Java生物信息学-获取字符串中多个特定单词的所有索引
我在大学的生物信息学课程中有一个项目，其中一个项目是基因预测 我今天的问题是如何获取字符串中多个特定单词的所有索引。例如，在我这里的例子中，我想查找 起始密码子Java生物信息学-获取字符串中多个特定单词的所有索引,java,bioinformatics,biojava,Java,Bioinformatics,Biojava,我在大学的生物信息学课程中有一个项目，其中一个项目是基因预测 我今天的问题是如何获取字符串中多个特定单词的所有索引。例如，在我这里的例子中，我想查找 起始密码子（“AUG”）和终止密码子（“UAA”、“UAG”、“UGA”）并使用它们预测基因，只需尝试做开放阅读框（ORF） 这是我的初始代码： private void jButton3ActionPerformed(java.awt.event.ActionEvent evt) {
（“AUG”）（“UAA”、“UAG”、“UGA”）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..");
}
}
}
private void jButton3ActionPerformed（java.awt.event.ActionEvent evt）{
//TODO在此处添加您的处理代码：
//textArea1.setText（空）\
字符串str=jTextField1.getText（），y=，gene=，dnax=，text=；
SymbolList dna=null；
int起始密码子索引=-1，终止密码子索引=-1；
如果（“.”等于（str））{
jTextArea1.setText（“未输入DNA链”）；
}否则{
if（校验和（str）==100）{
试一试{
dna=DNATools.createDNA（str）；
}捕获（非法SYMBOLEXCEPTION）{
Logger.getLogger（m.class.getName（））.log（Level.SEVERE，null，ex）；
}
试一试{
dna=DNATools.toRNA（dna）；
}捕获（IllegalHabetException例外）{
Logger.getLogger（m.class.getName（））.log（Level.SEVERE，null，ex）；
}
dnax=dna.seqString（）.toUpperCase（）；
如果（dnax.length（）%3！=0）{
如果（dnax.length（）%3==1）{
dnax+=“-”；
}
如果（dnax.length（）%3==2）{
dnax+=“-”；
}
}
//系统输出打印LN（dnax）；
对于（int g=0；g私有静态整数校验和（字符串x）{
int i=0，checks=0，count=0；
字符c；
x=x.toUpperCase（）；
而（i我尝试过其他的解决办法，但都不管用。欢迎任何帮助/建议。我想你是在问如何找到这些特定密码子的索引？dnax是您要检查的字符串吗 您可以使用
indexOf（String str，int from index）List<Integer> startCodonIndices = new ArrayList<Integer>();
int index;
for (int i=0; i+3<dnax.length(); i++) {
index = indexOf("AUG", i);
startCodonIndices.add(index);
}
List startDonIndexes=new ArrayList（）；
整数指数；
对于（int i=0；i+3这是我根据您在我的代码中的建议更改和添加的内容：
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);
}
}
}
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)
它返回时，您可以看到一个基因，但编辑的代码有问题
编辑：代码终于完成了它应该做的事情：从我的RNA序列中获取起始密码子和终止密码子
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");
}}
List startDonIndexes=new ArrayList（）；
int指数=0；
对于（int i=0；i+3
谢谢pepers的帮助！这对起始密码子非常有效；虽然，终止密码子仍然给我带来麻烦这是我添加到代码中的内容，它产生了正确的基因，但有一个例外（IndexOutOfBounds）-听着，对不起，我忍不住了，我在第一次发表评论后就上床睡觉了，哈哈，但最好是你自己想出来。干得好！
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)
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");
}}