jalview.git
16 years agorefactored method for registering instance of a dbSource with the SequenceFetcher...
jprocter [Thu, 31 Jul 2008 10:15:50 +0000 (10:15 +0000)]
refactored method for registering instance of a dbSource with the SequenceFetcher from the factory method for creating a dbSource instance

16 years agoquick fix for the new uniprot name schema - description line for retrieved uniprot...
jprocter [Thu, 31 Jul 2008 10:11:57 +0000 (10:11 +0000)]
quick fix for the new uniprot name schema - description line for retrieved uniprot sequences gets the first recommendedName.fullName string found in the entry.

16 years agoadded specific retrieval arguments to SequneceFetcher's main method.
jprocter [Thu, 31 Jul 2008 10:09:55 +0000 (10:09 +0000)]
added specific retrieval arguments to SequneceFetcher's main method.

16 years agoresolve 1:many mappings for sequence associated annotation to all alignment sequence...
jprocter [Fri, 18 Jul 2008 15:10:29 +0000 (15:10 +0000)]
resolve 1:many mappings for sequence associated annotation to all alignment sequence(s) with same ID

16 years agoresolve 1:many mappings from feature sequence ID to alignment sequence(s) with same ID
jprocter [Fri, 18 Jul 2008 15:05:30 +0000 (15:05 +0000)]
resolve 1:many mappings from feature sequence ID to alignment sequence(s) with same ID

16 years agoallow findSeq to begin *after* a given sequence in the alignment
jprocter [Fri, 18 Jul 2008 15:03:36 +0000 (15:03 +0000)]
allow findSeq to begin *after* a given sequence in the alignment

16 years agoSequence label colour stored for each sequence group
jprocter [Fri, 18 Jul 2008 13:31:02 +0000 (13:31 +0000)]
Sequence label colour stored for each sequence group

16 years agocomment
jprocter [Fri, 18 Jul 2008 13:27:57 +0000 (13:27 +0000)]
comment

16 years agoannotation file format updated to take idColour and specify single colour groups...
jprocter [Fri, 18 Jul 2008 12:32:02 +0000 (12:32 +0000)]
annotation file format updated to take idColour and specify single colour groups with rgb triplets and names

16 years agoSequence label colour stored for each sequence group
jprocter [Fri, 18 Jul 2008 12:31:53 +0000 (12:31 +0000)]
Sequence label colour stored for each sequence group

16 years agoUser defined colourschemes are automatically generated from colour names or RGB colou...
jprocter [Fri, 18 Jul 2008 12:30:57 +0000 (12:30 +0000)]
User defined colourschemes are automatically generated from colour names or RGB colour triplets

16 years agoprevent exception when no default timeout is specified
jprocter [Fri, 18 Jul 2008 12:29:54 +0000 (12:29 +0000)]
prevent exception when no default timeout is specified

16 years agoensure annotationElements in non-graphical annotation objects do not automatically...
jprocter [Fri, 11 Jul 2008 15:07:03 +0000 (15:07 +0000)]
ensure annotationElements in non-graphical annotation objects do not automatically get values

16 years agojavadoc and constraint to ensure annotation labels are not wider than alignment frame
jprocter [Mon, 30 Jun 2008 10:49:49 +0000 (10:49 +0000)]
javadoc and constraint to ensure annotation labels are not wider than alignment frame

16 years agojava 1.1 compatibility
jprocter [Mon, 30 Jun 2008 09:50:27 +0000 (09:50 +0000)]
java 1.1 compatibility

16 years agotiming of 'on load' output before any gui thread operations
jprocter [Mon, 30 Jun 2008 09:50:13 +0000 (09:50 +0000)]
timing of 'on load' output before any gui thread operations

16 years agosafer retrieval of groovy scripts from URLs
jprocter [Mon, 30 Jun 2008 09:49:44 +0000 (09:49 +0000)]
safer retrieval of groovy scripts from URLs

16 years agoincluded includeGaps flag in clustalW colour calculation - behaviour for includeGaps...
jprocter [Mon, 30 Jun 2008 09:48:06 +0000 (09:48 +0000)]
included includeGaps flag in clustalW colour calculation - behaviour for includeGaps=false is not verified to match ClustalX as yet.

16 years agoadded URLEncoder.encode to properly escape CGI encoded arguments so they are safely...
jprocter [Thu, 26 Jun 2008 17:13:17 +0000 (17:13 +0000)]
added URLEncoder.encode to properly escape CGI encoded arguments so they are safely transmitted to the launchApp servlet.

