在Java中将RNA序列转换为蛋白质的有效方法，以及arrayoutofbound错误

Below is my highly inefficient and non working code for converting RNA sequence to Protein:

下面是我将RNA序列转换为蛋白质的非常低效且无法工作的代码：

String translation(String temp)
{
    char[] result;
    int k=temp.length();
    int i=0;
    int z=0;
    char[] pro=new char[100];
    result=new char[temp.length()];
    result = temp.toCharArray();
    while(i<k-3)
    {
     char[] store;
     store=new char[1];
     store[0]=result[i];
     String tempstore1 = new String(store);
     store[0]=result[i+1];
     String tempstore2 = new String(store);
     store[0]=result[i+2];
     String tempstore3 = new String(store);
     String storefinal=tempstore1+tempstore2+tempstore3;

     if(storefinal.matches("UUU")||storefinal.matches("UUC"))
     {
         pro[z]='F';
         z++;
         continue;
     }
     if(storefinal.matches("UUA")||storefinal.matches("UUG")||storefinal.matches("CUU")||storefinal.matches("CUC")||storefinal.matches("CUA")||storefinal.matches("CUA")||storefinal.matches("CUG"))
     {
         pro[z]='L';
         z++;
         continue;
     }
     if(storefinal.matches("AUU")||storefinal.matches("AUC")||storefinal.matches("AUA"))
     {
         pro[z]='I';
         z++;
         continue;
     }
     if(storefinal.matches("AUG"))
     {
         pro[z]='M';
         z++;
         continue;
     }
     if(storefinal.matches("GUU")||storefinal.matches("GUC")||storefinal.matches("GUA")||storefinal.matches("GUG"))
     {
         pro[z]='V';
         z++;
         continue;
     }
     if(storefinal.matches("UCU")||storefinal.matches("UCC")||storefinal.matches("UCA")||storefinal.matches("UCG"))
     {
         pro[z]='S';
         z++;
         continue;
     }
     if(storefinal.matches("AGA")||storefinal.matches("AGG"))
     {
         pro[z]='R';
         z++;
         continue;
     }
     if(storefinal.matches("AGU")||storefinal.matches("AGC"))
     {
         pro[z]='S';
         z++;
         continue;
     }
     if(storefinal.matches("UGG"))
     {
         pro[z]='W';
         z++;
         continue;
     }
     if(storefinal.matches("UGU")||storefinal.matches("UGC"))
     {
         pro[z]='C';
         z++;
         continue;
     }
     if(storefinal.matches("GAA")||storefinal.matches("GAG"))
     {
         pro[z]='E';
         z++;
         continue;
     }
     if(storefinal.matches("GAU")||storefinal.matches("GAC"))
     {
         pro[z]='D';
         z++;
         continue;
     }
     if(storefinal.matches("AAA")||storefinal.matches("AAG"))
     {
         pro[z]='K';
         z++;
         continue;
     }
     if(storefinal.matches("AAU")||storefinal.matches("AAC"))
     {
         pro[z]='N';
         z++;
         continue;
     }
     if(storefinal.matches("CAA")||storefinal.matches("CAG"))
     {
         pro[z]='Q';
         z++;
         continue;
     }
     if(storefinal.matches("CAU")||storefinal.matches("CAC"))
     {
         pro[z]='H';
         z++;
         continue;
     }
     if(storefinal.matches("UAU")||storefinal.matches("UAC"))
     {
         pro[z]='Y';
         z++;
         continue;
     }
     if(storefinal.matches("CCG")||storefinal.matches("CCA")||storefinal.matches("CCC")||storefinal.matches("CCU"))
     {
         pro[z]='P';
         z++;
         continue;
     }
     if(storefinal.matches("ACG")||storefinal.matches("ACA")||storefinal.matches("ACC")||storefinal.matches("ACU"))
     {
         pro[z]='T';
         z++;
         continue;
     }
     if(storefinal.matches("GCG")||storefinal.matches("GCA")||storefinal.matches("GCC")||storefinal.matches("GCU"))
     {
         pro[z]='A';
         z++;
         continue;
     }
     if(storefinal.matches("CGG")||storefinal.matches("CGA")||storefinal.matches("CGC")||storefinal.matches("CGU"))
     {
         pro[z]='R';
         z++;
         continue;
     }
     if(storefinal.matches("GGG")||storefinal.matches("GGA")||storefinal.matches("GGC")||storefinal.matches("GGU"))
     {
         pro[z]='G';
         z++;
         continue;
     }
     if(storefinal.matches("UAG")||storefinal.matches("UAA")||storefinal.matches("UGA"))
     {
         pro[z]='.';
         z++;
         continue;
     }
     i++;
    }    
    String finalreturn = new String(pro);
 return finalreturn;
}

