WU-BLAST parser modified to handle EMBOSS header content containing
    leading '>' characters.
  Removed spurious cursor increment in main loop of
    Bio::MView::Display::Reverse_Ruler.
  Clustal parser supports trailing numbers for clustal 2.1 FASTA parsers
    extended to handle some more FASTA3 formats.
  Sequence assembly mechanism changed to preserve earlier fragments at the
    expense of overlapping ones seen later by the parser; this only visibly
    affects blast/fasta searches involving sequence fragments in mixed
    reading frames.


Version 1.52  2011-01-20
  Fasta parsing extended to handle versions 34,35,36. Only tested for fasta
  itself on protein sequences and not for other members of the fasta suite.
  Bug fixes:
  - SRS.pm did not truncate trailing garbage on identifiers correctly.
  - EBI SRS wgetz URL templates updated.
  - HSSP.pm parser now refers to uniprot instead of swiss in identifiers.


Version 1.51.1  2009-10-24
  HSSP output no longer produces the chain discontinuity symbol '!' in
  unaligned regions.


Version 1.51  2008-05-20
  Extended SRS links to handle NCBI identifiers of form "ref|accession|".

  Added 'pcid' option to control normalisation method for all percent
  identity calculations: 'reference' (normalises with respect to the query
  or reference sequence, 'aligned' (was the only option, normalises with
  respect to the length of the aligned region), and 'hit' (normalises with
  respect to the length of the matched or hit sequence).

  Added 'minident' option to allow filtering on sequences over some
  threshold of percent identity.

  Changed output header text to give information on percent identity
  normalisation method unless disabled with 'label4' or 'minident' or
  'maxident' in operation.

  Fixed syntax problem in some parsers for perl v5.10.0.


Version 1.50  2008-04-20
  Added 'find' option to search for strings and regexps.

  Renamed old 'clustal' colourmap to 'nardi' (its author) and added new
  'clustal' colourmap based on clustalx2. The 'cclustal' consensus
  colourmap still uses the old nardi clustal colour scheme.

  Tidied SRS sequence identifier link code: now contains NCBI entrez
  protein link and EBI protein and nucleotide link patterns.


Version 1.49.0  2005-12-03
  SourceForge relocation
  Switched to GPL.


Version 1.48.3  2005-11-14
  Refactored parser tree.


Version 1.48.2  2005-07-13

  Added T-COFFEE 1.37 parser.


Version 1.48.1  2004-11-04

  Minor change to BLAST2 family parser delimiting hits more accurately in
  special case that hit description section contains leading 'Score='
  referring to some cross-reference.

  Minor change to generic alignment BLAST parser to work around space
  padding inserted in mid-alignment by psiblast 2.2.9 in rare cases.


Version 1.48  2004-04-27

  Relaxed fasta 3.3 parsing of bits field in rank (was integer, now
  string).

  Fixed bug in discrete HSP processing for blastx,tblastn,tblastx where
  known HSP frames were being truncated to orientation only.

  Parsers extended and tested for:
    o ncbi blast 2.2.6
    o wu-blast 2.0 [13-Apr-2004]
    o fasta 3.4t23
    0 clustalw 1.83

  Relocated CVS tree to Unibas.

  Better input file checking.


Version 1.47.5  1-4-03

  Fixed plain output format which did not correctly process '#identifier'
  lines (user-supplied rows such as annotation that should not be processed
  in the normal way).


Version 1.47.4  1-1-03

  Changes to blast processing code; minor parser change for blastn 2.0.14;
  minor parser change for MSF; fixed missing percent identity calculation!
  As usual, this label is switched off with '-label4'.


Version 1.47.3  31-5-02

  Fixed 'exists' bug in Sequence.pm.


Version 1.47.2  29-4-02

  Minor changes and tidying of html documentation.


Version 1.47.1  23-4-02

  Fixed fasta family parse error caused by a short sequence stub on the
  first line of alignment, which gave negative sequence positions for the
  query (or subject).