16 years agolocal sequence properties are preserved in SeqCigar representation of sequence using...
jprocter [Mon, 23 Jun 2008 07:45:38 +0000 (07:45 +0000)]
local sequence properties are preserved in SeqCigar representation of sequence using SeqHash/SeqUnhash in jalview.analysis.SeqsetUtils. Ensures input data and alignment results from webservice have same visible names as original sequences input.

16 years agoUniprot is not actually a multi-acc capable source any more. see bug https://mantis...
jprocter [Mon, 26 May 2008 10:24:08 +0000 (10:24 +0000)]
Uniprot is not actually a multi-acc capable source any more. see bug https://mantis.lifesci.dundee.ac.uk/view.php?id=32464

16 years agobugfix so MULTI_ACC capable sources value property is actually used by DBRefFetcher
jprocter [Mon, 26 May 2008 10:23:30 +0000 (10:23 +0000)]
bugfix so MULTI_ACC capable sources value property is actually used by DBRefFetcher

16 years agominor bugfix for case when PDB sequence strings are not parsed and added new javascri...
jprocter [Mon, 26 May 2008 09:55:37 +0000 (09:55 +0000)]
minor bugfix for case when PDB sequence strings are not parsed and added new javascript API methods for getting selected sequences (https://mantis.lifesci.dundee.ac.uk/view.php?id=32977)

16 years agofixed Jalview project archive bug where alignment view is not written to Jar that...
jprocter [Mon, 12 May 2008 07:56:53 +0000 (07:56 +0000)]
fixed Jalview project archive bug where alignment view is not written to Jar that was introduced through refactoring JarEntry output code.

16 years agobugfix to avoid null pointer exceptions being raised for groups with no colourscheme...
jprocter [Fri, 2 May 2008 13:04:01 +0000 (13:04 +0000)]
bugfix to avoid null pointer exceptions being raised for groups with no colourscheme set.

16 years agofix for unicode char labels causing arrayOutOfBoundsException bug spotted by cameron...
jprocter [Thu, 1 May 2008 09:22:43 +0000 (09:22 +0000)]
fix for unicode char labels causing arrayOutOfBoundsException bug spotted by cameron weadicks

16 years agocomments and version wget ping timeout fix for when www connection is unavailable...
jprocter [Tue, 29 Apr 2008 10:53:40 +0000 (10:53 +0000)]
comments and version wget ping timeout fix for when www connection is unavailable due to proxy taking too long to respond

16 years agoadded SeqSearch service interface. Documented and refactored web service client ...
jprocter [Tue, 29 Apr 2008 10:51:04 +0000 (10:51 +0000)]
added SeqSearch service interface. Documented and refactored web service client (tbc - more refactors to come).

16 years agotrial fix for parsing NHX style trees to extract the bootstrap values
jprocter [Tue, 29 Apr 2008 10:15:04 +0000 (10:15 +0000)]
trial fix for parsing NHX style trees to extract the bootstrap values

16 years agopotential fix for hang on opening of application window when run in a proxied network...
jprocter [Fri, 25 Apr 2008 13:18:48 +0000 (13:18 +0000)]
potential fix for hang on opening of application window when run in a proxied network environment (splashscreen constructor blocks whilst jalview.jnlp is fetched)

16 years agotypo on Jalview help url
jprocter [Tue, 22 Apr 2008 10:14:34 +0000 (10:14 +0000)]
typo on Jalview help url

16 years agodocumented and refactored to facilitate headless feature file generation
jprocter [Mon, 21 Apr 2008 17:34:41 +0000 (17:34 +0000)]
documented and refactored to facilitate headless feature file generation

16 years agoadded centre column labels menu entry to format menu
jprocter [Mon, 21 Apr 2008 17:27:54 +0000 (17:27 +0000)]
added centre column labels menu entry to format menu

16 years agoadded centre annotation labels menu entry (and commented out SeqSearch web service...
jprocter [Mon, 21 Apr 2008 17:27:08 +0000 (17:27 +0000)]
added centre annotation labels menu entry (and commented out SeqSearch web service handler builder code)

16 years agocentrecolumnlabels format menu item and parameter added to applet
jprocter [Mon, 21 Apr 2008 17:19:03 +0000 (17:19 +0000)]
centrecolumnlabels format menu item and parameter added to applet

16 years agocastor debug option cleared
jprocter [Mon, 21 Apr 2008 17:18:05 +0000 (17:18 +0000)]
castor debug option cleared

16 years agobugfix for refactoring (webservice windows wouldn't open!!)
jprocter [Thu, 17 Apr 2008 16:37:47 +0000 (16:37 +0000)]
bugfix for refactoring (webservice windows wouldn't open!!)

