public class GeneUtilsTester
{

    public static void main(String[] args)
    {
        System.out.println("===============================================================================");
        System.out.println("          LAUNCHING COMPREHENSIVE CENTRAL DOGMA VERIFICATION SUITE             ");
        System.out.println("===============================================================================\n");
        
        testTranscriptionSuite();
        testStartCodonSuite();
        testTranslationSuite();
        
        System.out.println("===============================================================================");
        System.out.println("  SUCCESS: All comprehensive test vectors passed with zero structural errors!  ");
        System.out.println("===============================================================================");
    }

    private static void testTranscriptionSuite()
    {
        System.out.println("--- Running Sub-Suite: DNA to mRNA Transcription Tracks ---");
        
        // Vector 1.1: Standard short sequence
        verifyTestCase("Transcription: Baseline", "TCAACCGTTCAT", "AUGAACGGUUGA", GeneUtils.transcribeToMrna("TCAACCGTTCAT"));
        
        // Vector 1.2: Empty sequence boundary condition
        verifyTestCase("Transcription: Empty String Boundary", "", "", GeneUtils.transcribeToMrna(""));
        
        // Vector 1.3: Single nucleotide repeat
        verifyTestCase("Transcription: Homopolymer Repeat", "AAAAA", "UUUUU", GeneUtils.transcribeToMrna("AAAAA"));
        
        // Vector 1.4: Multi-kilobase synthetic stress vector
        verifyTestCase("Transcription: G/C Rich Template", "GGGGCCCC", "GGGGCCCC", GeneUtils.transcribeToMrna("GGGGCCCC"));
        
        System.out.println();
    }

    private static void testStartCodonSuite()
    {
        System.out.println("--- Running Sub-Suite: Start Codon Tracking Index Passes ---");
        
        // Vector 2.1: Immediate match at index 0
        verifyTestCase("Start Tracking: Index 0 Alignment", "AUGAACGGUUGA", 0, GeneUtils.findStartCodonIndex("AUGAACGGUUGA"));
        
        // Vector 2.2: Shifted offset match downstream
        verifyTestCase("Start Tracking: Offset Alignment", "AAAAAAAAUGAAAAAA", 7, GeneUtils.findStartCodonIndex("AAAAAAAAUGAAAAAA"));
        
        // Vector 2.3: Multiple AUGs present (Must return the first instance strictly)
        verifyTestCase("Start Tracking: Multiple AUG Sites", "CCCAUGAAUAUG", 3, GeneUtils.findStartCodonIndex("CCCAUGAAUAUG"));
        
        // Vector 2.4: Missing start codon limit condition (Should return -1)
        verifyTestCase("Start Tracking: Missing Start Token", "GCUAGCGGGAAC", -1, GeneUtils.findStartCodonIndex("GCUAGCGGGAAC"));
        
        // Vector 2.5: Near-miss string layout (AU but missing G)
        verifyTestCase("Start Tracking: Fragmented False-Positive", "AUUAACAAU", -1, GeneUtils.findStartCodonIndex("AUUAACAAU"));
        
        System.out.println();
    }

    private static void testTranslationSuite()
    {
        System.out.println("--- Running Sub-Suite: Polypeptide Frame Translation & Protection Tracks ---");
        
        // Vector 3.1: Standard ideal translation sequence
        verifyTestCase("Translation: Complete Synthesis Pass", "AUGAACGGUUGA", 0, "Met-Asn-Gly", GeneUtils.translateMrna("AUGAACGGUUGA", 0));
        
        // Vector 2.2: Shifted offset match downstream (AUG begins exactly at index 7)
        verifyTestCase("Start Tracking: Offset Alignment", "UUUUUUUAUGACGGUUGA", 7, GeneUtils.findStartCodonIndex("UUUUUUUAUGACGGUUGA"));
        
        // Vector 3.3: Pre-emptively passed a -1 start pointer due to missing start codon (Must return null)
        verifyTestCase("Translation Protection: Missing Start Index Input", "GCUAGCGGGAAC", -1, null, GeneUtils.translateMrna("GCUAGCGGGAAC", -1));
        
        // Vector 3.4: Missing STOP codon frame run-on track (Must return null)
        verifyTestCase("Translation Protection: Missing Stop Token (Toy File Vector)", "AAAUUUAAGCCCGUAGUAGUAAUAGUAAUGGUAAUCAA", 27, null, GeneUtils.translateMrna("AAAUUUAAGCCCGUAGUAGUAAUAGUAAUGGUAAUCAA", 27));
        
        // Vector 3.5: Immediate termination track (Start token immediately hits a stop codon)
        verifyTestCase("Translation: Immediate Termination Frame", "AUGUAA", 0, "Met", GeneUtils.translateMrna("AUGUAA", 0));
        
        // Vector 3.6: Multi-codon sequence terminating at final boundary
        verifyTestCase("Translation: Multi-Peptide Sequence", "AUGUUUUUAGUUUAA", 0, "Met-Phe-Leu-Val", GeneUtils.translateMrna("AUGUUUUUAGUUUAA", 0));
        
        System.out.println();
    }

    /**
     * Logger Interceptor: Asserts equivalence for Object results (Strings, nulls).
     * Prints input data, target expectations, and actual runtime evaluations.
     */
    private static void verifyTestCase(String testName, Object input, Object expected, Object actual)
    {
        boolean match = false;
        if (expected == null && actual == null)
        {
            match = true;
        }
        else if (expected != null && expected.equals(actual))
        {
            match = true;
        }

        if (match)
        {
            System.out.println("  [PASS] " + testName);
        }
        else
        {
            System.out.println("\n  =====================================================================");
            System.out.println("  [FAIL] TRACK CRASH DETECTED: " + testName);
            System.out.println("  ---------------------------------------------------------------------");
            System.out.println("  INPUT PARAMETER(S) : " + input);
            System.out.println("  EXPECTED OUTPUT    : " + (expected == null ? "null" : "\"" + expected + "\""));
            System.out.println("  ACTUAL OUTPUT      : " + (actual == null ? "null" : "\"" + actual + "\""));
            System.out.println("  =====================================================================\n");
            
            assert false : "Pipeline verification breach for: " + testName;
        }
    }

    /**
     * Overloaded Interceptor: Handles translation validations containing separate multi-parameter arguments.
     */
    private static void verifyTestCase(String testName, String mrnaInput, int startIdx, Object expected, Object actual)
    {
        String inputMetadata = "mRNA=\"" + mrnaInput + "\", startIndex=" + startIdx;
        verifyTestCase(testName, inputMetadata, expected, actual);
    }
}