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basic implementation of profile display and todos
[jalview.git]
/
src
/
jalview
/
datamodel
/
2009-08-21
jprocter
basic implementation of profile display and todos
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commitdiff
2009-08-21
jprocter
todo
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commitdiff
2009-07-24
jprocter
implement new insert annotation row method and ensure...
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commitdiff
2009-07-24
jprocter
insert annotation at specific position
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2009-07-24
jprocter
optional sequencegroup ref for annotation row
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commitdiff
2009-07-24
jprocter
sequence groups carry their own conservation and consen...
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commitdiff
2009-06-24
jprocter
fix to cope with EMBL records containing a CDS fragment...
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commitdiff
2009-06-19
jprocter
parent db references and mappings added to retrieved...
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commitdiff
2009-06-19
jprocter
intersect did not intersect (used in selection listener)
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commitdiff
2009-06-08
jprocter
apply gpl development license
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commitdiff
2009-06-01
jprocter
apply method for a NodeTransform to nodes in a tree
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commitdiff
2009-06-01
jprocter
javadoc
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commitdiff
2009-04-14
jprocter
patch to fix occasional arrayoutofbounds exception...
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commitdiff
2009-02-24
jprocter
bugfix for occasional nullpointer exceptions when selec...
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commitdiff
2009-02-06
jprocter
showUnconserved group attribute
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commitdiff
2008-12-19
jprocter
avoid null pointer exception when groupName is not set
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commitdiff
2008-12-19
jprocter
left and right justify method
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commitdiff
2008-12-05
jprocter
support for multiple accession retrieval from a databas...
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commitdiff
2008-11-12
jprocter
jdk1.2 compatibility
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commitdiff
2008-11-12
jprocter
new copy constructor and intersect method
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commitdiff
2008-11-12
jprocter
involvesSequence to check if searchResults intersect...
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commitdiff
2008-11-12
jprocter
javadoc and new method to get alignment sequence index...
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commitdiff
2008-11-04
jprocter
beginning of implementation of new properties for hide...
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commitdiff
2008-09-04
jprocter
merge from 2_4_Release branch
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commitdiff
2008-08-20
jprocter
tooltip displays formatted annotation row description...
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commitdiff
2008-08-15
jprocter
safer copy constructor
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commitdiff
2008-08-06
jprocter
getDBRefs now always returns DBRefArray if it exists...
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commitdiff
2008-07-18
jprocter
allow findSeq to begin *after* a given sequence in...
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commitdiff
2008-07-18
jprocter
Sequence label colour stored for each sequence group
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commitdiff
2008-06-23
jprocter
local sequence properties are preserved in SeqCigar...
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commitdiff
2008-05-01
jprocter
fix for unicode char labels causing arrayOutOfBoundsExc...
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commitdiff
2008-02-22
jprocter
CDS segment index
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commitdiff
2008-02-22
jprocter
possible fix for stockhom ss-annotation re-creation...
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commitdiff
2008-02-22
jprocter
index number for contiguous part of mapped sequence...
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commitdiff
2008-02-22
jprocter
javadoc
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commitdiff
2008-01-22
jprocter
new method to get map of sequence positions correspondi...
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commitdiff
2007-12-21
jprocter
sequence db fetcher metadata for multiple sequence...
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commitdiff
2007-12-21
jprocter
temporary bugfix ?
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commitdiff
2007-12-21
jprocter
bugfix
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commitdiff
2007-12-21
jprocter
equivalence for transferring/updating references
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commitdiff
2007-11-30
jprocter
null pointer bugfix
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commitdiff
2007-11-30
jprocter
javadoc and transferAnnotation method
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commitdiff
2007-11-30
jprocter
case insensitive matching of database ids
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commitdiff
2007-11-30
jprocter
case invariant matching of seqeunce feature to sequence...
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commitdiff
2007-11-16
jprocter
javadoc
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commitdiff
2007-11-08
jprocter
end must be greater than blockstart
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commitdiff
2007-10-31
jprocter
javadoc
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commitdiff
2007-10-31
jprocter
fix parsing of embl entries like S75919 which have...