16 years agojavadoc and refactor of setWebService method to allow headless client operation
jprocter [Thu, 17 Apr 2008 15:47:56 +0000 (15:47 +0000)]
javadoc and refactor of setWebService method to allow headless client operation

16 years agotodo for refactoring webservice GUI creation mechanism
jprocter [Thu, 17 Apr 2008 15:06:43 +0000 (15:06 +0000)]
todo for refactoring webservice GUI creation mechanism

16 years agojavadoc for webservice client tutorial
jprocter [Thu, 17 Apr 2008 15:06:02 +0000 (15:06 +0000)]
javadoc for webservice client tutorial

16 years agotodos
jprocter [Thu, 17 Apr 2008 15:04:16 +0000 (15:04 +0000)]
todos

16 years agojavadoc and quiet flag
jprocter [Thu, 17 Apr 2008 15:03:48 +0000 (15:03 +0000)]
javadoc and quiet flag

16 years agofix JPred thread so job aborts if submission fails.
jprocter [Fri, 11 Apr 2008 12:28:17 +0000 (12:28 +0000)]
fix JPred thread so job aborts if submission fails.

16 years agoquick fix for conservation calculation when residue ambiguity codes are used.
jprocter [Thu, 10 Apr 2008 13:01:31 +0000 (13:01 +0000)]
quick fix for conservation calculation when residue ambiguity codes are used.

16 years agobug fix for Features/Annotations file parameter parsing in JalviewLite reported and...
jprocter [Thu, 10 Apr 2008 12:56:32 +0000 (12:56 +0000)]
bug fix for Features/Annotations file parameter parsing in JalviewLite reported and fixed by Daron Standley and Reiko Yamashita. Also enhanced Jmol to allow  it to be used to view PDB files retrieved via Classloader in the Applet

16 years agofirst hack to get true DNA and Sequence highlighting from Structure mouseovers
jprocter [Sat, 8 Mar 2008 02:52:04 +0000 (02:52 +0000)]
first hack to get true DNA and Sequence highlighting from Structure mouseovers

16 years agocorrection to Jnet service documentation
jprocter [Sat, 8 Mar 2008 02:51:06 +0000 (02:51 +0000)]
correction to Jnet service documentation

16 years agosequenceId is a string, not an integer - allows generation of unlimited unique sequen...
jprocter [Sun, 24 Feb 2008 20:08:56 +0000 (20:08 +0000)]
sequenceId is a string, not an integer - allows generation of unlimited unique sequential sequence Ids

16 years agosequenceId is a string, not an integer - allows generation of unlimited unique sequen...
jprocter [Sun, 24 Feb 2008 19:52:19 +0000 (19:52 +0000)]
sequenceId is a string, not an integer - allows generation of unlimited unique sequential sequence Ids

16 years agosequenceId is a string, not an integer - allows generation of unlimited unique sequen...
jprocter [Fri, 22 Feb 2008 16:32:57 +0000 (16:32 +0000)]
sequenceId is a string, not an integer - allows generation of unlimited unique sequential sequence Ids

16 years agovalid format for writing test
jprocter [Fri, 22 Feb 2008 16:31:40 +0000 (16:31 +0000)]
valid format for writing test

16 years agoprobably unnecessary optimisation (SequenceGroup.addSequence is probably rate limitin...
jprocter [Fri, 22 Feb 2008 16:31:03 +0000 (16:31 +0000)]
probably unnecessary optimisation (SequenceGroup.addSequence is probably rate limiting step here)

16 years agoOn 'save' menu entry check to see if fileformat is a valid output format and open...
jprocter [Fri, 22 Feb 2008 16:29:56 +0000 (16:29 +0000)]
On 'save' menu entry check to see if fileformat is a valid output format and open save as dialog if it isn't.

