Exemple #1
0
 public String get_normalized_observed_bases() {
   String result;
   if (strand.equals("+")) {
     result = observed_bases;
   } else {
     char[] res = observed_bases.toCharArray();
     for (int i = 0; i < res.length; i++) {
       if (res[i] != '/') res[i] = RefGene.complement(res[i]);
     }
     result = new String(res);
     //      System.err.println("before:"+observed_bases + " after:" +result);  // debug
   }
   return result;
 }
Exemple #2
0
  public void run() {
    String line;
    String id = null;
    config.refgenes = new ArrayList<RefGene>();
    config.dbsnp = new ArrayList<dbSNP>();

    try {
      //      System.err.println("quality read start");  // debug
      boolean need_ruler_rebuild = false;
      boolean need_title = false;
      SAMRegion sr = null;
      while (true) {
        line = br.readLine();
        if (line == null) break;
        // EOF
        String[] stuff = line.split("\t");
        if (stuff[0].equals("sample2id")) {
          Sample sample = Sample.get_sample(stuff[1]);
          for (int i = 2; i < stuff.length; i++) {
            config.read2sample.put(new String(stuff[i]), sample);
          }
        } else if (stuff[0].equals("consensus_label")) {
          config.CONSENSUS_TAG = new String(stuff[1]);
        } else if (stuff[0].equals("ruler_start")) {
          config.ruler_start = Integer.parseInt(stuff[1]);
          need_ruler_rebuild = true;
        } else if (stuff[0].equals("title")) {
          config.title = stuff[1];
          need_title = true;
        } else if (stuff[0].equals("refGene")) {
          config.refgenes.add(new RefGene(stuff));
        } else if (stuff[0].equals("dbsnp")) {
          config.dbsnp.add(new dbSNP(stuff));
        } else if (stuff[0].toUpperCase().indexOf("SAM_") == 0) {
          // FUGLY
          SAMResourceTags v = SAMResourceTags.valueOf(stuff[0].toUpperCase());
          if (v.equals(SAMResourceTags.SAM_URL)) config.sams.add(new SAMResource());
          config.sams.get(config.sams.size() - 1).import_data(v, stuff[1]);
        } else if (stuff[0].equals("reference_sequence")) {
          StringBuffer target_sequence = new StringBuffer();
          while (true) {
            line = br.readLine();
            if (line.equals(">")) {
              //	      config.target_sequence = target_sequence.toString().toCharArray();
              config.target_sequence = target_sequence.toString().getBytes();
              break;
            } else {
              target_sequence.append(line);
            }
          }
        } else if (stuff[0].equals("target_region")) {
          sr = new SAMRegion();
          sr.tname = new String(stuff[1]);
          sr.range = new Range(Integer.parseInt(stuff[2]), Integer.parseInt(stuff[3]));
          //	  System.err.println("range " + sr.tname + " " + sr.range.start + " " + sr.range.end);
          // // debug
        } else {
          System.err.println("error, don't recognize tag " + stuff[0]); // debug
        }
      }

      if (config.ruler_start > 0) {
        for (dbSNP snp : config.dbsnp) {
          snp.consensus_adjust(config.ruler_start);
        }

        for (RefGene rg : config.refgenes) {
          rg.consensus_adjust(config.ruler_start);
        }
      }

      if (config.dbsnp != null) {
        for (dbSNP snp : config.dbsnp) {
          //	  System.err.println("adding snp at " + snp.start + " = " + (snp.start +
          // config.ruler_start));  // debug
        }

        config.snp_config.snp_query = new dbSNPSet(config.dbsnp);
      }

      for (SAMResource sre : config.sams) {
        sre.set_region(sr);
      }

      if (av != null) {
        while (av.get_acepanel().is_built() == false) {
          // spin until dependency built
          try {
            System.err.println("MarkupReader spin..."); // debug
            Thread.sleep(50);
          } catch (Exception e) {
          }
        }

        PadMap pm = av.get_acepanel().get_assembly().get_padmap();
        for (RefGene rg : config.refgenes) {
          rg.consensus_setup(pm);
        }

        Runnable later;

        if (need_title) {
          //	  System.err.println("title="+config.title);  // debug
          later =
              new Runnable() {
                public void run() {
                  av.setTitle(config.title);
                  av.repaint();
                }
              };
          javax.swing.SwingUtilities.invokeLater(later);
        }

        if (need_ruler_rebuild) {
          //
          //  ruler labeling has changed.
          //
          later =
              new Runnable() {
                public void run() {
                  //		av.get_acepanel().get_canvas().build_ruler();

                  if (config.start_unpadded_offset != 0) {
                    AcePanel ap = av.get_acepanel();
                    PadMap pm = ap.get_assembly().get_padmap();
                    int upo = (config.start_unpadded_offset - config.ruler_start) + 1;
                    // +1: convert to 1-based offset
                    int po = pm.get_unpadded_to_padded(upo);
                    System.err.println("upo=" + upo + " po=" + po); // debug
                    SNPList sl = new SNPList();
                    sl.addElement(new SNP(po, 0.0));
                    ap.ace.set_snps(sl);
                    ap.get_canvas().center_on(po);
                    ap.get_canvas().repaint();
                  }
                }
              };
          javax.swing.SwingUtilities.invokeLater(later);
        }

        if (config.enable_exon_navigation) {
          if (false) {
            System.err.println("DEBUG: exon nav disabled");
          } else {
            av.get_acepanel().init_exon_navigation();
          }
        }

        av.get_acepanel().get_assembly().build_summary_info();
        // group samples by tumor/normal, if applicable
        //      av.repaint();

        later =
            new Runnable() {
              public void run() {
                av.repaint();
              }
            };
        javax.swing.SwingUtilities.invokeLater(later);
      }

      //      System.err.println("quality read end");  // debug
    } catch (Exception e) {
      e.printStackTrace(); // debug
    }
  }