user generated file does not get displayed correctly(?)

Dear Jalview Team,

I am trying to use Jalview with an user generated feature/annotation file. However, I get the following errors:

  1. For the BAR_GRAPH command, only the histogram bars get displayed (not the labels below the histogram).

  2. For the SEQUENCE_GROUP/PROPERTIES commands, it seems that nothing gets loaded into Jalview.

I am running Jalview on a Mac OS X 10.6 (I also tried on Windows XP with similar results). I was very careful in using tab delimited values and I have tried different possibilities assuming that Jalview may not parse correctly dashes or other symbols.

I really like Jalview and I would like to be able to import my annotations, but so far I was not able to go very far.

I pasted a shortened version of the sequence and feature/annotation files below. I can provide anyone with the original fasta and feature/annotation files. As an additional test, to make sure I am using thre proper format, I have tried to export the features and reload them - when the BAR_GRAPHs get reloaded the histogram labels do not get displayed correctly.

I would really appreciate if you can give me any type of feedback.

Thank you so much,
Andrea

···

Fasta file:
^^^^^^^^^

SEQ1
----MSFSGK
SEQ2
----MAFDST
SEQ3
–MVDAFLGT


Features file:
^^^^^^^^^^^^
JALVIEW_ANNOTATION

Created: Fri Mar 19 16:17:33 PDT 2010

BAR_GRAPH Mutants1 Description1 -,1.2,[00ff00]|-,1.2,[00ff00]|-,1.2,[00ff00]|-,1.2,[00ff00]|-,1.2,[00ff00]|-,1.2,[00ff00]|-,1.2,[00ff00]|-,1.2,[00ff00]|-,1.2,[00ff00]|-,1.2,[00ff00]|

BAR_GRAPH Mutants2 Description2 M,12.0,[4d0000]|-,[4d0000]|-,5.0,[4d0000]|1,1.0,[5d1500]|5,5.0,[9e6800]|3,3.0,[7d3f00]|8,8.0,[cea700]|3,3.0,[7d3f00]|8,8.0,[cea700]|6,6.0,[ae7d00]|

SEQUENCE_GROUP JGroup:0 4 4 -1 *
PROPERTIES JGroup:0 colour=% Identity outlineColour=a00000 displayBoxes=true displayText=true colourText=true

SEQUENCE_GROUP JGroupA 6 6 -1 1-3
PROPERTIES JGroupA colour=% Identity outlineColour=a0ff00 displayBoxes=true displayText=true colourText=true


Dear Andrea.

Thanks for reposting the email about your problems with the annotations format -
I've verified what you observed using the image attached to your original mail - and have some fixes for you.

I am trying to use Jalview with an user generated feature/annotation file. However, I get the following errors:

1) For the BAR_GRAPH command, only the histogram bars get displayed (not the labels below the histogram).

This is a problem with the annotationFile parser. If you try out the jalview development version (http://www.jalview.org/versions.html), you'll find that your annotation rows now get displayed with the labels.

2) For the SEQUENCE_GROUP/PROPERTIES commands, it seems that nothing gets loaded into Jalview.

This was actually a problem with your annotation file. The SEQUENCE_GROUP lines should be:

SEQUENCE_GROUP JGroup:0 4 4 *
SEQUENCE_GROUP JGroupA 6 6 1-3

In both cases, you had a '-1' in the 5th column - which indicates to Jalview that it should expect the 6th column to contain a series of comma separated sequence ID strings (ie SEQ1,SEQ2,SEQ3).

As an additional test, to make sure I am using thre proper format, I have tried to export the features and reload them - when the BAR_GRAPHs get reloaded the histogram labels do not get displayed correctly.

Regarding the importing of exported annotation - there has been an inconsistency in the jalview annotations file parser and generator for a number of jalview releases and I am trying to resolve this for the next major jalview release. Your files were very helpful - since they exhibited a couple of subtle bugs in both the parser and the file emitter! If you can, I suggest you try using the jalview development version until the next release.

Cheers
Jim.

···

On 22/03/2010 16:39, Andrea Rossi wrote:

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