Structure statistics

Structure Statistics

The RNAStatisticsCalculator class exposes static methods to analyze an RNAFile. Import them statically for concise usage:

import static it.unicam.cs.bdslab.rna2dformatIO.tarnas.model.utils.RNAStatisticsCalculator.*;

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Available Methods

Method	Returns	Requires sequence?
getNucleotideCount(file)	Total number of nucleotides	❌
getBondCount(file)	Total number of weak bonds	❌
getACount(file)	Count of adenine (A) bases	✅
getCCount(file)	Count of cytosine (C) bases	✅
getGCount(file)	Count of guanine (G) bases	✅
getUCount(file)	Count of uracil (U) bases	✅
getGcBonds(file)	Number of G-C bonds	✅
getAuBonds(file)	Number of A-U bonds	✅
getGuBonds(file)	Number of G-U bonds	✅

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Usage Example

RNAFile file = io.loadFile(Path.of("structure.bpseq"));
 
System.out.println("Total nucleotides : " + getNucleotideCount(file));
System.out.println("Total bonds       : " + getBondCount(file));
System.out.println("GC bonds          : " + getGcBonds(file));
System.out.println("AU bonds          : " + getAuBonds(file));
System.out.println("GU bonds          : " + getGuBonds(file));
System.out.println("A count           : " + getACount(file));
System.out.println("C count           : " + getCCount(file));
System.out.println("G count           : " + getGCount(file));
System.out.println("U count           : " + getUCount(file));

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Limitations

Methods that require the nucleotide sequence return 0 when the format does not carry one:

Format	Sequence-dependent methods
DB_NO_SEQUENCE	Return 0
AAS_NO_SEQUENCE	Return 0
FASTA	Return 0 (no bond data either)

Statistics CSVs generated via saveFiles use these same methods and will contain 0 for the affected columns.

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See Also

• Saving Files — generate statistics CSV on save
• Supported Formats
• Home