Java File reader - Reading file line by line and compare some content of one line with rest of the lines

Java File reader - Reading file line by line and compare some content of one line with rest of the lines

I would like to read file line by line and compare them.
for example
file.tex ChapterInput[x,y,z] sectionInput[x,y,z] sectionInput[x,y] sectionInput[z,k,m] ChapterInput[k,d,l] sectionInput[k,d,h] sectionInput[l] sectionInput[l,r]
if i read line AAA and wanted to check whether ChapterInput[x,y,z] contains all the letters(in [x,y,z]) in lines sectionInput[x,y,z],sectionInput[x,y],sectionInput[x,k,m] if not i wanted to include missing letter (ex: k,m is missing in ChapterInput) so file will be re written as follows
file.tex
ChapterInput[x,y,z,k,m] sectionInput[x,y,z] sectionInput[x,y] sectionInput[z,k,m] ChapterInput[k,d,l,h,r] sectionInput[k,d,h] sectionInput[l] sectionInput[l,r]
import java.util.Scanner; import java.io.; import java.util.;//StringTokenizer; import java.util.Stack; import java.util.regex.*; import java.io.LineNumberReader;
class sample {
public static void main (String args[])
{ 
    String line;
    String nextData = null;
    int lineCount=0;
    try{
    File file=new File("waste.tex");
    Scanner scanFile = new Scanner(file);
    boolean flag = true;
while(scanFile.hasNextLine())
    {      
           lineCount++;
           line= scanFile.nextLine();
       StringTokenizer tok = new StringTokenizer(line);
       while(tok.hasMoreElements())
       {
           nextData = tok.nextToken();
           if(nextData.contains("chapterInput"))
           {
              System.out.println("Line : "+lineCount+ ": "+ nextData);            
                           Pattern p1 = Pattern.compile(\\[(.*?)\\]);
                           Matcher m1 = p1.matcher(nextData);
                           while(m1.find())
                              { System.out.println(m1.group(1)); }
               String nxt_line = scanFile.nextLine();  
                           Scanner scanFile_1 = new Scanner(file);                             
               while((scanFile_1.hasNextLine()) && (flag=true) )                          
               {                                 
                System.out.println("");
                                if(nxt_line.contains("sectionInput"))                                   
                  {
                                   System.out.println("Line : "+lineCount+ ": "+nxt_line);
                                   Pattern p2= Pattern.compile(\\[(.*?)\\]);
                                   Matcher m2=p2.matcher(nxt_line);
                                   while (m2.find())
                   {System.out.println(m2.group(1));}                                   
                                  }
                else
                  {flag=false;}
               }                
           }
       }
    }  
}
    catch(Exception e){e.printStackTrace();}    
} }
But i cannot Access lines in between chapterInputs.
Thanks in Advance
Uma