slightly larger window edit name/desc
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edit annotation name/description
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Can edit annotation name/description
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Consensus, conservation, quality labels may have changed
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aligned not used
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Dont export annotations if not visible
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Unique name for new group and treegroup
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Adjust features when cutting and pasting
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make new dataset seq if residues deleted
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copy feature: check for null values
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aligned not used
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Check valid residues in ss
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Check seqs in group exist in this alignment
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Any character non aa or nucleotide is a space
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moved painting routine
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consensusColouring never used
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Draw helices correctly
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Use util toHexString
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Output groups in annotation file
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Dont clear graphics g before drawing the image
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Image for labels, stops flickering
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New view copies annotations across
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Tooltips for group names, descriptions
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Description added
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SequenceGroup parsing added to annotation file
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ID_ITALICS option in preferences
47 lines of code changed in:
scaleAbove, left and right set when tab selection changes
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Marios annotation bug fixed
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AnnotationId is hashcode of object
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Only set the sequence oncecvs diff datamodel/Alignment.java
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Adjusts annotations for sequence edits
69 lines of code changed in:
If its null, set tip empty
0 lines of code changed in:
preliminary documentation for DNA->protein codon features and EMBL coding region parsing
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added doc for PDBResNum features
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Command takes alignment, not gapChar
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Annotations move when full alignment edited
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Annotation adjustment moved to EditCommand
125 lines of code changed in:
Remove unneccessary lines
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AlignmentAnnotations require id
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Allow for hidden columns
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Only output visible annotations
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load/get Annotation
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Remove unnecessary line
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Output annotations
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1.1 enabled
273 lines of code changed in:
reinstating class implementation.
1525 lines of code changed in:
checks for irreflexive mapping in main tester
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Conservation etc have autoCalculated flag set true
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AdjustAnnotations needs position, number and insert
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This constructor is never called
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Features output for javascript
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output now takes alignment, not just sequences
49 lines of code changed in:
Extension to fastaFile for myhits
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refactored to use jalview.analysis.Finder for searching alignment.
432 lines of code changed in:
kkv change
278 lines of code changed in:
Map arbitrary series of non-overlapping integer intervals on one range to another on another range - with an integer ratio for each range
278 lines of code changed in:
Page setup added
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boolean for internal copies
8 lines of code changed in:
Hidden representatives moved from sequence to viewport
312 lines of code changed in:
refactoring (added seqIndex/resIndex state for incremental search)
39 lines of code changed in:
refactored search algorithm from gui classes
235 lines of code changed in:
transfer resnum features now returns features (could be passed to feature renderer)
4 lines of code changed in:
reoganization of PDB sequence fetching for sequence annotation generated by PDBFile
84 lines of code changed in:
PDBChain maintains reference to dataset of sequences created by PDBfile reader.
30 lines of code changed in:
datasetSequence derive method and some checks
41 lines of code changed in:
export features/annotations not for import
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Applet can output and load annotations, features
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Neeed to know protocol for annotation loading
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Need to know protocol to load anntotations
0 lines of code changed in:
javadoc
8 lines of code changed in:
added sequence feature copy constructor.
260 lines of code changed in:
transfer and update of sequenceFeatures for associated alignment sequence
fixed mapping bug for sequences that do not start at 1.
673 lines of code changed in:
random ';'
181 lines of code changed in:
transfer and update of sequenceFeatures for associated alignment sequence
179 lines of code changed in:
fixed last-residue bug and added sequence feature creation and transfer for resNum+insCode annotation for each sequence residue
302 lines of code changed in:
added resNum+insCode string field for truly unambiguous PDB atom entry referencing/display
4 lines of code changed in:
Add the last sequence before annotations
4 lines of code changed in:
Take scrollOffset into account
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Tool tip for annotation description
285 lines of code changed in:
Set description on copy
7 lines of code changed in:
Set tooltip
3 lines of code changed in:
1.1 enabled
7 lines of code changed in:
put vamsas bit back in
47 lines of code changed in:
File Parsing returns Alignments, not Sequence[]
140 lines of code changed in:
Is secondary structure label modified
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Display description
12 lines of code changed in:
Descriptions can be added to annotations
0 lines of code changed in:
Edit name/description added to applet
60 lines of code changed in:
Fit to Window bug fixed
12 lines of code changed in:
made atom attributes public (rather than put in get/set pairs)
62 lines of code changed in:
Dont set the font of alignFrameMenubarcvs update appletgui/AlignFrame.java
0 lines of code changed in:
Send new sequences when firing alignment changed
11 lines of code changed in:
Reads in anything following seq id as a description
14 lines of code changed in:
HEADER and ATOM must be position 0
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