2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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24 import jalview.datamodel.*;
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25 import jalview.schemes.*;
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28 * Parse and create Jalview Features files
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29 * Detects GFF format features files and parses.
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30 * Does not implement standard print() - call specific printFeatures or printGFF.
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31 * Uses AlignmentI.findSequence(String id) to find the sequence object for the features annotation - this normally works on an exact match.
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33 * @version $Revision$
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35 public class FeaturesFile
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39 * Creates a new FeaturesFile object.
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41 public FeaturesFile()
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46 * Creates a new FeaturesFile object.
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48 * @param inFile DOCUMENT ME!
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49 * @param type DOCUMENT ME!
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51 * @throws IOException DOCUMENT ME!
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53 public FeaturesFile(String inFile, String type)
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56 super(inFile, type);
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58 public FeaturesFile(FileParse source) throws IOException
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64 * The Application can render HTML, but the applet will
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65 * remove HTML tags and replace links with %LINK%
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66 * Both need to read links in HTML however
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68 * @throws IOException DOCUMENT ME!
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70 public boolean parse(AlignmentI align,
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74 return parse(align, colours, null, removeHTML);
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78 * The Application can render HTML, but the applet will
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79 * remove HTML tags and replace links with %LINK%
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80 * Both need to read links in HTML however
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82 * @throws IOException DOCUMENT ME!
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84 public boolean parse(AlignmentI align,
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86 Hashtable featureLink,
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92 SequenceI seq = null;
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93 String type, desc, token = null;
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95 int index, start, end;
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99 String featureGroup = null, groupLink = null;
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100 Hashtable typeLink = new Hashtable();
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102 boolean GFFFile = true;
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104 while ( (line = nextLine()) != null)
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106 if (line.startsWith("#"))
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111 st = new StringTokenizer(line, "\t");
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112 if (st.countTokens() > 1 && st.countTokens() < 4)
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115 type = st.nextToken();
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116 if (type.equalsIgnoreCase("startgroup"))
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118 featureGroup = st.nextToken();
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119 if (st.hasMoreElements())
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121 groupLink = st.nextToken();
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122 featureLink.put(featureGroup, groupLink);
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125 else if (type.equalsIgnoreCase("endgroup"))
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127 //We should check whether this is the current group,
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128 //but at present theres no way of showing more than 1 group
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130 featureGroup = null;
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135 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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136 colours.put(type, ucs.findColour('A'));
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137 if (st.hasMoreElements())
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139 String link = st.nextToken();
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140 typeLink.put(type, link);
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141 if (featureLink == null)
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143 featureLink = new Hashtable();
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145 featureLink.put(type, link);
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152 while (st.hasMoreElements())
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157 // Still possible this is an old Jalview file,
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158 // which does not have type colours at the beginning
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159 token = st.nextToken();
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160 seq = align.findName(token, true);
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163 desc = st.nextToken();
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164 type = st.nextToken();
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166 start = Integer.parseInt(st.nextToken());
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167 } catch (NumberFormatException ex)
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172 end = Integer.parseInt(st.nextToken());
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174 catch (NumberFormatException ex)
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180 score = new Float(st.nextToken()).floatValue();
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182 catch (NumberFormatException ex)
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187 sf = new SequenceFeature(type, desc, start, end, score, null);
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191 sf.setValue("STRAND", st.nextToken());
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192 sf.setValue("FRAME", st.nextToken());
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194 catch (Exception ex)
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197 if (st.hasMoreTokens())
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199 StringBuffer attributes = new StringBuffer();
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200 while (st.hasMoreTokens())
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202 attributes.append("\t" + st.nextElement());
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204 sf.setValue("ATTRIBUTES", attributes.toString());
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207 seq.addSequenceFeature(sf);
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213 if (GFFFile && seq == null)
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219 desc = st.nextToken();
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221 if (!st.hasMoreTokens())
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223 System.err.println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");
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224 // in all probability, this isn't a file we understand, so bail quietly.
