java - Linked List Optimization -

i'm working on program emulates restriction enzymes , dna splicing. i'm using dnasequencenode[s] linked list nodes.

i have problem 1 of function in code, cutsplice() supposed create new dnastrand clone of current dnastrand, every instance of enzyme replaced splicee.

for example, if linkeddnastrand instantiated "ttgatcc", , cutsplice("gat", "ttaagg") called, linked list should become (previous pointers not shown):

first -> "tt" -> "ttaagg" -> "cc" -> null

my function works. however, method cutsplice() takes more 80 seconds splice 200 dnas. i'm supposed bring 80 seconds 2 seconds.

this code class : linkeddnastrand.java

and here's code method cutsplice()

public dnastrand cutsplice(string enzyme, string splicee) {     dnastrand newstrand = null;     string original_dna = this.tostring();     string new_dna = original_dna.replaceall(enzyme, splicee);     string[] splicee_split = new_dna.split(splicee); // splits new dna string dnastrand     newstrand = null;     int = 0;     if (original_dna.startswith(enzyme)) {         newstrand = new linkeddnastrand(splicee);     } else {         newstrand = new linkeddnastrand(splicee_split[0]);         newstrand.append(splicee);     }     (i = 1; < splicee_split.length - 1; i++) {          string node = splicee_split[i];         newstrand.append(node);         newstrand.append(splicee);      }     newstrand.append(splicee_split[splicee_split.length - 1]);      if (original_dna.endswith(enzyme)) {         newstrand.append(splicee);     }       return newstrand; } 

does see make critical difference on time function takes process 200 dnas sample?

well, comfortable use string methods, losing time in converting string, sequence, , (as pointed out in previous comments) regex based string functions.

it consume less time operate on linked list directly, although require implement replacement algorithm yourself:

@override public linkeddnastrand cutsplice(string enzyme, string splicee) {     linkeddnastrand strand = new linkeddnastrand();     dnasequencenode end = null;     dnasequencenode begin = top;     int pos = 0;     dnasequencenode tmpstart, tmpend;     (dnasequencenode current = top; current != null; current = current.next)     {         if(current.value != enzyme.charat(pos))         {             tmpstart = tmpend = new dnasequencenode(begin.value);             (dnasequencenode n = begin.next; n != current.next; n = n.next)             {                 dnasequencenode c = new dnasequencenode(n.value);                 tmpend.next = c;                 c.previous = tmpend;                 tmpend = c;             }         }         else if(++pos == enzyme.length())         {             tmpstart = tmpend = new dnasequencenode(splicee.charat(0));             (int = 1; < splicee.length(); ++i)             {                 dnasequencenode c = new dnasequencenode(splicee.charat(i));                 tmpend.next = c;                 c.previous = tmpend;                 tmpend = c;             }         }         else         {             continue;         }          if(end == null)         {             strand.top = end = tmpstart;         }         else         {             end.next = tmpstart;             tmpstart.previous = end;         }         end = tmpend;         begin = current.next;         pos = 0;     }      return strand; } 

i not claim there not opportunity further optimize, should lot faster original version. tested example gave, if yet find bug, feel free fix yourself...

note 1: did explicitely create new sequence string (instead of using constructor) end of sequence without having iterate on again.

note 2: assumed existing constructor dnasequencenode(char value) , dnasequencenode having member public char value. might have adjust code appropriately if of these assumptions fails.