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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. Thanks to sfrye@rr-research.no for the last 4 items. 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 (reported by Jiuhai Zhao). WU-BLAST parser modified to handle EMBOSS header content containing leading '>' characters (identified by Weizhong Li). Removed spurious cursor increment in main loop of Bio::MView::Display::Reverse_Ruler (Weizhong Li). Clustal parser supports trailing numbers for clustal 2.1 (Weizhong Li). 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 as requested by Shiraz Shah. Only tested for fasta itself on protein sequences and not for other members of the fasta suite. Bug fixes suggested by Rob Sheridan/Chris Sander: 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. Reported by Rainer Merkl. 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 reported by Lins1@wyeth.com. 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 (reported by agibbs@uvic.ca), 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 - thanks to michael.spitzer@uni-muenster.de and others who have asked for this. o Fixed inoperative '-minopt' bug for fasta, reported by gkutish@asrr.arsusda.gov. 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 (requested by andrade@stork.embl-heidelberg.de), specified with '-in jnet'. This only reads the 'jnet -z' (columnar) style output. o CLUSTAL-like colormaps added (thanks to Frederico.Nardi@astrazeneca.com). o Kuang Lin's 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 for Gert Vriend/EMBL, 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 (requested by tdeboer@hgmp.mrc.ac.uk). 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: thanks to m.mitchell@icrf.icnet.uk. 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 (suggested kauffman_e_wayne_ii@lilly.com). 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 (reported by m.mitchell@icrf.icnet.uk) 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 (reported by J.Stoye@dkfz-heidelberg.de). Version 1.39 11-11-98 Added -con_gaps option to control use of gaps in consensus calculation (suggested by J.Stoye@dkfz-heidelberg.de). 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 found by Chris Upton. Version 1.27.1 26-2-98 Fixed MSF.pm bug reported by Martin Simmen. Version 1.27 10-2-98 Various compiler bugs under perl5.004 reported by Alex Whittaker 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. ###########################################################################
Source: README.txt, updated 2015-01-24