Selecting Arbitrary Nth Column in Syntax

[ababaian]

Selecting Arbitrary Nth Column in Syntax

[ababaian]

Even simpler version with an open-ended scope for all columns greater then 5.

Robust Nth Column Selection

%YAML 1.2
---
name: faidx
file_extensions: [fa.fai,fasta.fai]
scope: source.faidx

# Fasta Index Filetype Description
# NAME  Name of this reference sequence
# LENGTH  Total length of this reference sequence, in bases
# OFFSET  Offset within the FASTA file of this sequence's first base
# LINEBASES The number of bases on each line
# LINEWIDTH The number of bytes in each line, including the newline

contexts:
  main:
    # COLUMN 1
    - match: '^[\S]*\t'
      scope: coord.Chr.faidx
      push: col2

  col2:
    # COLUMN 2
    - match: '[\S]*'
      scope: coord.Start.faidx
    - match: \t
      push: col3
    - match: $
      pop: true

  col3:
    # COLUMN 3
    - match: '[\S]*'
      scope: constant.numeric.faidx
    - match: \t
      push: col4
    - match: $
      pop: true

  col4:
    # COLUMN 4
    - match: '[\S]*'
      scope: comment.line.faidx
    - match: \t
      push: col5
    - match: $
      pop: true

  col5:
    # COLUMN 5
    - match: '[\S]*'
      scope: comment.line.faidx
    - match: \t
      push: colast
    - match: $
      pop: true

  colast:
    # Any COLUMN >5
    - match: .*
      scope: comment.line.faidx
      pop: true

[cpan-chu]

This is really cool.

I think it looks pretty robust as it is. Though, would it work for files with >5 columns? Might need to do some figuring out on how to encode the 5th column if there is a 6th column. Maybe something along the lines of '(?<=\t[\S]\t)[\S]\t'?

[cpan-chu]

brilliant!

[ababaian]

I think this same logic could be applied for gedit and Vim syntax as well. There is a Match Start // Match End logic which can be extended in this way. I would say if we figure this out soon we'll simplify our lives greatly.

Maybe read some syntax highlighting files for other complex langauges (C / XML etc...) to learn how other people solved similar problems.

[Ebedthan]

Can we get a screenshot of what it looks like @ababaian ?

[ababaian]

[Ebedthan]

Please can you give me the colors you used to do this colors scheme?

[ababaian]

I'd say let's not worry 100% about all the color schemes just yet. This was based off of bioMonokai for Sublime which is dark background. Gedit is based off of Kate and is light background so it might not work. The third column is simply the default 'numeric' color, fourth + fifth are comment colored.

We're going to have to formalize all the colors and/or set one dark one light theme to make the same for all the different programs. We can worry about this last; now we need the syntax files to work reliably for all the different software as the highest priority.

[ababaian]

Also faidx-gedit syntax

Check out Fasta Index Language File for an example of the logic. It's the same thing as in sublime / less where nested contexts can be used to select by column. This should make SAM/VCF/BED/GTF files much much easier to deal with.