Below is my highly inefficient and non working code for converting RNA sequence to Protein:
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:
Is there any way I can use regex to solve this problem? (I mean like in perl) Edit : whole exception
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)
To increase speed I would use a static Map for all available codons
Use a StringBuilder to build your finalresult
Be sure that your String input is a multiple of 3
Be sure that every triplet corresponds to a valid codon
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();
}