Dear all,
i would like to display the component sequences of assemblies (contigs) in one line
each.
The contig is produced in an EMBL like format from several tables of an oracle
database and
then imported via SeqIOTools.readEMBL().
The sequences in the resulting SequenceIterator are of type SimpleSequence and cannot
be
casted to SimpleAssembly. (I cannot determine a priori, if the sequence is an assembly
at
all. So, constructing an Assembly via e.g a temporary file does not work either.)
The component sequences appear as normal features like in this example:
ID 945136
AC CONTIG1;
DE |
FT EST_CONTIG complement(1..156)
FT /childID="907559"
FT /childAccNbr="AccNo1"
FT /description="desc 1"
FT EST_CONTIG complement(196..416)
FT /childID="916188"
FT /childAccNbr="AccNo2"
FT /description="desc 2"
FT EST_CONTIG complement(4..527)
FT /childID="910809"
FT /childAccNbr="AccNo 3"
FT /description="desc 3"
FT EST_CONTIG complement(407..509)
FT /childID="911471"
FT /childAccNbr="AccNo 4"
FT /description="desc 4"
SQ SEQUENCE
...
//
I tried RectangularBeadRenderer and setBeadDisplacement(10.0) but that only seems to
add
some padding to the complete renderer line.
To make the story short:
Can anyone hint me on a class or technique that results in a display like this ?
\
+---------+ |
|child 1 | |
+---------+ |
|
+---------------+ |
|child 2 | |- Renderer line
+---------------+ |
|
+--------------------------------+ |
|child 3 | |
+--------------------------------+ /
Thanks
Frank
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