Version 1.47  21-4-02

  o  Blast and fasta processing now always outputs strand
     orientations/frames as a part of the score data field controllable
     with '-label3' (except for blastp, since strand orientations are
     always '+'.
  o  Blast and fasta processing now outputs query and hit sequence
     positions as reported in those formats. This can be switched off
     with '-label5' option (no query positions) and '-label6' (no hit
     positions).
  o  Pearson, PIR, RDB, HTML output formats now report rank, description,
     score information, strand orientations, and query/hit positional
     data.
  o  Fixed inoperative '-minopt' bug for fasta.
  o  Colormap now uses a palette of colors by name, run with -listcolors to
     see the extended syntax. Backwards compatible with previous versions.
  o  Input sequences having sequence identifiers that start with a hash
     character '#' will be treated as special rows for coloring
     purposes. The user can supply corresponding colormaps using
     '-colorfile FILENAME'. For example, if the input alignment contains a
     line identified by '#sec-struct' then a colormap called [sec-struct]
     would apply to any rows containing that string in their identifier.
  o  Options -disc/-keep/-nops now accept '*' meaning all rows.
  o  New option '-labcolor' to specify the color for the label portion of
     the output alignment.
  o  JNET secondary structure prediction parser added, with own color
     scheme, specified with '-in jnet'. This only reads the 'jnet -z'
     (columnar) style output.
  o  CLUSTAL-like colormaps added.
  o  New neural network derived colour scheme added (-colormap kxlin).
  o  Option '-out plain' added for completeness.


Version 1.41.11  12-5-01

  Fixed Substring.pm _close() which gave warning in perl5.6.0 when called
  more than once.


Version 1.41.10  9-3-01

  Fasta version 3.3t07 'fasta' format added percent identity ungapped.


Version 1.41.9  20-10-00

  Start of some support for NCBI psi-blast web page (text-only) output.


Version 1.41.8  1-12-99

  Parser for FASTA suite 'fasta' version 3.3 added.


Version 1.41.7

22-11-99  GPCRdb colour scheme added, selected with command line option
          '-colormap gpcr' as for other coloring schemes.


Version 1.41.6

13-9-99   PHI-BLAST 2.0.9 supported.


Version 1.41.5

31-8-99   o Modified BLAST2 parser to recognise ungapped (blastall -g F)
            output. Note, the default behaviour of MView when processing
            BLAST2 output is to display only the first sequence fragment
            found, which is reasonable for gapped output. If you want to
            use BLAST2 ungapped output and see the HSPs merged (the default
            behaviour of MView with old BLAST1 output) use the '-hsp all'
            option. Likewise to see all HSPs separately use '-hsp discrete'.
          o Modified BLAST2 BLAST[NX] parsers to recognise strand and frame
            orientation fields added in (or before?) BLAST2.0.9.
          o Modified FASTA3 parsers for multi-line descriptions
            (fasta... -L) output.


Version 1.41.4

30-7-99   Options -help, -listcolors, -listgroups now output on stdout
          rather than stderr; use of -html option adds markup to these -
          in particular with -listcolors, the output is marked up in colour
          (useful for documentation Web pages). Comments within each
          colormap or groupmap definition are now retained for output with
          the corresponding -list options.


Version 1.41.3

1-7-99    o Coloring by identity now uses the colormap's '*' color (if
            defined) preferentially instead of 'symcolor', defaulting to
            the latter if '*' is undefined in the colormap: if coloring by
            identity is selected, symbols matching the reference sequence
            will receive their given colors from the colormap, while
            mismatches will receive the wildcard '*' color, if defined in
            the colormap, otherwise the 'symcolor'.
          o New DNA colormap 'D2' for use with coloring by identity:
            blue/red for match/mismatch.


Version 1.41.2

18-5-99   o Fixed bug in FASTA 32t05 parser.


Version 1.41.1

13-5-99   o Parser modification for newly released FASTA 32t05.
          o New parser for MIPS-ALN format (experimental).


Version 1.41

15-4-99   o Condensed CSS HTML output so loading pages should be faster.
          o Added limited experimental support for GCG 9.1 versions of
            BLAST and FASTA suites: known to work for: blastp (1.4.8),
            fasta (2).
          o Added support for fasta (3.2) with strand orientations.
          o Changed -disc/-keep policy again! List precedence is:
              -keep > -disc
            ie., -keep list overrides the -disc list. Regular expressions
            can now be used in -keep/-disc/-nop lists, so something like:
              -disc '/.*/'  -keep '2,3,6..10,/^pdb/'
            would discard everything except rows 2, 3, 6 through 10, and
            any hits beginning with the string 'pdb'. Regular expressions
            inside a list must be enclosed by '/' characters and matches
            are case-insensitive.
          o The currently set reference row is still used for percent
            identity and colouring operations, but the row will be
            invisible if excluded by the -disc list, so you must explicitly
            keep it in that situation if desired. This is arguably a more
            useful behaviour that still satisfies the need addressed in
            version 1.39.1 (see above) allowing '-disc query'.
          o Use of a reference row can be completely switched off by
            specifying any non-existent value, eg., -ref -1, thereby
            disabling percent identity column calculation and identity
            coloring schemes.
          o The keeplist is no-longer reported in the output.
          o Memory use extensively reduced in various places; essential for
            massive psi-blast jobs that process all cycles.
          o New option '-register on|off' to control registration of
            columns in multi-pass output (eg., blastn strands, psi-blast
            cycles). With the default setting 'on', MView saves all output
            in memory until the end to ensure alignments and labels are
            output in register. Much memory can be saved by setting to
            'off'.


