Details
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Type:
Bug
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Status: Open
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Priority:
Minor
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Resolution: Unresolved
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Affects Version/s: 2.10.3
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Fix Version/s: None
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Component/s: Datamodel
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Labels:None
Description
Load uniref50.fa and make a group of 3 sequences.
Select any sequence in the group and Edit | Cut (or Delete).
Right-click in the group and Output to Textbox as Fasta.
No output produced, ArrayIndexOutOfBoundsException in the console.
Cause: the list of sequences in SequenceGroup still includes the deleted sequences. SequenceGroup.size() returns 3 but getSequencesInOrder(alignment) (intersection) returns 2 sequences.
This is one symptom, there may be others.
Note the group consensus calculation does calculate correctly: AAFrequency.calculate() receives the deleted sequence, but it has zero length, so is ignored in the calculation.
Is this a bug or by design?
If sequence were to be deleted from any sequence groups as well, would want to ensure that Undo restored it...
Select any sequence in the group and Edit | Cut (or Delete).
Right-click in the group and Output to Textbox as Fasta.
No output produced, ArrayIndexOutOfBoundsException in the console.
Cause: the list of sequences in SequenceGroup still includes the deleted sequences. SequenceGroup.size() returns 3 but getSequencesInOrder(alignment) (intersection) returns 2 sequences.
This is one symptom, there may be others.
Note the group consensus calculation does calculate correctly: AAFrequency.calculate() receives the deleted sequence, but it has zero length, so is ignored in the calculation.
Is this a bug or by design?
If sequence were to be deleted from any sequence groups as well, would want to ensure that Undo restored it...