private volatile int lineNumber;
volatile public static ArrayList<CodeString> applicationSourceCode = new ArrayList<CodeString>();

while (lineNumber < WorkData.applicationSourceCode.size()) {
    if (isLineComplete) {
        isLineComplete = false;
        runOnUiThread(runnable);
    }
}

line = WorkData.applicationSourceCode.get(lineNumber);
...
isLineComplete = true;
lineNumber++;

public class Analyzer {

    public void verify(ArrayList<String> applicationSourceCode) {
        AtomicInteger line = new AtomicInteger(0);
        while (line.get() < applicationSourceCode.size()) {
            runOnUiThread(applicationSourceCode.get(line.getAndIncrement()));
        }
    }

    private void runOnUiThread(String line) {
        //создаём новый объект Runnable и скармливаем потоку line.
        //не задерживаясь выходим.
    }
}