16 years agoCDS segment index
jprocter [Fri, 22 Feb 2008 16:29:01 +0000 (16:29 +0000)]
CDS segment index

16 years agopossible fix for stockhom ss-annotation re-creation after it is saved to Jalview...
jprocter [Fri, 22 Feb 2008 16:28:47 +0000 (16:28 +0000)]
possible fix for stockhom ss-annotation re-creation after it is saved to Jalview project

16 years agoindex number for contiguous part of mapped sequence feature
jprocter [Fri, 22 Feb 2008 16:28:08 +0000 (16:28 +0000)]
index number for contiguous part of mapped sequence feature

16 years agojavadoc
jprocter [Fri, 22 Feb 2008 16:27:29 +0000 (16:27 +0000)]
javadoc

16 years agotypo for AXISLOGLEVEL constant
jprocter [Fri, 22 Feb 2008 15:38:06 +0000 (15:38 +0000)]
typo for AXISLOGLEVEL  constant

16 years agoexplicit quote of chaincode in errror message
jprocter [Fri, 22 Feb 2008 15:37:07 +0000 (15:37 +0000)]
explicit quote of chaincode in errror message

16 years agominor change to output of main method for testing file IO
jprocter [Tue, 29 Jan 2008 14:43:17 +0000 (14:43 +0000)]
minor change to output of main method for testing file IO

16 years agogroovy from stdin
jprocter [Tue, 29 Jan 2008 10:32:50 +0000 (10:32 +0000)]
groovy from stdin

16 years agomemory usage information and flag to indicate if warning dialog boxes should be raise...
jprocter [Tue, 29 Jan 2008 10:17:56 +0000 (10:17 +0000)]
memory usage information and flag to indicate if warning dialog boxes should be raised when problems occur.

16 years agoadd methods to read from current position of existing fileParse object.
jprocter [Tue, 29 Jan 2008 10:17:07 +0000 (10:17 +0000)]
add methods to read from current position of existing fileParse object.

16 years agoensure mark is set before identification is started.
jprocter [Tue, 29 Jan 2008 10:15:36 +0000 (10:15 +0000)]
ensure mark is set before identification is started.

16 years agoFileParse object can be re-used to read different files concatenated together
jprocter [Tue, 29 Jan 2008 10:15:09 +0000 (10:15 +0000)]
FileParse object can be re-used to read different files concatenated together

16 years agoflag to indicate if errors are raised as warning dialog boxes or not.
jprocter [Tue, 29 Jan 2008 10:12:51 +0000 (10:12 +0000)]
flag to indicate if errors are raised as warning dialog boxes or not.

16 years agoexplicitly allow access to showMemoryUsage flag in myDesktopPane
jprocter [Tue, 29 Jan 2008 10:12:17 +0000 (10:12 +0000)]
explicitly allow access to showMemoryUsage flag in myDesktopPane

16 years agojavadoc
jprocter [Tue, 29 Jan 2008 10:11:45 +0000 (10:11 +0000)]
javadoc

16 years agogroovy scripts can be read from stdin
jprocter [Tue, 29 Jan 2008 10:11:32 +0000 (10:11 +0000)]
groovy scripts can be read from stdin

16 years agoreinstated proper case insensitive searching for both upper and lower case
jprocter [Tue, 29 Jan 2008 09:16:28 +0000 (09:16 +0000)]
reinstated proper case insensitive searching for both upper and lower case

16 years agotimings and memory usage for reading in a file
jprocter [Tue, 22 Jan 2008 16:17:03 +0000 (16:17 +0000)]
timings and memory usage for reading in a file

16 years agomore efficient parsing of large files, do not create sequence features from GR annota...
jprocter [Tue, 22 Jan 2008 16:16:30 +0000 (16:16 +0000)]
more efficient parsing of large files, do not create sequence features from GR annotation positions with '.'

16 years agoensured that seqeunce feature shift takes into account start position difference...
jprocter [Tue, 22 Jan 2008 16:14:54 +0000 (16:14 +0000)]
ensured that seqeunce feature shift takes into account start position difference w.r.t. db seqeunce

16 years agonew method to get map of sequence positions corresponding to alignment columns
jprocter [Tue, 22 Jan 2008 16:14:19 +0000 (16:14 +0000)]
new method to get map of sequence positions corresponding to alignment columns

16 years agofix regex for annotation subtype to use non-whitespace presence rather than word...
jprocter [Mon, 21 Jan 2008 16:57:16 +0000 (16:57 +0000)]
fix regex for annotation subtype to use non-whitespace presence rather than word boundary tokens

16 years agojavadoc and main method for testing file input routines
jprocter [Mon, 21 Jan 2008 16:55:51 +0000 (16:55 +0000)]
javadoc and main method for testing file input routines

16 years agojavadoc
jprocter [Mon, 21 Jan 2008 16:55:36 +0000 (16:55 +0000)]
javadoc

