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copied!<pre><code> public static void main(String[] args) { Scanner s = new Scanner("Shortest path(2)::RV3280-RV0973C-RV2888C" + "\nShortest path(1)::RV3280-RV2502C" + "\nShortest path(2)::RV3280-RV2501C-RV1263" + "\nShortest path(2)::RV2363-Rv3285-RV3280"); while (s.hasNextLine()) { s.findInLine("Shortest path\\((\\d+)\\)::(\\w+).*-(\\w+)"); // at each line, look for this pattern MatchResult result = s.match(); // results from for (int i = 1; i <= result.groupCount(); i++) { System.out.println(result.group(i)); } s.nextLine(); // line no. 29 } s.close(); } } run: 2 RV3280 RV2888C 1 RV3280 RV2502C 2 RV3280 RV1263 2 RV2363 RV3280 BUILD SUCCESSFUL (total time: 0 seconds) </code></pre> <p>This works well for me, maybe you have some weird characters or empty lines in your file?</p> <p>2 empty lines at the end give me that: Exception in thread "main" java.lang.IllegalStateException: No match result available</p> <p>If your input file is that strictly formatted, you can do something like that, which is way easier because you can get rid of that nasty regex ;)</p> <pre><code> String[] lines = new String[]{"Shortest path(2)::RV3280-RV0973C-RV2888C", "Shortest path(1)::RV3280-RV2502C", "Shortest path(2)::RV3280-RV2501C-RV1263", "Shortest path(2)::RV2363-Rv3285-RV3280", "\n", "\n"}; final int positionOfIndex = 14; final int startPositionOfProteins = 18; for (String line : lines) { if (!line.trim().isEmpty()) { System.out.print(line.charAt(positionOfIndex) + ": "); String[] proteins = line.substring(startPositionOfProteins).split("-"); System.out.println(proteins[0] + " " + proteins[proteins.size() -1]); } } </code></pre>

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