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 contextdnaMoleculeArchive
: 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 moleculeReturns: 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 pixelsReturns: This builder for method chaining |
setBorderHeight(int height) |
Set the border height around the DNA molecule in pixels. Parameters: height - Border height in pixelsReturns: 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.