src/org/vamsas/objects/utils/Seq.java

   1 /*
   2  * Created on 17-May-2005
   3  *
   4  * TODO To change the template for this generated file go to
   5  * Window - Preferences - Java - Code Style - Code Templates
   6  */
   7 package org.vamsas.objects.utils;
   8
   9 import java.io.BufferedWriter;
  10 import java.io.IOException;
  11 import java.io.OutputStream;
  12 import java.io.OutputStreamWriter;
  13 import java.util.regex.Pattern;
  14
  15 import org.vamsas.objects.core.AlignmentSequence;
  16 import org.vamsas.objects.core.Sequence;
  17 import org.vamsas.objects.core.SequenceType;
  18
  19 /**
  20  * @author jimp
  21  *
  22  * TODO To change the template for this generated type comment go to
  23  * Window - Preferences - Java - Code Style - Code Templates
  24  */
  25 public class Seq {
  26
  27         public static void write_PirSeq(OutputStream os, SequenceType seq, int wid) throws IOException {
  28                 BufferedWriter pir_out = new BufferedWriter(new OutputStreamWriter(os));
  29                 pir_out.write(">P1;"+seq.getName()+"\n");
  30                 int width = (wid<1) ? 80 : wid;
  31                 for (int j=0,k=seq.getSequence().length(); j<k; j+=width)
  32                         if (j+width<k)
  33                                 pir_out.write(seq.getSequence().substring(j,j+width)+"\n");
  34                         else
  35                                 pir_out.write(seq.getSequence().substring(j)+"\n");
  36                 pir_out.flush();
  37           }
  38
  39         public static void write_FastaSeq(OutputStream os, SequenceType seq) throws IOException {
  40                 BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
  41                 fasta_out.write(">"+seq.getName()+"\n");
  42                 fasta_out.write(seq.getSequence()+"\n");
  43                 fasta_out.flush();
  44           }
  45
  46         public static void write_FastaSeq(OutputStream os, SequenceType seq, int wid) throws IOException {
  47                 BufferedWriter fasta_out = new BufferedWriter(new OutputStreamWriter(os));
  48                 fasta_out.write(">"+seq.getName()+"\n");
  49                 int width = (wid<1) ? 80 : wid;
  50                 for (int j=0,k=seq.getSequence().length(); j<k; j+=width)
  51                         if (j+width<k)
  52                                 fasta_out.write(seq.getSequence().substring(j,j+width)+"\n");
  53                         else
  54                                 fasta_out.write(seq.getSequence().substring(j)+"\n");
  55                 fasta_out.flush();
  56           }
  57         /**
  58    *validate a SequenceType object as an info:iubmb.org/aminoacid SequenceType
  59    *This version resolves references to Sequence objects from AlignmentSequence
  60    *TODO: Define info: urn for dictionary string (could also be regex of valid characters!)
  61    * @param s
  62    * @return true if a valid amino acid sequence object
  63          */
  64         private static boolean valid_aadictionary_string(String s) {
  65     if (s==null)
  66       return false;
  67     // validate against dictionary
  68     // TODO generalise to resolve dictionary against info: urn for dictionary type
  69       Pattern aa_repl = Pattern.compile("[ARNDCQEGHILKMFPSTWYVUX]+", Pattern.CASE_INSENSITIVE);
  70       String remnants = aa_repl.matcher(s).replaceAll("");
  71       return !remnants.matches("//S+");
  72   }
  73
  74   public static boolean is_valid_aa_seq(SequenceType s) {
  75     Sequence q;
  76     boolean validref=false;
  77     if (s instanceof Sequence) {
  78       q=(Sequence) s;
  79       if (q.getDictionary()!=null
  80
  81         && q.getDictionary().length()>0
  82         || !q.getDictionary().equals("info:iubmb.org/aminoacid"))
  83         return false;
  84       return valid_aadictionary_string(q.getSequence());
  85     }
  86
  87     // follow references
  88     if (s instanceof AlignmentSequence) {
  89       Object w = (((AlignmentSequence) s).getRefid());
  90       if (w!=null && w!=s && w instanceof SequenceType)
  91         return is_valid_aa_seq((SequenceType) w)
  92         && valid_aadictionary_string(((AlignmentSequence) s).getSequence());
  93     }
  94
  95     return false;
  96   }
  97 }