[Jalview-discuss] user generated file does not get displayed correctly(?)

[Andrea Rossi]

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
__________________
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