[Biojava-l] Display components of an assembly (contig) multilined

[Matthew Pocock]

Hi,

Wrap the renderer for the contigs in a BumpedRenderer. This will spread 
them over multiple lines.

Matthew

f.maiwald at nexgo.de wrote:
> 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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