Odtnhj

I have two lists (Matches and Motifpoisitions). I want to combine the list in the following way: For all i such that i%2 = 1, look for Motifpoistions(k) = Matches(i) +1. And then set Matches(i)=Motifpostions(k+1). Additionally, I want to remove i and i-1 if k could not be found.

For example, If matches are (1,3,10,12) and Motifpositions is (4,8) then the final vector should be (1,8). Since 4 = 3+1, I replaced 3 with 8. And since there is no value in Motifpositions equal to 12+1, remove 10 and 12.
Here is what I am trying so far

for( int i = 1; i < matches.size(); i = i+2)
 int motifmatched = 0;
 for(int k = 0; k <motifpositions.size(); k++)
 if(motifpositions.get(k) == matches.get(i)+1)
 matches(i) = motifpositions(k+1); 
 motifmatched ++; 
 
 
 if(motifmatched ==0)
 matches.remove(i);
 matches.remove(i-1);
 
 

Not sure why you've used nested loops.

Try this code, which prints [1, 8] as requested:-

List<Integer> matches = new LinkedList<>();
matches.add(1);
matches.add(3);
matches.add(10);
matches.add(12);

List<Integer> motifPositions = new LinkedList<>();
motifPositions.add(4);
motifPositions.add(8);

for (int i = 1; i < matches.size(); i += 2) 
 int indexOfSumInMotifpositions = motifPositions.indexOf(matches.get(i) + 1);
 if (indexOfSumInMotifpositions > -1) 
 matches.set(i, motifPositions.get(indexOfSumInMotifpositions + 1));
 else 
 matches.remove(i);
 matches.remove(i - 1);
 

System.out.println(matches);