public MarkupReader(BufferedReader br, AceViewerConfig config, boolean async) { this.br = br; this.av = null; this.config = config; config.read2sample = new HashMap<String, Sample>(); if (async) { Thread t = new Thread(this); // t.setPriority(Thread.MIN_PRIORITY); t.start(); } else { run(); } }
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 } }