16 years agodraft of 2.4 features in feature list
jprocter [Tue, 15 Jan 2008 14:05:29 +0000 (14:05 +0000)]
draft of 2.4 features in feature list

16 years agoadded groovy documentation to contents
jprocter [Fri, 11 Jan 2008 13:54:43 +0000 (13:54 +0000)]
added groovy documentation to contents

16 years agojalview memory monitor instructions added
jprocter [Fri, 11 Jan 2008 13:54:27 +0000 (13:54 +0000)]
jalview memory monitor instructions added

16 years agodesktop tools menu updated
jprocter [Fri, 11 Jan 2008 13:54:15 +0000 (13:54 +0000)]
desktop tools menu updated

16 years agogroovy and das fetching stuff in command line argument list
jprocter [Fri, 11 Jan 2008 13:54:03 +0000 (13:54 +0000)]
groovy and das fetching stuff in command line argument list

16 years agodocumentation for groovy console and basic groovy scripting support
jprocter [Fri, 11 Jan 2008 13:53:39 +0000 (13:53 +0000)]
documentation  for groovy console and basic groovy scripting support

16 years agoadded groovy argument for launching a groovy script from the command line
jprocter [Fri, 11 Jan 2008 13:52:16 +0000 (13:52 +0000)]
added groovy argument for launching a groovy script from the command line

16 years agomemory monitor, garbage collection and changed menu item for groovy console opening
jprocter [Fri, 11 Jan 2008 13:51:37 +0000 (13:51 +0000)]
memory monitor, garbage collection and changed menu item for groovy console opening

16 years agouniprotxml format comment (ebi changed service parameter)
jprocter [Fri, 21 Dec 2007 15:13:19 +0000 (15:13 +0000)]
uniprotxml format comment (ebi changed service parameter)

16 years agosource directory tree documentation
jprocter [Fri, 21 Dec 2007 15:08:45 +0000 (15:08 +0000)]
source directory tree documentation

16 years agoautomatic dbref fetching and sequence validation for arbitrary databases
jprocter [Fri, 21 Dec 2007 15:08:26 +0000 (15:08 +0000)]
automatic dbref fetching and sequence validation for arbitrary databases

16 years agofurther bugfix and annotation transfer for dna/protein (still issues with non-codon...
jprocter [Fri, 21 Dec 2007 15:06:06 +0000 (15:06 +0000)]
further bugfix and annotation transfer for dna/protein (still issues with non-codon translation mapping generation)

16 years agojavadoc and bugfix
jprocter [Fri, 21 Dec 2007 15:05:33 +0000 (15:05 +0000)]
javadoc and bugfix

16 years agosequence db fetcher and db reference validation/annotation transfer
jprocter [Fri, 21 Dec 2007 15:03:56 +0000 (15:03 +0000)]
sequence db fetcher and db reference validation/annotation transfer

16 years agosequence db fetcher metadata for multiple sequence fetch capacity
jprocter [Fri, 21 Dec 2007 15:02:36 +0000 (15:02 +0000)]
sequence db fetcher metadata for multiple sequence fetch capacity

16 years agotemporary bugfix ?
jprocter [Fri, 21 Dec 2007 15:00:13 +0000 (15:00 +0000)]
temporary bugfix ?

16 years agobugfix
jprocter [Fri, 21 Dec 2007 14:59:52 +0000 (14:59 +0000)]
bugfix

16 years agoequivalence for transferring/updating references
jprocter [Fri, 21 Dec 2007 14:59:49 +0000 (14:59 +0000)]
equivalence for transferring/updating references

16 years agobugfixes
jprocter [Fri, 21 Dec 2007 14:55:02 +0000 (14:55 +0000)]
bugfixes

16 years agoincorrect colour-by-sequence when gaps are present in alignment sequence and pdb...
jprocter [Tue, 18 Dec 2007 13:20:18 +0000 (13:20 +0000)]
incorrect colour-by-sequence when gaps are present in alignment sequence and pdb-sequence mapping start>1

16 years agojava 1.1 compatibility (again)
jprocter [Thu, 13 Dec 2007 17:47:45 +0000 (17:47 +0000)]
java 1.1 compatibility (again)

16 years agojava 1.1 compatibility (again)
jprocter [Thu, 13 Dec 2007 17:35:24 +0000 (17:35 +0000)]
java 1.1 compatibility (again)

16 years agonull pointer bugfix
jprocter [Fri, 30 Nov 2007 13:55:15 +0000 (13:55 +0000)]
null pointer bugfix