cs321-project/GeneBankCreateBTree.java at master · aidanvanleuven/cs321-project · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
import java.io.BufferedReader;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.FileReader;
import java.io.RandomAccessFile;
import java.util.Scanner;
/*
 * This class is invoked and creates
 * @author davidMarcial nathanJones
 */
public class GeneBankCreateBTree
{
    public static BTree tree;
    public static File gbk;
    public static File fileName;
    public static int size = 4096;
    public static int degree = 0;
    public static final int MAX_SEQUENCE_LENGTH = 31;
    public static final int MIN_SEQUENCE_LENGTH = 1;
    public static int sequenceLength = 0;
    public static boolean cache;
    public static int cacheSize = 0;
    public static void main (String args[])
    {
        try
        {

        if (args.length < 4 || args.length > 6)
        {
            System.out.println("Incorrect number of arguments! Please use the following usage.");
            printUsage();
        }

        /*
         *read cache argument and set appropriately
         */
        cache = (Integer.parseInt(args[0]) == 1) ? true:false;

        /*
         * read degree argument and set appropriately
         */
        if(Integer.parseInt(args[1]) == 0)
        {
            degree = (size - 4)/ 32;
        }
        else
        {
            degree = Integer.parseInt(args[1]);
        }

        /*
         * read and set stringLength argument
         */
        int stringLength = Integer.parseInt(args[3]);
        if(stringLength >= MIN_SEQUENCE_LENGTH && stringLength <= MAX_SEQUENCE_LENGTH)
        {
            sequenceLength = stringLength;
        }
        else
        {
            System.out.println("The integer for the sequence length must be between 1 and 31 inclusive");
            printUsage();
        }

        /*
         * read and set file argument
         */
        String fileName = (args[2]);
        try
        {
            gbk = new File(fileName);
        }
        catch(NullPointerException e)
        {
            System.out.println("File does not exist " + gbk.toPath());
        }

        /*
         * TODO optional cache size argument
         */
        if(args.length>=5)
        {
        	cacheSize = Integer.parseInt(args[4]);
        }

        /*
         * Build the tree
         */
        tree = new BTree(degree,fileName,sequenceLength,cache, cacheSize);
        BufferedReader currentInput = new BufferedReader(new FileReader(gbk));
        String currentLine = currentInput.readLine();
        boolean start = false;
        boolean completeSequence = false;
        boolean containedSlash = false;
        while(currentLine != null)
        {

        	if(start && (currentLine.contains("N") || currentLine.contains("n"))) {
        		completeSequence = true;
        	}
            currentLine = currentLine.replaceAll("\\s","").replaceAll("\\d","").replaceAll("[Nn]","");

            if(containedSlash)
            {
            	completeSequence = true;
            	currentLine.replace("//", "");
            	containedSlash = true;
            }

            if(start == true && completeSequence && currentLine.length()>0)
            {
            	while(currentLine.length() >= sequenceLength) {
            		String tmp = currentLine.substring(0, sequenceLength);
            		tree.insert(TreeObject.sequenceToLong(tmp));
            		currentLine = currentLine.substring(1);
            		System.out.println(tmp);
            	}
            	completeSequence = false;
            	if(containedSlash) {
            		start = false;
            	}
            	System.out.println(currentLine);
            }

            if(currentLine.equals("ORIGI"))
            {
                start = true;
                currentLine = currentInput.readLine();
            }

            if(start) {
            	String curr = currentInput.readLine();
            	if(curr.contains("//")) {
            		curr = "";
            		containedSlash = true;
            	}
            	currentLine += curr;
            }
            else {
            	currentLine = currentInput.readLine();
            }
        }
        currentInput.close();

        /*
         * create dump file if requested
         */
        if(args.length==6)
        {
        	if(Integer.parseInt(args[5])==1)
        	{
        		File f = new File(fileName + ".btree.dump." + sequenceLength + "." + degree);
        		RandomAccessFile dump = new RandomAccessFile(f, "rw");

        	}
        }
    }
        catch(FileNotFoundException e)
        {
            System.out.println("File not found");
        }

        catch(IOException b)
        {

        }

    }

    public static void printUsage()
    {
        System.out.println("java GenebankCreateBTree <0/1(no/with Cache)> <degree> <gbk file> <sequence length> [<cache size>] [<debug level]>");
    }


}