Dna Archive Region

The DnaArchiveMoleculeRegionBuilder class extracts regions from DNA molecules stored in a DnaMoleculeArchive. It provides a flexible way to extract a bounded region around a DNA molecule for further processing or visualization.

Constructor

DnaArchiveMoleculeRegionBuilder(Context context, DnaMoleculeArchive dnaMoleculeArchive)

Creates a new builder for extracting DNA molecule regions.

Parameters:

context: The SciJava context
dnaMoleculeArchive: The archive containing the DNA molecules

Methods

Setting the Molecule

Method	Description
`setMolecule(DnaMolecule dnaMolecule)`	Set the molecule to use for region extraction. Returns: This builder for method chaining
`setMolecule(String UID)`	Set the molecule to use by its UID. Parameters: `UID` - The unique identifier of the molecule Returns: This builder for method chaining

Setting Border Size

Method	Description
`setBorderWidth(int width)`	Set the border width around the DNA molecule in pixels. Parameters: `width` - Border width in pixels Returns: This builder for method chaining
`setBorderHeight(int height)`	Set the border height around the DNA molecule in pixels. Parameters: `height` - Border height in pixels Returns: This builder for method chaining

Building the Region

Method	Description
`build()`	Extracts the region around the DNA molecule. The region is defined by the `Dna_Top_X1`, `Dna_Top_Y1`, `Dna_Bottom_X2`, and `Dna_Bottom_Y2` parameters of the DNA molecule, with added borders. Returns: An `ImgPlus<?>` containing the extracted region
`getMontage()`	Get the built image (same as returned by `build()`). Returns: The `ImgPlus<?>` containing the extracted region

Example Usage

// Create the builder
DnaArchiveMoleculeRegionBuilder regionBuilder = 
    new DnaArchiveMoleculeRegionBuilder(context, archive);

// Configure and build
ImgPlus<?> imgPlus = regionBuilder
    .setMolecule("moleculeUID")
    .setBorderWidth(10)
    .setBorderHeight(10)
    .build();

Implementation Details

The class uses the MarsIntervalExporter to export an interval from the archive that contains the DNA molecule. The interval is computed based on the DNA molecule’s top and bottom coordinates with added borders.