| 2006-12-28 |
cjfields | Moving BLAST XML SAX methods to separate class
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commit | commitdiff | tree |
| 2006-12-21 |
cjfields | XML::SAX::PurePerl works with older BLAST XML report...
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commit | commitdiff | tree |
| 2006-12-21 |
cjfields | add tests for 'unisave', move to Test::More, minor...
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commit | commitdiff | tree |
| 2006-12-21 |
cjfields | added 'unisave'
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commit | commitdiff | tree |
| 2006-12-20 |
cjfields | Bug fix for env_proxy
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commit | commitdiff | tree |
| 2006-12-13 |
cjfields | If parser overheats, turn off and back slowly away...
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commit | commitdiff | tree |
| 2006-12-13 |
cjfields | Very experimental Infernal (cmsearch) parser.
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commit | commitdiff | tree |
| 2006-12-12 |
cjfields | small change for phase test
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commit | commitdiff | tree |
| 2006-12-12 |
cjfields | Add convenience parameter '-phase' to spliced_seq()
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commit | commitdiff | tree |
| 2006-12-12 |
cjfields | spliced_seq() phase tests
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commit | commitdiff | tree |
| 2006-12-06 |
cjfields | Update from wiki
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commit | commitdiff | tree |
| 2006-12-06 |
cjfields | Update from wiki
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commit | commitdiff | tree |
| 2006-12-05 |
cjfields | Grr...refix Bug 2159
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commit | commitdiff | tree |
| 2006-12-05 |
cjfields | bug 2159
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commit | commitdiff | tree |
| 2006-12-05 |
cjfields | Bug 2160
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commit | commitdiff | tree |
| 2006-11-30 |
cjfields | change for block to a map
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commit | commitdiff | tree |
| 2006-11-30 |
cjfields | Bug 2152
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commit | commitdiff | tree |
| 2006-11-27 |
cjfields | throw, not warn, since this dies 99% of the time anyway...
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commit | commitdiff | tree |
| 2006-11-27 |
cjfields | small fixes for AnnotationFactory
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commit | commitdiff | tree |
| 2006-11-26 |
cjfields | Bug 2124
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commit | commitdiff | tree |
| 2006-11-26 |
cjfields | Bug 2151
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commit | commitdiff | tree |
| 2006-11-23 |
cjfields | Bug 2146
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commit | commitdiff | tree |
| 2006-11-23 |
cjfields | Bug 2146
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commit | commitdiff | tree |
| 2006-11-16 |
cjfields | Convert to Test::More
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commit | commitdiff | tree |
| 2006-11-16 |
cjfields | Convert to Test::More
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commit | commitdiff | tree |
| 2006-11-16 |
cjfields | Bug 2145
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commit | commitdiff | tree |
| 2006-11-14 |
cjfields | Add CVS tags, move dependencies to new file
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commit | commitdiff | tree |
| 2006-11-14 |
cjfields | New INSTALL.WIN doc (from wiki)
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commit | commitdiff | tree |
| 2006-11-14 |
cjfields | Add POD
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commit | commitdiff | tree |
| 2006-11-13 |
cjfields | bug 2139; change to Test::More
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commit | commitdiff | tree |
| 2006-11-13 |
cjfields | Bug 2139
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commit | commitdiff | tree |
| 2006-11-13 |
cjfields | typo (bug 2141)
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commit | commitdiff | tree |
| 2006-11-13 |
cjfields | change test file data
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commit | commitdiff | tree |
| 2006-11-11 |
cjfields | ARP tests
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commit | commitdiff | tree |
| 2006-11-11 |
cjfields | Simple ARP parser
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commit | commitdiff | tree |
| 2006-11-10 |
cjfields | use single quotes for system calls to prevent interpolation
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commit | commitdiff | tree |
| 2006-11-10 |
cjfields | Changed or removed VERSION
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commit | commitdiff | tree |
| 2006-11-09 |
cjfields | delete output test files
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commit | commitdiff | tree |
| 2006-11-09 |
cjfields | Add xmfa alignment tests
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commit | commitdiff | tree |
| 2006-11-09 |
cjfields | add xmfa write_aln() method, stk and xmfa file extensions...
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commit | commitdiff | tree |
| 2006-11-09 |
cjfields | using 'our'
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commit | commitdiff | tree |
| 2006-11-09 |
cjfields | first pass at xmfa parser (next_aln() implemented only)
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commit | commitdiff | tree |
| 2006-11-09 |
cjfields | Bug 2134 (change output to conform with rel. 9 ID changes)
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commit | commitdiff | tree |
| 2006-11-09 |
cjfields | Bug 2134 (added tests for new swiss format); changed...
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commit | commitdiff | tree |
| 2006-11-09 |
cjfields | Bug 2134 (fix parsing)
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commit | commitdiff | tree |
| 2006-11-09 |
cjfields | Changed name
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commit | commitdiff | tree |
| 2006-11-08 |
cjfields | Bug 2134
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commit | commitdiff | tree |
| 2006-11-08 |
cjfields | Some modules don't define VERSION, default to 0
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commit | commitdiff | tree |
| 2006-11-08 |
cjfields | Remove extraneous debugging staatements
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commit | commitdiff | tree |
| 2006-11-08 |
cjfields | typo
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commit | commitdiff | tree |
| 2006-11-08 |
cjfields | Using DBLinks for database refs
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commit | commitdiff | tree |
| 2006-11-07 |
cjfields | Additional fun stuff; write_aln() test added; may move...
