Details
-
Type: Bug
-
Status: Closed
-
Priority: Major
-
Resolution: Not A Bug
-
Affects Version/s: 2.11.3.3
-
Fix Version/s: 2.11.4.0
-
Component/s: None
-
Labels:
-
Environment:Jalview 2.11.3.3 and Java version 8 update 241
Description
I use a groovy script to highlight peptides in a sequence alignment. It reads a txt file and and basically searches peptides and colours them differently.
This worked fine for a long time, but now out of a sudden, the script reports problems in the import commands.
I can't remember updating either Jalview nor Java, but the problem is now on different computers where the script worked fine before.
The error message is:
groovy.lang.MissingPropertyException: No such property: currentAlignFrame for class: jalview.bin.Jalview
Possible solutions: currentAlignFrame
at highlight_peptides.run(highlight_peptides.groovy:6)
And the groovy script:
import jalview.util.ColorUtils
import jalview.datamodel.SequenceFeature
import jalview.schemes.FeatureColour
import jalview.analysis.Finder
def af = jalview.bin.Jalview.currentAlignFrame
def av = af.viewport
def fr = af.featureRenderer
def finder = new Finder(av)
new File("/Users/user/Downloads/jalview/motifs.txt").eachLine
{
line ->
if (!line.startsWith('#'))
{
tokens = line.split("\\t")
motif = tokens[0]
featureName = tokens[1]
featureColour = ColorUtils.parseColourString(tokens[2])
featureScore = (tokens.length < 4 ? 0 : Float.parseFloat(tokens[3]))
fr.setColour(featureName, new FeatureColour(featureColour))
finder.findAll(motif, false, false, false)
matches = finder.searchResults.results
matches.each
{
sf = new SequenceFeature(featureName, motif, it.start, it.end, featureScore, null)
it.sequence.addSequenceFeature(sf)
}
}
}
av.setShowSequenceFeatures(true)
af.alignPanel.paintAlignment(false, false)
So, somehow the currentAlignFrame is no longer available?
Where can I get some help on this issue and where is the best place to ask?
Thanks in advance
Mario
This worked fine for a long time, but now out of a sudden, the script reports problems in the import commands.
I can't remember updating either Jalview nor Java, but the problem is now on different computers where the script worked fine before.
The error message is:
groovy.lang.MissingPropertyException: No such property: currentAlignFrame for class: jalview.bin.Jalview
Possible solutions: currentAlignFrame
at highlight_peptides.run(highlight_peptides.groovy:6)
And the groovy script:
import jalview.util.ColorUtils
import jalview.datamodel.SequenceFeature
import jalview.schemes.FeatureColour
import jalview.analysis.Finder
def af = jalview.bin.Jalview.currentAlignFrame
def av = af.viewport
def fr = af.featureRenderer
def finder = new Finder(av)
new File("/Users/user/Downloads/jalview/motifs.txt").eachLine
{
line ->
if (!line.startsWith('#'))
{
tokens = line.split("\\t")
motif = tokens[0]
featureName = tokens[1]
featureColour = ColorUtils.parseColourString(tokens[2])
featureScore = (tokens.length < 4 ? 0 : Float.parseFloat(tokens[3]))
fr.setColour(featureName, new FeatureColour(featureColour))
finder.findAll(motif, false, false, false)
matches = finder.searchResults.results
matches.each
{
sf = new SequenceFeature(featureName, motif, it.start, it.end, featureScore, null)
it.sequence.addSequenceFeature(sf)
}
}
}
av.setShowSequenceFeatures(true)
af.alignPanel.paintAlignment(false, false)
So, somehow the currentAlignFrame is no longer available?
Where can I get some help on this issue and where is the best place to ask?
Thanks in advance
Mario