November 2010 Archives by date

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Starting: Mon Nov 1 20:40:06 EDT 2010
Ending: Mon Nov 29 16:13:32 EST 2010
Messages: 82

• [Bioperl-guts-l] [Bug 3152] New: Order of elements in phyloXML   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3153] New: SeqIO::swiss TagTree logic bomb   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3153] SeqIO::swiss TagTree logic bomb   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [bioperl/bioperl-live] a9d671: display_name should be settable, like name()   noreply at github.com
• [Bioperl-guts-l] [Bug 3154] New: SearchIO:blastxml does not return correct query name for blastp (2.2.24)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3154] SearchIO:blastxml does not return correct query name for blastp (2.2.24)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [bioperl/bioperl-live] 7c64e8: check for definedness prior to calling methods   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 71ba1d: initial checkin of revamped Blat wrapper   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] d9db11: add an uppercase alias for db, tests pass   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 8339f2: tests for regions, require a .2bit database so onl...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 651990: allow other SearchIO formats and parameters (thoug...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 533b37: remove cruft, gunge, and implement searchio()   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 71ba1d: initial checkin of revamped Blat wrapper   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] db373a: simplify some bits, pass on query/target types to ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 9c59fd: t/SearchIO/hmmer.t: Fix trailing whitespace   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 322ac7: Rewrite the TreeIO nhx and newick parser and add a...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 2eca6f: updated FASTA result parsing for version 3.6; FAST...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 948af1: kill our reliance on Switch, but add a temp relian...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] e75244: remove given/when :(   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 58e9c3: add simple test for number of nodes returned   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] dd7a31: Merge branch 'topic/gjuggler_tree_fixes'   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 9ac617: change default perms to remove +x for a module   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b4aa25: test remove comment here   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 0ea2d4: commit some parts of the development - this has so...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] bee00a: Small documentation fix.   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 5376d7: Revert "Merge branch 'topic/tree_dbsqlite_memoryfi...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d10cc3: moved some of the documentation to main POD   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 1ed2b0: test commit   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 7dcf3d: fixes to deal with changes in sort order of nodes ...   noreply at github.com
• [Bioperl-guts-l] [Bug 3128] phyloxml and wrong element order   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3152] Order of elements in phyloXML   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [bioperl/bioperl-live] 81bf58: some more functions rolled in   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 1ae693: no more $   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] a08e42: test for NodeDB -- minimal   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 505c4b: Added developer and method documentation.   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b7e5b7: This file was a mistake, Chris says.   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] c22909: Added developer and method documentation.   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 45d9fe: Adding new() method and documentation.   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 022413: use throw() as a class method, since next_token() ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 873940: initial check-in of code for rewrite of phyloxml o...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d3e1cb: initiate work on dispatching to generic methods to...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d0b3b5: First stab at rewriting the even processing for en...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 825565: basic DB backed Tree object   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] cf9bee: (1) Add some convenience / alias methods to Node a...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 5245f8: Rename ascii_art method to print_tree.   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 090cb6: Added insert_node(), update_node(), with API docum...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 7213f8: add a simple class to generate XML nodes, which ma...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 67fedb: added schemaLocation method and constants for XML ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 1bec49: Add is_rooted method to TreeI and a rooted() gette...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 47b1fe: fix test that relied on the highly optional Error....   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] f0e3be: add Error as a recommends, but indicate it as very...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 318f92: check in latest phyloxml commits, may move code fr...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] a953a2: write_xml now catching more nested data, a few mor...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 20ebaa: beginnings of sequence information   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] c0a7df: Added fetch_tree method. Finished insert_tree impl...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 2d4422: fixing glob behavior on MacOS X when there are spa...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 439c4c: Minor doc cleanup.   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 4e8e24: (somewhere over Ohio) <sequence> now working   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 4514fb: Completely gutted, refactored, rehashed, and revam...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] a0a499: more relation fixes   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 4dfe14: Changed root_node to root in Tree to match TreeI s...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b32814: document sorting option   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 6c51dd: either/or for ordering   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] fa7a68: Make NodeFunctionsI not inherit from NodeI -- Node...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 062113: some formatting   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 3e4f5a: Test script for parsing trees into a database.   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d54ece: do sub-tree analysis   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] ef1d89: Fix uninitialized value error if called from outsi...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 44b68d: Add documentation and re-work the interfaces.   noreply at github.com
• [Bioperl-guts-l] GO annotation   Christos Noutsos
• [Bioperl-guts-l] [bioperl/bioperl-live] db88f1: initial checkin of rewritten psl code   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d7685b: add .qual file ext to file extension guessing in S...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 5376d7: Revert "Merge branch 'topic/tree_dbsqlite_memoryfi...   Chris Fields
• [Bioperl-guts-l] [bioperl/bioperl-live] e9b25c: add length so this matches to_string documentation...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 612d92: formatting and compact some code   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 2c95cb: handle nexus guessing too   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] f93dbb: mild formatting   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] ac1696: add seq() method to PrimaryQual, which is similar ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 558467: Switching to File::Glob for file globbing. It use...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] ecf558: few more updates   noreply at github.com
• [Bioperl-guts-l] [Bug 3157] New: Bio::Restriction::Analysis 'sizes' method is broken   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [bioperl/bioperl-live] 78f60d: update Bio::Annotation::Relation to be more graph-...   noreply at github.com

Last message date: Mon Nov 29 16:13:32 EST 2010
Archived on: Mon Nov 29 16:13:38 EST 2010

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