Commit 2b50c997 authored by Hyun Soo Kim's avatar Hyun Soo Kim
Browse files

add command for generating and adding proteins to database

parent cf2e2fbf

src/Main.java

+39 −3
Original line number Diff line number Diff line
@@ -4,11 +4,16 @@ import java.io.*; 
import java.net.ConnectException;

import java.net.ServerSocket;

import java.net.Socket;

import java.nio.file.*;

import java.nio.file.attribute.BasicFileAttributes;



public class Main {



    static MoleculeDatabase moleculeDb = null;

    static boolean verbose = false;

    static int MINUTE = 60 * 1000;



    public static ProteinFactory proteinFactory = ProteinFactory.getInstance();



    public static void initDb(String dbName) throws IOException {

        // Load the database
@@ -17,6 +22,7 @@ public class Main { 
        if (dbFile.exists()) {

            moleculeDb.load(dbName);

        }

        moleculeDb.name = dbName;

    }



    public static void printVerbose(String s) {
@@ -25,9 +31,10 @@ public class Main { 
        }

    }



    public static void commandHandler1(String cmd) {

    public static void commandHandler1(String cmd) throws IOException {

        switch (cmd) {

            case "--printDb":

                System.out.println(moleculeDb.name);

                moleculeDb.printDb();

                break;

            case "--verbose":
@@ -39,17 +46,46 @@ public class Main { 
                verbose = !verbose;

                moleculeDb.verbose = verbose;

                break;

            case "--manySimple":

                ProteinFactory.manySimpleProteins();

                break;

            case "--fewComplex":

                ProteinFactory.fewComplexProteins();

                break;

            case "--marco":

                System.out.println("polo");

                break;

            default:

                printVerbose("unrecognized command: " + cmd);

                break;

        }

    }



    public static void commandHandler2(String cmd, String moleculePath) {

    public static void addProteins(String proteinPath) throws IOException {

        Files.walkFileTree(Paths.get(proteinPath), new SimpleFileVisitor<>() {

            @Override

            public FileVisitResult visitFile(Path file, BasicFileAttributes attrs) {

                if (!Files.isDirectory(file)) {

                    moleculeDb.addMolecule(new Molecule(proteinPath + "/" +

                            file.getParent().toString() + "/" + file.getFileName().toString()));

                }

                return FileVisitResult.CONTINUE;

            }

        });

    }



    public static void commandHandler2(String cmd, String moleculePath) throws IOException {

        switch (cmd) {

            case "--addMolecule":

                moleculeDb.addMolecule(new Molecule(moleculePath));

                break;

            case "--addProteins":

                try {

                    addProteins(moleculePath);

                } catch (Exception e) {

                    System.err.println(e.getMessage());

                }

                break;

            case "--findMolecule":

                Molecule molecule = moleculeDb.findMolecule(new Molecule(moleculePath));

                if (molecule == null) {
@@ -153,7 +189,7 @@ public class Main { 
        } catch (ConnectException e) {

            // If a client connection fails, run the server side of the program

            ServerSocket serverSocket = new ServerSocket(PORT_NUMBER);

            serverSocket.setSoTimeout(60 * 1000);

            serverSocket.setSoTimeout(10 * MINUTE);



            // Set the default filename for the database

            String dbName = "molecule.db";