BioJava Protein Model

import java.util.ArrayList;
import java.util.List;
import java.util.Objects;

/**
 * Represents a functional domain within a protein sequence.
 * This class models common data found in databases like Pfam or InterPro.
 */
class ProteinDomain {
    private final String domainId;
    private final String name;
    private final int startPosition;
    private final int endPosition;

    /**
     * Constructs a ProteinDomain object.
     * @param domainId Unique identifier for the domain (e.g., Pfam accession).
     * @param name Descriptive name of the domain (e.g., 'Kinase domain').
     * @param startPosition 1-based start index in the protein sequence.
     * @param endPosition 1-based end index in the protein sequence.
     */
    public ProteinDomain(String domainId, String name, int startPosition, int endPosition) {
        if (startPosition <= 0 || endPosition <= 0 || startPosition > endPosition) {
            throw new IllegalArgumentException("Invalid domain positions.");
        }
        this.domainId = domainId;
        this.name = name;
        this.startPosition = startPosition;
        this.endPosition = endPosition;
    }

    // Standard getter methods
    public String getDomainId() { return domainId; }
    public String getName() { return name; }
    public int getStartPosition() { return startPosition; }
    public int getEndPosition() { return endPosition; }

    @Override
    public String toString() {
        return String.format("%s (%s): %d-%d", name, domainId, startPosition, endPosition);
    }
}

/**
 * Represents a complete protein model, including its sequence and annotated domains.
 * This structure is suitable for integration into BioJava's core object model.
 */
public class ProteinModel {
    private final String accession;
    private final String sequence;
    private final List<ProteinDomain> domains;

    /**
     * Constructs a ProteinModel.
     * @param accession Unique protein identifier (e.g., UniProt ID).
     * @param sequence The full amino acid sequence (1-letter code).
     */
    public ProteinModel(String accession, String sequence) {
        this.accession = Objects.requireNonNull(accession, "Accession cannot be null.");
        this.sequence = Objects.requireNonNull(sequence, "Sequence cannot be null.");
        this.domains = new ArrayList<>();
    }

    /**
     * Adds a functional domain to the protein model.
     * Ensures the domain coordinates are valid relative to the sequence length.
     * @param domain The ProteinDomain object to add.
     * @return True if the domain was added successfully, false otherwise.
     */
    public boolean addDomain(ProteinDomain domain) {
        if (domain.getEndPosition() > this.sequence.length()) {
            System.err.println("Error: Domain ends at " + domain.getEndPosition() + 
                               " which is beyond sequence length " + this.sequence.length());
            return false;
        }
        return domains.add(domain);
    }

    // Standard getter methods
    public String getAccession() { return accession; }
    public String getSequence() { return sequence; }
    public int getLength() { return sequence.length(); }
    public List<ProteinDomain> getDomains() { return new ArrayList<>(domains); } // Return a copy

    /**
     * Provides a summary of the protein model.
     */
    public void summarize() {
        System.out.println("----------------------------------------");
        System.out.println("Protein Accession: " + accession);
        System.out.println("Sequence Length: " + getLength());
        System.out.println("Sequence Snippet: " + sequence.substring(0, Math.min(sequence.length(), 40)) + "...");
        System.out.println("Annotated Domains (" + domains.size() + "):");

        if (domains.isEmpty()) {
            System.out.println("  No domains annotated.");
        } else {
            for (ProteinDomain domain : domains) {
                System.out.println("  - " + domain);
            }
        }
        System.out.println("----------------------------------------");
    }

    // Example Main Method to Demonstrate Usage
    public static void main(String[] args) {
        
        // UniProt P00517: Proto-oncogene tyrosine-protein kinase Src
        String srcAccession = "P00517";
        String srcSequence = "MGSSKSKPKDASQRRRESLVRITRGLYGLTWNSSLDVLRDNAPVLYLPPEEGLCYCNPIAEQYRLYGEIKSPFRERLSEEEERLTLL" +
                             "SEELSDELARVLVDESHKPGIVLTGWQPLSDPLVTLLQAPQLWQLNPDTYQYSLRGYRTLSSVDAEEALRDIK";
        
        ProteinModel srcProtein = new ProteinModel(srcAccession, srcSequence);
        
        // Domain 1: SH3 domain (start-stop 50-100)
        ProteinDomain sh3 = new ProteinDomain("PF00018", "SH3 domain", 50, 100);
        // Domain 2: SH2 domain (start-stop 105-180)
        ProteinDomain sh2 = new ProteinDomain("PF00017", "SH2 domain", 105, 180);
        
        srcProtein.addDomain(sh3);
        srcProtein.addDomain(sh2);
        
        // Attempt to add an invalid domain (ends beyond sequence length)
        ProteinDomain invalidDomain = new ProteinDomain("PFXXXXX", "Invalid Test", 200, 500);
        srcProtein.addDomain(invalidDomain); // This should print an error

        srcProtein.summarize();
        // 
    }
}