Now there are two problems associated with it:

现在有两个与之相关的问题：

1. It is not working(Array out of bound exception)
2. 它不起作用（Array out of bound of exception）
3. I cannot figure out how to manage the flanking unassociated redundant codes, which don't code for anything.
4. 我无法弄清楚如何管理侧翼无关联的冗余代码，它们不代码任何东西。

Is there any way I can use regex to solve this problem? (I mean like in perl) Edit : whole exception

有什么方法可以使用正则表达式来解决这个问题吗？ （我的意思是在perl中）编辑：整个异常

Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 100
at JSATS2.transcriplation.translation(transcriplation.java:197)
at JSATS2.TabExp.jButton7ActionPerformed(TabExp.java:835)
at JSATS2.TabExp.access$1100(TabExp.java:14)
at JSATS2.TabExp$12.actionPerformed(TabExp.java:599)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.Component.processMouseEvent(Component.java:6527)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
at java.awt.Component.processEvent(Component.java:6292)
at java.awt.Container.processEvent(Container.java:2234)
at java.awt.Component.dispatchEventImpl(Component.java:4883)
at java.awt.Container.dispatchEventImpl(Container.java:2292)
at java.awt.Component.dispatchEvent(Component.java:4705)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)
at java.awt.Container.dispatchEventImpl(Container.java:2278)
at java.awt.Window.dispatchEventImpl(Window.java:2739)
at java.awt.Component.dispatchEvent(Component.java:4705)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:746)
at java.awt.EventQueue.access$400(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:697)
at java.awt.EventQueue$3.run(EventQueue.java:691)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)
at java.awt.EventQueue$4.run(EventQueue.java:719)
at java.awt.EventQueue$4.run(EventQueue.java:717)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:716)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

3 个解决方案

#1

To increase speed I would use a static Map for all available codons

为了提高速度，我会对所有可用的密码子使用静态Map

Use a StringBuilder to build your finalresult

使用StringBuilder构建最终结果

Be sure that your String input is a multiple of 3

确保您的String输入是3的倍数

Be sure that every triplet corresponds to a valid codon

确保每个三联体对应一个有效的密码子

private static final Map<String, Character> codonsMap;
static
{
    codonsMap = new HashMap<String, Character>();
    codonsMap.put("UUU", 'F');
    codonsMap.put("UUC", 'F');
    codonsMap.put("UUA", 'L');
    //and so on for all codons
}

//be sure that length of temp is a multiple of 3 and that every 3 characters correspond to a valid codon
public String translation(String temp)
{
    //Use StringBuilder for adding Characters, it is by far faster than adding chars to a mutable String
    StringBuilder finalreturn = new StringBuilder();
    String codon;       
    for (int i = 0; i < temp.length() - 2; i++) {
        codon = temp.substring(i, i+3);
        finalreturn.append(codonsMap.get(codon));
    }
    return finalreturn.toString();
}

#2

First, you can build the substring in one go with the substring() method. Then, you can build the output with a StringBuilder. Finally, you can use a switch statement, which makes the code more readable. The result looks like this:

首先，您可以使用substring（）方法一次构建子字符串。然后，您可以使用StringBuilder构建输出。最后，您可以使用switch语句，这使代码更具可读性。结果如下：

static String translation (String rna) {
    StringBuilder sb = new StringBuilder();

    for (int i = 0; i < rna.length() - 2; i++) {
        String triplet = rna.substring(i, i+3);

        switch (triplet) {
        case "UUU":
        case "UUC":
            sb.append("F");
            break;
        case "UUA":
        case "UUG":
        case "CUU":
        case "CUC":
        case "CUA":
        case "CUG":
            sb.append("L");
            break;
        case "AUU":
        case "AUC":
        case "AUA":
            sb.append("I");
            break;
        case "AUG":
            sb.append("M");
            break;
        case "GUU":
        case "GUC":
        case "GUA":
        case "GUG":
            sb.append("V");
            break;
            // and so on
        default:
            // do nothing;
        }           
    }       

    return sb.toString();
}

public static void main(String[] args) {
    System.out.println(translation("UUCGUGAUU"));
}

Also, I am not sure if incrementing i by one unit is really what you want since I don't know anything in this area, maybe it should be incremented by 3 if a translation is made ?