Version 1.40.5

18-3-99   Fixed: -strand {+,-,*} options failed with new Getopt.pm because
          of +/- character conflicts: now use -strand {p,m,*}.


Version 1.40.4

9-3-99    Fixed: -colormap/-groupmap failed to recognise maps loaded by
          -colorfile/-groupfile; -srs option had no effect.


Version 1.40.3

2-3-99    Fixed: -groupfile called missing method.


Version 1.40.2

1-3-99    Fixed: -label switches were being ignored; -listgroups called
          missing method; -minbits called missing mehod; SRS.pm built-in
          URLs now refer to SRS version 5 sites.


Version 1.40.1

18-2-99   Added explicit CORE::{warn,die} for perl 5.005. Default alignment
          color '-symcolor' set to #222222 (dark grey) instead of #000000
          (black).


Version 1.40

12-2-99   Added Cascading Style Sheets for blocked coloured backgrounds.
          Colour palettes changed to use Netscape 216 cross-platform
          colours.
          New HTML markup options: -html, -title, -pagecolor, -textcolor,
          -linkcolor, -alinkcolor, -vlinkcolor, -alncolor, -symcolor,
          -gapcolor. New option -dna for selecting default nucleotide
          colours and consensus group definitions, -css for switching on
          style sheets. Colouring schemes augmented with '-coloring
          group'. Built-in palette and consensus group names changed. Old
          options -contrast -body removed. New Getopt.pm class. Colouring
          mode methods clearer.


Version 1.39.5

1-12-98   Minor parser change for PSI-BLAST 2.0.6.


Version 1.39.4

18-11-98  Fixed bug in -con_gaps option which left blanks in the consensus
          sequence when the number of gaps in the column dominated non-gaps.


Version 1.39.3

16-11-98  Perl 5.003 problem fixed for backward compatibility. This
          concerned use lexically scoped $a (or $b) inside a function
          passed to the sort() builtin; solved by renaming the my()
          variable(s).


Version 1.39.2

11-11-98  Blast filters -maxpval, -maxeval, -minscore, -minbits were broken
          as access methods were missing.


Version 1.39.1

11-11-98  Changed interoperation of -keep and -disc options: formerly,
          -keep overrode -disc where an id was present in both. Now, the
          converse is true. This allows the query sequence to be discarded
          from a search, which was not possible before.


Version 1.39

11-11-98  Added -con_gaps option to control use of gaps in consensus
          calculation. The default behaviour is equivalent to '-con_gaps
          on' which computes consensus colours and consensus lines counting
          gaps. This often results in columns of alignment that are
          uncoloured or have no consensus because they contain too many
          gaps that force the consensus below the threshold. Setting
          '-con_gaps off' causes gaps to be ignored for consensus
          calculations.


Version 1.38.2

11-11-98  Fixed bug in Plain.pm causing parse failure on trailing white
          space in alignments.


Version 1.38.1

04-11-98  Changed default consensus calcualtion threshold to 70% (from 75%)
          to match the 70% line available by default when consensus lines
          are switched on.


Version 1.38

02-11-98  Added -hsp {ranked,all,discrete} option allowing some control of
          ungapped BLAST HSP or gapped BLAST alignments for processing.


Version 1.37.1,1.37.2

          Minor bug fixes and omissions in 1.37.


Version 1.37

12-10-98  Ftp/Web site relocated to NIMR.
          Parsers extended to cover the full BLAST program suite (*=new) :
             NCBI BLAST (2.0 series)
               blastp, blastn, (*)blastx, (*)tblastn, (*)tblastx, psi-blast
             NCBI BLAST (1.4 series)
               blastp, blastn, (*)blastx, (*)tblastn, (*)tblastx
             WashU BLAST2 (2.0)
               blastp, blastn, (*)blastx, (*)tblastn, (*)tblastx
          BLAST (1.4 series) HSP stacking mechanism is now more
          conservative: only the HSPs forming the set reported in the hit
          ranking are stacked (where this can be determined). Other HSPs
          are ignored. Input format detection using preferentially 1) -in
          option, 2) filename extension, 3) non-directory part of filename
          prefix to infer format. Multiple files in different formats can
          thus be processed as one. Column names added to numeric fields
          (score, expect, etc) for search programs in BLAST/FASTA
          suites. Added -minopt to for FASTA filtering (was -minscore, but
          this was ambiguous). Added -range M:N option giving limited
          output sequence number range control from command line.
          Bug fixes: Ordering of HSPs in reverse complemented query strands
          was wrong for blastn (series 1.4). Better memory usage. Rulers
          now decrement for reverse oriented query sequences (BLASTN, etc).