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commit | commitdiff | tree |
| 2006-11-06 |
cjfields | more Stockholm tests; skipping two for now (dropping...
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commit | commitdiff | tree |
| 2006-11-06 |
cjfields | Add alignment meta string output
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commit | commitdiff | tree |
| 2006-11-06 |
cjfields | remove old initialization parameter; will add builder...
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commit | commitdiff | tree |
| 2006-11-06 |
cjfields | Add sequence-based meta output
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commit | commitdiff | tree |
| 2006-11-06 |
cjfields | stockholm alignment tests
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commit | commitdiff | tree |
| 2006-11-06 |
cjfields | Add experimental stockholm write_aln() support
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commit | commitdiff | tree |
| 2006-11-05 |
cjfields | Use Test::More
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commit | commitdiff | tree |
| 2006-11-01 |
cjfields | Implement AnnotatableI (for alignment-specific annotation)
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commit | commitdiff | tree |
| 2006-10-31 |
cjfields | remove redundant sub_Location_by_order()
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commit | commitdiff | tree |
| 2006-10-31 |
cjfields | Bug 2130
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commit | commitdiff | tree |
| 2006-10-28 |
cjfields | remove extraneous use statement
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commit | commitdiff | tree |
| 2006-10-26 |
cjfields | Bullet-proof some tests
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commit | commitdiff | tree |
| 2006-10-24 |
cjfields | Bug 2060
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commit | commitdiff | tree |
| 2006-10-24 |
cjfields | our $VERSION (perl 5.6.1-ish)
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commit | commitdiff | tree |
| 2006-10-20 |
cjfields | Typo
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commit | commitdiff | tree |
| 2006-10-19 |
cjfields | Bug 2101 (tentative fix)
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commit | commitdiff | tree |
| 2006-10-17 |
cjfields | Change to Test::More; skip XML tests if problems arise...
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commit | commitdiff | tree |
| 2006-10-11 |
cjfields | Bug 2121
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commit | commitdiff | tree |
| 2006-10-10 |
cjfields | Bug 2120
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commit | commitdiff | tree |
| 2006-10-05 |
cjfields | Updates to POD and egquery (getting it up to speed)
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commit | commitdiff | tree |
| 2006-10-05 |
cjfields | Fixes to get EGQuery working correctly
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commit | commitdiff | tree |
| 2006-10-04 |
cjfields | Added tests for new DocSum methods; will probably cut...
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commit | commitdiff | tree |
| 2006-10-04 |
cjfields | POD cleanup (thanks Sendu), remove some debugging stuff...
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commit | commitdiff | tree |
| 2006-10-04 |
cjfields | ESummary tests
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commit | commitdiff | tree |
| 2006-10-04 |
cjfields | Fixes for tests
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commit | commitdiff | tree |
| 2006-10-03 |
cjfields | About to add a few tests for Esummary (not implemented...
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commit | commitdiff | tree |
| 2006-10-03 |
cjfields | Add POD
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commit | commitdiff | tree |
| 2006-10-03 |
cjfields | Adding methods to DocSum and esummary (still experimental)
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commit | commitdiff | tree |
| 2006-10-03 |
cjfields | Add simple docsum container object for esummary
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commit | commitdiff | tree |
| 2006-10-03 |
cjfields | Setting DB from cookie is bad for elink; it should...
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commit | commitdiff | tree |
| 2006-10-03 |
cjfields | Force IDs to be an array at all times
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commit | commitdiff | tree |
| 2006-10-03 |
cjfields | Remove tests for deprecated modules
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commit | commitdiff | tree |
| 2006-10-02 |
cjfields | warn, not warning (duh....)
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commit | commitdiff | tree |
| 2006-10-02 |
cjfields | Added more deprecated modules
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commit | commitdiff | tree |
| 2006-10-02 |
cjfields | Add deprecation warnings
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commit | commitdiff | tree |
| 2006-10-02 |
cjfields | Add link not present from wiki2txt conversion
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commit | commitdiff | tree |
| 2006-10-02 |
cjfields | Update to include Torsten's wiki changes for http_proxy
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commit | commitdiff | tree |
| 2006-09-29 |
cjfields | remove numbers in contents
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commit | commitdiff | tree |
| 2006-09-29 |
cjfields | First draft of new INSTALL (from wiki)
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commit | commitdiff | tree |
| 2006-09-28 |
cjfields | Remove extra quote
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commit | commitdiff | tree |
| 2006-09-28 |
cjfields | now with 'our'
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commit | commitdiff | tree |
| 2006-09-28 |
cjfields | Add proxy authorization, small fixes to POD
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commit | commitdiff | tree |
| 2006-09-28 |
cjfields | Pass to SUPER::proxy (bug 2109)
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commit | commitdiff | tree |
| 2006-09-28 |
cjfields | Did I forget to mention, now with Test::More? Small...
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commit | commitdiff | tree |
| 2006-09-28 |
cjfields | Minor changes (deal with evalue perliness)
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commit | commitdiff | tree |
| 2006-09-28 |
cjfields | Add ERPIN tests
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commit | commitdiff | tree |
| 2006-09-28 |
cjfields | for ERPIN tests
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commit | commitdiff | tree |
| 2006-09-27 |
cjfields | change use var to our; comment out Dumper lines
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commit | commitdiff | tree |
