Details
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Type:
Bug
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Status: Open
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: 2.11.1.3
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Fix Version/s: None
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Component/s: jvdesktop
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Labels:None
Description
Stumbled across this.
Load example file estrogenReceptorCdna_aln.fa and Calculate | Translate as cDNA.
Now align the protein using e.g. TCoffee with defaults.
Realigned split frame fails to display, console has message and stack trace
Can't align cds as protein (length mismatch 1593/1594): EMBLCDS|ADZ17331
Exception in thread "Thread-33" java.lang.ArrayIndexOutOfBoundsException: 3039
at jalview.analysis.AlignmentUtils.alignCdsSequenceAsProtein(AlignmentUtils.java:1054)
at jalview.analysis.AlignmentUtils.alignCdsAsProtein(AlignmentUtils.java:916)
at jalview.datamodel.Alignment.alignAs(Alignment.java:1825)
at jalview.datamodel.Alignment.alignAs(Alignment.java:1786)
at jalview.ws.jws2.MsaWSThread.displayResults(MsaWSThread.java:988)
...
Load example file estrogenReceptorCdna_aln.fa and Calculate | Translate as cDNA.
Now align the protein using e.g. TCoffee with defaults.
Realigned split frame fails to display, console has message and stack trace
Can't align cds as protein (length mismatch 1593/1594): EMBLCDS|ADZ17331
Exception in thread "Thread-33" java.lang.ArrayIndexOutOfBoundsException: 3039
at jalview.analysis.AlignmentUtils.alignCdsSequenceAsProtein(AlignmentUtils.java:1054)
at jalview.analysis.AlignmentUtils.alignCdsAsProtein(AlignmentUtils.java:916)
at jalview.datamodel.Alignment.alignAs(Alignment.java:1825)
at jalview.datamodel.Alignment.alignAs(Alignment.java:1786)
at jalview.ws.jws2.MsaWSThread.displayResults(MsaWSThread.java:988)
...