Commit 48dadd41 authored by Hyun Soo Kim's avatar Hyun Soo Kim
Browse files

more printouts when making proteins, no longer singleton

parent 0dbf87bb

src/ProteinFactory.java

+22 −30
Original line number Diff line number Diff line
@@ -3,26 +3,7 @@ import java.util.ArrayList; 


public class ProteinFactory {



    private static ProteinFactory INSTANCE;



    private ProteinFactory() {

        ALANINE.symbol1 = "A";

        CYSTEINE.symbol1 = "C";

        GLYCINE.symbol1 = "G";

        ISOLEUCINE.symbol1 = "I";

        LEUCINE.symbol1 = "L";

        METHIONINE.symbol1 = "M";

        PROLINE.symbol1 = "P";

        SERINE.symbol1 = "S";

        THREONINE.symbol1 = "T";

        VALINE.symbol1 = "V";

    }



    public static ProteinFactory getInstance() {

        if (INSTANCE == null) {

            INSTANCE = new ProteinFactory();

        }

        return INSTANCE;

    public ProteinFactory() {

    }



    static final AminoAcid ALANINE;
@@ -63,6 +44,19 @@ public class ProteinFactory { 
        }

    }



    static public void initAminoAcids() {

        ALANINE.symbol1 = "A";

        CYSTEINE.symbol1 = "C";

        GLYCINE.symbol1 = "G";

        ISOLEUCINE.symbol1 = "I";

        LEUCINE.symbol1 = "L";

        METHIONINE.symbol1 = "M";

        PROLINE.symbol1 = "P";

        SERINE.symbol1 = "S";

        THREONINE.symbol1 = "T";

        VALINE.symbol1 = "V";

    }



    static final int AMINO_ACID_COUNT = 10;



    static public class AminoAcid {
@@ -155,14 +149,6 @@ public class ProteinFactory { 
            terminusC = newTerminusC;

        }



        public void print() {

            System.out.println(atomCount);

            System.out.println(atomBuffer);

            System.out.println(bondList);

            System.out.println(terminusC);

            System.out.println(complete);

        }



        public void write(String folderName) throws IOException {

            BufferedWriter writer = new BufferedWriter(new FileWriter(folderName + "/" + name + ".txt"));

            writer.write(name + "\n");
@@ -281,13 +267,16 @@ public class ProteinFactory { 
        for (int ii = 0; ii < 100; ii++) {

            System.out.println(ii + "% done generating simple proteins (< 137 atoms)");

            File simpleDirNested = new File(simpleDir, "simple" + ii);

            simpleDirNested.mkdirs();

            if (simpleDirNested.mkdirs()) {

                System.out.println("made new directory: " + simpleDirNested);

            }

            for (int jj = 0; jj < 100000; jj++) {

                Protein protein = generateProtein(simpleIdx, 7);

                protein.write(simpleDirNested.toString());

                simpleIdx++;

            }

        }

        System.out.println("done");

    }



    public static void fewComplexProteins() throws IOException {
@@ -296,7 +285,9 @@ public class ProteinFactory { 
        for (int ii = 0; ii < 10; ii++) {

            System.out.println(ii + "0% done generating complex proteins (>= 10006 atoms)");

            File complexDirNested = new File(complexDir, "complex" + ii);

            complexDirNested.mkdirs();

            if (complexDirNested.mkdirs()) {

                System.out.println("made new directory: " + complexDirNested);

            }

            for (int jj = 0; jj < 1000; jj++) {

                Protein protein = generateProtein(complexIdx, 1429);

                protein.name = "protein" + complexIdx;
@@ -304,6 +295,7 @@ public class ProteinFactory { 
                complexIdx++;

            }

        }

        System.out.println("done");

    }



    public static void main(String[] args) throws IOException {