Bioinformatics/Subsequence: Difference between revisions
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=={{header|Phix}}== |
=={{header|Phix}}== |
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Note: match_all() is due to become a builtin in the next release, so the version below may or may not need renaming/deleting before it will run. |
Note: match_all() is due to become a builtin in the next release, so the version below may or may not need renaming/deleting before it will run.<br> |
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Currently only searches for non-overlapped sequences, but it should be pretty obviuous how to change that, in which case the next underline will simply partially overwrite the previous, so you'll get eg "<=<==>". |
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<lang Phix>constant cheat = false |
<lang Phix>constant cheat = false |
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end procedure |
end procedure |
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function match_all(object needle, sequence haystack) |
function match_all(object needle, sequence haystack, bool bOverlap = false) |
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if atom(needle) then return find_all(needle,haystack) end if |
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integer start = 1 |
integer start = 1 |
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sequence res = {} |
sequence res = {} |
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if start=0 then exit end if |
if start=0 then exit end if |
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res = append(res,start) |
res = append(res,start) |
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start += length(needle) |
start += iff(bOverlap?1:length(needle)) |
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end while |
end while |
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return res |
return res |
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