获得字符串中多个特定单词的所有索引

Question

我在大学的生物信息学课程上有一个项目，其中一个项目是基因预测。

我今天的问题是如何获得一个字符串中多个特定单词的所有索引。例如，在我的例子中，我想找到所有出现的开始密码子("AUG")和停止密码子("UAA","UAG", "UGA")，并使用它们预测基因，简单地尝试做开放阅读框(ORF)

这是我的初始代码:

private void jButton3ActionPerformed(java.awt.event.ActionEvent evt) {                                         
    // TODO add your handling code here:
    //   textArea1.setText(null);
    String str = jTextField1.getText(), y = "", gene = "", dnax = "", text = "";
    SymbolList dna = null;
    int start_codon_index = -1, stop_codon_index = -1;
if ("".equals(str)) {
    jTextArea1.setText("No DNA strand entered.. ");
} else {
    if (checksum(str) == 100) {
        try {
            dna = DNATools.createDNA(str);
        } catch (IllegalSymbolException ex) {
            Logger.getLogger(m.class.getName()).log(Level.SEVERE, null, ex);
        }
        try {
            dna = DNATools.toRNA(dna);
        } catch (IllegalAlphabetException ex) {
            Logger.getLogger(m.class.getName()).log(Level.SEVERE, null, ex);
        }
        dnax = dna.seqString().toUpperCase();
        if (dnax.length() % 3 != 0) {
            if (dnax.length() % 3 == 1) {
                dnax += "-";
            }
            if (dnax.length() % 3 == 2) {
                dnax += "-";
            }
        }
        //  System.out.println(dnax);
        for (int g = 0; g < dnax.length(); g += 3) {
            y = dnax.substring(g, g + 3);
            if ("AUG".equals(y)) {
                start_codon_index = g;
            } else if (start_codon_index != -1 && ("UGA".equals(y) || "UAG".equals(y) || "UAA".equals(y))) {
                stop_codon_index = g + 3;
            }
        }
        if (stop_codon_index != -1 && start_codon_index != -1) {
            String k = "";
            int a = 0;
            for (a = start_codon_index; a < stop_codon_index; a++) {
                gene += dnax.charAt(a);
            }
            text += "nGene start position:  " + start_codon_index + "nGene end position:  " + a + "n Gene: " + gene;
            jTextArea1.setText(text);
        } else {
            jTextArea1.setText("No genes found in Seq: " + dnax);
        }
    } else {
        jTextArea1.setText("Text entered is not a DNA strand..");
    }
}
}

下面是checksum()方法:

private static int checksum(String x) {
    int i = 0, checks = 0, count = 0;
    char c;
    x = x.toUpperCase();
    while (i < x.length()) {
        c = x.charAt(i);
        if (c == 'A' || c == 'T' || c == 'G' || c == 'C' || c == '-') {

    count++;
    }
    i++;
}
try {
    checks = (count / x.length()) * 100;
} catch (Exception e) {
    e.printStackTrace();
}
return checks;
}

我已经尝试了其他的解决方法，但都不适合我。欢迎任何帮助/建议

Answer 1

我想你是在问如何找到这些特定密码子的索引?您要检查的字符串是什么?

你可以用indexOf(String str, int fromIndex)。如果没有找到子字符串，则返回-1。

所以像这样的东西可能会有帮助，

List<Integer> startCodonIndices = new ArrayList<Integer>();
int index;
for (int i=0; i+3<dnax.length(); i++) {
    index = indexOf("AUG", i);
    startCodonIndices.add(index);
}

Answer 2

这是我根据您的建议在我的代码中更改和添加的内容:

 for (int i = 0; i + 3 < dnax.length(); i++) {
                    index = indexOf("AUG", i);
                    startCodonIndices.add(index);
                }
                List stopCodonIndices = new ArrayList();
                int i2, i3, i4;
                for (int j = 0; j + 3 < dnax.length(); j++) {
                    i2 = indexOf("UGA", j);
                    i3 = indexOf("UAA", j);
                    i4 = indexOf("UAG", j);
                    stopCodonIndices.add(i2);
                    stopCodonIndices.add(i3);
                    stopCodonIndices.add(i4);
                }
                for (int n = 0; n < dnax.length(); n++) {
                    for (int k = 0; k < startCodonIndices.size() - 1; k++) {
                        for (int h = 0; h < stopCodonIndices.size() - 1; h++) {
                            gene = dnax.substring(k, h);
                            jTextArea1.append("n" + gene);
                        }
                    }
                }

Seq=ATGACCTGA的结果:

A
AU
AUG
AUGA
AUGAC
AUGACC
AUGACCU
AUGACCUG
AUGACCUGA

错误:

Exception in thread "AWT-EventQueue-0" java.lang.StringIndexOutOfBoundsException: String index out of range: 10
at java.lang.String.substring(String.java:1951)
    at bio.m.jButton3ActionPerformed(m.java:365)
    at bio.m.access$200(m.java:36)
    at bio.m$3.actionPerformed(m.java:142)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
    at javax.swing.AbstractButton$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 com.jtattoo.plaf.BaseButtonListener.mouseReleased(BaseButtonListener.java:60)
    at java.awt.Component.processMouseEvent(Component.java:6525)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
    at java.awt.Component.processEvent(Component.java:6290)
    at java.awt.Container.processEvent(Container.java:2234)
    at java.awt.Component.dispatchEventImpl(Component.java:4881)
    at java.awt.Container.dispatchEventImpl(Container.java:2292)
    at java.awt.Component.dispatchEvent(Component.java:4703)
    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:2750)
    at java.awt.Component.dispatchEvent(Component.java:4703)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:702)
    at java.awt.EventQueue$3.run(EventQueue.java:696)
    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:724)
    at java.awt.EventQueue$4.run(EventQueue.java:722)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:721)
    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)

它返回，你可以看到一个基因，但有一些错误的编辑代码

编辑:代码终于做了它应该做的事情:从我的RNA序列中获得开始和停止密码子这是我最后的编辑:

        List startCodonIndices = new ArrayList();
        int index = 0;
        for (int i = 0; i + 3 < dnax.length(); i++) {
            index = dnax.indexOf("AUG", i);
            if (index != -1) {
                startCodonIndices.add(index);
            }
            List stopCodonIndices = new ArrayList();
            int i2, i3, i4;
            for (int j = 0; j + 3 < dnax.length(); j++) {
                i2 = dnax.indexOf("UGA", j);
                System.out.println("i2: "+i2);
                if (i2 != -1) {
                    stopCodonIndices.add(i2);
                }
                i3 = dnax.indexOf("UAA", j);
                System.out.println("i3: "+i3);
                if (i3 != -1) {
                    stopCodonIndices.add(i3);
                }
                i4 = dnax.indexOf("UAG", j);
                System.out.println("i4: "+i4);
                if (i4 != -1) {
                    stopCodonIndices.add(i4);
                }
            }
            for (int v = 0; v < startCodonIndices.size(); v++) {
                for (int h = 0; h < stopCodonIndices.size(); h++) {
               gene = dnax.substring((int)startCodonIndices.get(v), (int)stopCodonIndices.get(h)+3);
                jTextArea1.setText(gene+"n");
            }}

谢谢pepper的帮助!