src/jalview/io/DnaUtils.java

   1 package jalview.io;
   2
   3 import jalview.io.xdb.genbank.GenBankFeature;
   4 import jalview.io.xdb.genbank.GenBankSequence;
   5
   6 import java.util.ArrayList;
   7 import java.util.List;
   8 import java.util.Vector;
   9
  10 public class DnaUtils {
  11
  12         /**
  13          * @param gbf CDS feature data
  14          * @param sequences ORIGIN data
  15          * @return Nucleotid String (sequence) of CDS
  16          */
  17         public static String getSequence(GenBankFeature gbf, Vector<GenBankSequence> sequences){
  18                 if (!gbf.getType().equals(GenBankFeature.CDS)){
  19                         //If the feature is not a CDS, no sequence is returned
  20                         return null;
  21                 }else{
  22                         String range = gbf.getQualifier("range");
  23                         if (range.startsWith("join")){
  24                                 //TODO
  25                                 //It's a composed sequence
  26                         }else{
  27                                 //It's a simple range
  28                                 String[] positions = range.split("..");
  29                                 int initRange = Integer.parseInt(positions[0]);
  30                                 int endRange = Integer.parseInt(positions[1]);
  31                                 String sourceSequence = getNucleotidesFromSequenceVector(sequences);
  32                                 return sourceSequence.substring(initRange, endRange);
  33                         }
  34                 }
  35                 return null;
  36
  37         }
  38         private static boolean isSequenceInRange(int initRange, int endRange, GenBankSequence gbs){
  39                 return ((initRange>=gbs.getId()) && (endRange>=gbs.getId()));
  40         }
  41         private static String getNucleotidesInRangeFromSequence(int initRange, int endRange, GenBankSequence gbs){
  42                 return "";
  43         }
  44         public static String getNucleotidesFromSequenceVector(Vector<GenBankSequence> v){
  45                 StringBuffer sb = new StringBuffer();
  46                 for (GenBankSequence gbs:v){
  47                         Vector<String> seqs = gbs.getSequences();
  48                         for (String s:seqs)
  49                                 sb.append(s);
  50                 }
  51                 return sb.toString();
  52         }
  53         /**
  54          * @param args
  55          */
  56         public static void main(String[] args) {
  57                 // TODO Auto-generated method stub
  58
  59         }
  60
  61 }