Version 1.36.2

3-9-98    Fixed empty psi-blast iteration bug: if no hits are found MView
          skips that iteration.


Version 1.36.1

1-9-98    Added GCG style checksums to MSF output format for Name lines.


Version 1.36

24-8-98   OPERATIONAL changes:
          Support for HTML TABLE output dropped (too complex and
          compromising efficiency). BLASTP/BLASTN parser minor bug
          fix. BLAST2 parser supports choice of one or more search cycles
          to be processed using -cycle option. Selective exclusion of
          alignment rows from colour or identity calculations added through
          -nop (no process) option. Complete removal of explicit rows and
          ranges of rows through -disc (discard) option. Same ability to
          handle row ranges (eg., 10..15) added to existing -keep (force
          retention of rows despite other filters) option. New PIR format
          parser added (-in option). New output formats PIR and MSF added
          (-out option). The MSF output does not presenty; compute
          checksums, so this may cause a problem for those programs that
          are fussy about this.

          MAJOR PERFORMANCE changes:
          The memory footprint has been massively reduced for large
          alignments through closure or several memory leaks concerning
          (lack of) garbage collection of circular references in perl. The
          input file is no longer read into memory for parsing, but is read
          on demand using seek(), which also saves memory.


Version 1.35.1

27-7-98   MSF parser modified. -help text use of -threshold corrected.


Version 1.35

16-6-98   Added consensus colouring/line code. Added MULTAS parser. Added
          new output mode 'pearson' which allows any valid input format to
          be dumped as a Pearson/FASTA library for import to other tools.


Version 1.33/34  Experimental - not released.


Version 1.32.1

5-6-98    Fixed TFASTX parser to differentiate from FASTA when no
          interactive header is present.


Version 1.32

4-6-98    Added TFASTX parser; BLASTN parser splits alignments on strand
          orientations, but this is a memory hog - only works for small
          alignments or with limiting -topn.


Version 1.31.1

27-5-98   Changed calculation of percent identities reported in alignments
          to follow that used by BLAST:

                         number of identical residues
                   --------------------------------------  x 100
                     length of query over aligned region,
                           excluding gaps in the query

          In the case of BLAST MView output, deviations from the
          percentages reported by BLAST are due to 1) different rounding,
          and 2) the was MView assembles a single pseudo-sequence for a hit
          composed of multiple HSPs, giving an averaged percent identity.


Version 1.31

18-3-98   New/changed command line options:

          OLD                   NEW
          -ruler                -ruler on|off
                                -alignment on|off
          -color scheme         -coloring scheme
                                -colormap mapname
                                -listcolors

          Fixed '-contrast' option ignored by '-coloring any'.
          Changed COPYING file explicitly to allow free use of MView output.


Version 1.30

17-3-98   Added user control of coloring. Setting maxident is no longer
          overridden by topn: -maxident 75 -topn 10 now gives the top 10
          hits with maximum identity of 75%. Formerly, it gave the maximum
          75% identity hits of the top 10.


Version 1.29.1

20-3-98   Added BLASTN (NCBI 2.0.4) parser.


Version 1.29

12-3-98   Added CLUSTAL parser. Various small changes.


Version 1.28  Experimental - not released.


Version 1.27.3

6-3-98    Removed old PSI-BLAST parser (PBlastp.pm). Added NCBI BLAST2
          parser (Blast2.pm), which parses both new NCBI BLAST2 and
          PSI-BLAST formats.
          Added -minbits filtering to mview command line for use with
          these.


Version 1.27.2

3-3-98    Fixed Fasta.pm bug.


Version 1.27.1

26-2-98   Fixed MSF.pm bug.


Version 1.27

10-2-98   Various compiler bugs under perl5.004 corrected. JOB parsing
          removed.


Version 1.26

29-1-98   Added Pearson/Fasta parser for multiple alignments.

8-2-98    Minor changes to COPYING document.


Version 1.25

22-1-98   Added MSF parser for multiple alignments.

          build_old_alignment() now checks new 'class' attribute of Manager
          set by Search or Align constructors - this is used to control
          sequence numbering in left column. As conceived, this routine
          only numbered properly for searches, not for alignments. Obsolete
          routine anyway, but fixed for completeness.


Version 1.24.2

20-1-98   Fixed bug in colouring when an excised gap region was lowercased:
          identical residues weren't being coloured.


Version 1.24

Log started.

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