另外，我不确定是否一个单位增加i真的是你想要的，因为我在这个领域什么都不知道，如果翻译的话，它应该增加3？

As a final remark, this question would possibly be more at home on the Code Review Stack Exchange.

作为最后的评论，这个问题可能在Code Review Stack Exchange上更为重要。

#3

The reason why you are getting an ArrayIndexOutOfBoundsException is because you do not increase your the index variable i. Therefore you keep repeating for the first three characters.

您获得ArrayIndexOutOfBoundsException的原因是因为您没有增加索引变量i。因此，您不断重复前三个字符。

The underlying reason is that when you use "continue" you continue with the next iteration of the while loop. And because you only increment i after all possible matches, you will never reach this statement. Therefore try putting the increment just before the big if-then-else statement.

根本原因是，当您使用“继续”时，您将继续执行while循环的下一次迭代。而且因为你只在所有可能的匹配后增加i，所以你永远不会达到这个声明。因此，请尝试在大if-then-else语句之前添加增量。

Also, you might want to increment by 3, and loop while i is smaller than or equal to k -3.

此外，您可能希望增加3，并在i小于或等于k -3时循环。

A suggestion to reduce some of the unnessecary code would be:

减少一些不必要的代码的建议是：

public static String translation(String temp) {
    int i = 0;
    String result = "";
    while (i <= temp.length() - 3) {
    String triplet = temp.substring(i,i+=3);
        if (triplet.equals("UUU") || triplet.equals("UUC"))
            result += 'F';
        if (triplet.equals("UUA") || triplet.equals("UUG")
                || triplet.equals("CUU") || triplet.equals("CUC")
                || triplet.equals("CUA") || triplet.equals("CUA")
                || triplet.equals("CUG"))
            result += 'L';
        if (triplet.equals("AUU") || triplet.equals("AUC")
                || triplet.equals("AUA"))
            result += 'I';
        if (triplet.equals("AUG"))
            result += 'M';
        if (triplet.equals("GUU") || triplet.equals("GUC")
                || triplet.equals("GUA") || triplet.equals("GUG"))
            result += 'V';
        if (triplet.equals("UCU") || triplet.equals("UCC")
                || triplet.equals("UCA") || triplet.equals("UCG"))
            result += 'S';
        if (triplet.equals("AGA") || triplet.equals("AGG"))
            result += 'R';
        if (triplet.equals("AGU") || triplet.equals("AGC"))
            result += 'S';
        if (triplet.equals("UGG"))
            result += 'W';
        if (triplet.equals("UGU") || triplet.equals("UGC"))
            result += 'C';
        if (triplet.equals("GAA") || triplet.equals("GAG"))
            result += 'E';
        if (triplet.equals("GAU") || triplet.equals("GAC"))
            result += 'D';
        if (triplet.equals("AAA") || triplet.equals("AAG"))
            result += 'K';
        if (triplet.equals("AAU") || triplet.equals("AAC"))
            result += 'N';
        if (triplet.equals("CAA") || triplet.equals("CAG"))
            result += 'Q';
        if (triplet.equals("CAU") || triplet.equals("CAC"))
            result += 'H';
        if (triplet.equals("UAU") || triplet.equals("UAC"))
            result += 'Y';
        if (triplet.equals("CCG") || triplet.equals("CCA")
                || triplet.equals("CCC") || triplet.equals("CCU"))
            result += 'P';
        if (triplet.equals("ACG") || triplet.equals("ACA")
                || triplet.equals("ACC") || triplet.equals("ACU"))
            result += 'T';
        if (triplet.equals("GCG") || triplet.equals("GCA")
                || triplet.equals("GCC") || triplet.equals("GCU"))
            result += 'A';
        if (triplet.equals("CGG") || triplet.equals("CGA")
                || triplet.equals("CGC") || triplet.equals("CGU"))
            result += 'R';
        if (triplet.equals("GGG") || triplet.equals("GGA")
                || triplet.equals("GGC") || triplet.equals("GGU"))
            result += 'G';
        if (triplet.equals("UAG") || triplet.equals("UAA")
                || triplet.equals("UGA"))
            result += '.';
    }
    return result;
}