Details
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Type:
Bug
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Status: Resolved
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Priority:
Critical
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Resolution: Fixed
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Affects Version/s: 2.8
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Fix Version/s: 2.8.0b1
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Component/s: file format issue
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Labels:None
Description
An intuitive interpretation of the 'combine' statement in alignment annotation files is that each statement combines the given set of alignment annotation rows into one overlaid group.
The annotation file below demonstrates this, but in version 2.8, results in a single grouped annotation row:
#Comment lines follow the hash symbol
JALVIEW_ANNOTATION
SEQUENCE_REF FER1_MESCR 5
BAR_GRAPH Bar Graph 1 <html>an <em>html tooltip</em> for Bar graph 1.</html> ||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
LINE_GRAPH Green Values 1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
LINE_GRAPH Red Values 2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
LINE_GRAPH Blue Values 0|0|0|1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2
LINE_GRAPH Yellow Values 3.0|3.0|3.0|2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2
BAR_GRAPH Bar Graph 2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
NO_GRAPH Icons ||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
NO_GRAPH Purple Letters m|y|p|r|o|t|e|i|n
COLOUR Bar Graph 2 blue
COLOUR Red Values 255,0,0
COLOUR Green Values green
COLOUR Blue Values blue
COLOUR Yellow Values yellow
COLOUR Purple Letters 151,52,228
COMBINE Green Values Red Values
COMBINE Blue Values Yellow Values
GRAPHLINE Red Values 2.6 threshold black
SEQUENCE_GROUP Group_A 30 50 *
SEQUENCE_GROUP Group_B 1 351 2-5
SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0
PROPERTIES Group_B outlineColour=red
PROPERTIES Group_C colour=Clustal
The annotation file below demonstrates this, but in version 2.8, results in a single grouped annotation row:
#Comment lines follow the hash symbol
JALVIEW_ANNOTATION
SEQUENCE_REF FER1_MESCR 5
BAR_GRAPH Bar Graph 1 <html>an <em>html tooltip</em> for Bar graph 1.</html> ||-100,-|-200,-|-300,-|-400,-|200,+|300,+|150,+
LINE_GRAPH Green Values 1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2|2.1|-1.1|3.2
LINE_GRAPH Red Values 2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2|-1.1|1.1|3.2
LINE_GRAPH Blue Values 0|0|0|1.1|2.2|1.3|3.4|0.7|1.4|3.3|2.2
LINE_GRAPH Yellow Values 3.0|3.0|3.0|2.1|3.2|1.3|-1.4|5.5|1.4|1.3|4.2
BAR_GRAPH Bar Graph 2 1,.|2,*|3,:|4,.|5,*|4,:|3,.|2|1|1|2|3|4|5|4
NO_GRAPH Icons ||||E,Sheet1|E|E||||H,Sheet 2|H|H|H||||||
NO_GRAPH Purple Letters m|y|p|r|o|t|e|i|n
COLOUR Bar Graph 2 blue
COLOUR Red Values 255,0,0
COLOUR Green Values green
COLOUR Blue Values blue
COLOUR Yellow Values yellow
COLOUR Purple Letters 151,52,228
COMBINE Green Values Red Values
COMBINE Blue Values Yellow Values
GRAPHLINE Red Values 2.6 threshold black
SEQUENCE_GROUP Group_A 30 50 *
SEQUENCE_GROUP Group_B 1 351 2-5
SEQUENCE_GROUP Group_C 12 14 -1 seq1 seq2 seq3
PROPERTIES Group_A description=This is the description colour=Helix Propensity pidThreshold=0 outlineColour=red displayBoxes=true displayText=false colourText=false textCol1=black textCol2=black textColThreshold=0
PROPERTIES Group_B outlineColour=red
PROPERTIES Group_C colour=Clustal
Attachments
Issue Links
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JAL-1294 Cannot export and re-import IUPred protein disorder predictions as annotation file
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- Resolved
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