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commitdiff
2007-10-24
jprocter
ensure PDB ids are updated on the dataset sequence
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commitdiff
2007-10-04
jprocter
refactored invertColumnSelection as an object method
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commitdiff
2007-10-02
jprocter
convenience constructor for duplicating an annotation...
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commitdiff
2007-10-02
jprocter
javadoc and operator for editing AlignmentAnnotation...
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commitdiff
2007-10-02
jprocter
javadoc
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commitdiff
2007-09-29
jprocter
updatePDBEntry method to add any PDBEntry from the...
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commitdiff
2007-09-29
jprocter
friendlier sequence names for protein products
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commitdiff
2007-09-06
jprocter
args for emblfile parser main method
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commitdiff
2007-08-30
jprocter
moved dataset sequence creation onto sequence method
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commitdiff
2007-08-30
jprocter
create dataset sequence method
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commitdiff
2007-08-30
jprocter
removed autogenerated todo
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commitdiff
2007-08-24
jprocter
dataset alignments have a reference count which must...
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commitdiff
2007-08-24
jprocter
todo comments
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commitdiff
2007-08-22
jprocter
added failsafe fix for cases where null sequence names...
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commitdiff
2007-07-31
jprocter
debugging cross references and duplicate sequence db...
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commitdiff
2007-07-30
jprocter
javadoc
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commitdiff
2007-07-25
jprocter
uniprot synonym
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commitdiff
2007-07-13
jprocter
more semantic groupings of dbs
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commitdiff
2007-07-13
jprocter
debugged mappings and translated sequence recovery
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commitdiff
2007-07-13
jprocter
preliminary states for pca distribution io
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commitdiff
2007-07-13
jprocter
preliminary methods for detecting internal sequence...
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commitdiff
2007-07-13
jprocter
bugfix
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commitdiff
2007-07-13
jprocter
mapping bug fixes
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commitdiff
2007-07-13
jprocter
basic idea for recognising that a feature is a coding...
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commitdiff
2007-06-17
jprocter
AlignedCodonFrame holds mapping information between...
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commitdiff
2007-06-17
jprocter
searchresult highlighting on common dataset or specific...
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commitdiff
2007-06-17
jprocter
correct construction of new dataset sequence when resid...
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commitdiff
2007-06-17
jprocter
javadoc
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commitdiff
2007-05-28
jprocter
prototype DBRef and Feature Type semantics (for annotat...
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commitdiff
2007-05-28
jprocter
fix compact annotation array routine
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commitdiff
2007-05-28
jprocter
castor mapping unmarshalling logging
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commitdiff
2007-05-10
jprocter
ensure that only annotation referenced in given alignme...
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commitdiff
2007-05-10
jprocter
bugfix on copy only referenced annotation in copy const...
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commitdiff
2007-05-10
jprocter
fixed array index out of bounds when not removing align...
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commitdiff
2007-05-07
amwaterhouse
tIndex prevented deletion of last annotation
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commitdiff
2007-05-02
jprocter
feature locations are retrieved by associated accession...
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commitdiff
2007-05-02
jprocter
feature locations are retrieved by associated accession...
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commitdiff
2007-05-02
jprocter
documentation and proxy call to util.MapList.getToWord...
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commitdiff
2007-05-02
jprocter
only return non-empty subsequences when getting selecti...
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commitdiff
2007-05-02
jprocter
subsequence bound checks and constructor for selectivel...
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commitdiff
2007-05-02
jprocter
return flag indicating if annotations were actually...
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commitdiff
2007-05-02
jprocter
checks for negative start column in restrict
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commitdiff
2007-05-02
amwaterhouse
Padgaps is false by default
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commitdiff
2007-05-01
amwaterhouse
Pad gaps method
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commitdiff
2007-05-01
jprocter
javadoc
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commitdiff
2007-05-01
jprocter
removeAlignmentAnnotation only removes annotation objec...
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commitdiff
2007-04-30
jprocter
pad should leave null annotations array null
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commitdiff
2007-04-30
jprocter
convenient creation of 'score only' annotation.
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commitdiff
2007-04-27
amwaterhouse
padGaps moved
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commitdiff
2007-04-27
jprocter
getProperties returns nullk for no properties
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commitdiff
2007-04-27
jprocter
documentation and getProperties method
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commitdiff
2007-04-26
jprocter
get annotation by label string
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