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228 token = st.nextToken();
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230 if (!token.equals("ID_NOT_SPECIFIED"))
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232 seq = align.findName(token, true);
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239 index = Integer.parseInt(st.nextToken());
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240 seq = align.getSequenceAt(index);
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242 catch (NumberFormatException ex)
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250 System.out.println("Sequence not found: " + line);
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254 start = Integer.parseInt(st.nextToken());
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255 end = Integer.parseInt(st.nextToken());
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257 type = st.nextToken();
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259 if (!colours.containsKey(type))
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261 // Probably the old style groups file
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262 UserColourScheme ucs = new UserColourScheme(type);
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263 colours.put(type, ucs.findColour('A'));
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266 sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
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268 seq.addSequenceFeature(sf);
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270 if (groupLink != null && removeHTML)
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272 sf.addLink(groupLink);
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273 sf.description += "%LINK%";
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275 if (typeLink.containsKey(type) && removeHTML)
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277 sf.addLink(typeLink.get(type).toString());
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278 sf.description += "%LINK%";
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281 parseDescriptionHTML(sf, removeHTML);
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283 //If we got here, its not a GFFFile
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288 catch (Exception ex)
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290 System.out.println(line);
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291 System.out.println("Error parsing feature file: " + ex + "\n" + line);
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292 ex.printStackTrace(System.err);
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299 public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
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301 if (sf.getDescription() == null)
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306 if (removeHTML && sf.getDescription().toUpperCase().indexOf("<HTML>") == -1)
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308 removeHTML = false;
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311 StringBuffer sb = new StringBuffer();
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312 StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");
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313 String token, link;
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316 while (st.hasMoreElements())
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318 token = st.nextToken("&>");
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319 if (token.equalsIgnoreCase("html") || token.startsWith("/"))
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325 startTag = token.indexOf("<");
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329 tag = token.substring(startTag + 1);
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330 token = token.substring(0, startTag);
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333 if (tag != null && tag.toUpperCase().startsWith("A HREF="))
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335 if (token.length() > 0)
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339 link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);
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340 String label = st.nextToken("<>");
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341 sf.addLink(label + "|" + link);
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342 sb.append(label + "%LINK%");
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344 else if (tag != null && tag.equalsIgnoreCase("br"))
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348 else if (token.startsWith("lt;"))
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350 sb.append("<" + token.substring(3));
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352 else if (token.startsWith("gt;"))
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354 sb.append(">" + token.substring(3));
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356 else if (token.startsWith("amp;"))
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358 sb.append("&" + token.substring(4));
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368 sf.description = sb.toString();
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376 * @param s DOCUMENT ME!
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377 * @param len DOCUMENT ME!
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378 * @param gaps DOCUMENT ME!
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379 * @param displayId DOCUMENT ME!
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381 * @return DOCUMENT ME!
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383 public String printJalviewFormat(SequenceI[] seqs,
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386 StringBuffer out = new StringBuffer();
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387 SequenceFeature[] next;
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389 if (visible == null || visible.size() < 1)
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391 return "No Features Visible";
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394 Enumeration en = visible.keys();
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397 while (en.hasMoreElements())
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399 type = en.nextElement().toString();
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400 color = Integer.parseInt(visible.get(type).toString());
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401 out.append(type + "\t"
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402 + jalview.util.Format.getHexString(
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403 new java.awt.Color(color))
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407 //Work out which groups are both present and visible
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408 Vector groups = new Vector();
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409 int groupIndex = 0;
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411 for (int i = 0; i < seqs.length; i++)
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413 next = seqs[i].getSequenceFeatures();
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416 for (int j = 0; j < next.length; j++)
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418 if (!visible.containsKey(next[j].type))
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423 if (next[j].featureGroup != null
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424 && !groups.contains(next[j].featureGroup))
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426 groups.addElement(next[j].featureGroup);
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432 String group = null;
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437 if (groups.size() > 0 && groupIndex < groups.size())
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439 group = groups.elementAt(groupIndex).toString();
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440 out.append("\nSTARTGROUP\t" + group + "\n");
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447 for (int i = 0; i < seqs.length; i++)
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449 next = seqs[i].getSequenceFeatures();
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452 for (int j = 0; j < next.length; j++)
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454 if (!visible.containsKey(next[j].type))
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460 && (next[j].featureGroup == null
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461 || !next[j].featureGroup.equals(group))
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467 if (group == null && next[j].featureGroup != null)
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472 if (next[j].description == null || next[j].description.equals(""))
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474 out.append(next[j].type + "\t");
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478 if (next[j].links != null
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479 && next[j].getDescription().indexOf("<html>") == -1)
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481 out.append("<html>");
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484 out.append(next[j].description + " ");
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485 if (next[j].links != null)
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487 for (int l = 0; l < next[j].links.size(); l++)
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489 String label = next[j].links.elementAt(l).toString();
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490 String href = label.substring(label.indexOf("|") + 1);
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491 label = label.substring(0, label.indexOf("|"));
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493 if (next[j].description.indexOf(href) == -1)
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495 out.append("<a href=\""
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503 if (next[j].getDescription().indexOf("</html>") == -1)
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505 out.append("</html>");
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512 out.append(seqs[i].getName() + "\t-1\t"
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513 + next[j].begin + "\t"
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514 + next[j].end + "\t"
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515 + next[j].type + "\n"
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523 out.append("ENDGROUP\t" + group + "\n");
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532 while (groupIndex < groups.size() + 1);
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534 return out.toString();
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537 public String printGFFFormat(SequenceI[] seqs, Hashtable visible)
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539 StringBuffer out = new StringBuffer();
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540 SequenceFeature[] next;
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543 for (int i = 0; i < seqs.length; i++)
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545 if (seqs[i].getSequenceFeatures() != null)
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547 next = seqs[i].getSequenceFeatures();
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548 for (int j = 0; j < next.length; j++)
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550 if (!visible.containsKey(next[j].type))
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555 source = next[j].featureGroup;
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556 if (source == null)
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558 source = next[j].getDescription();
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561 out.append(seqs[i].getName() + "\t"
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563 + next[j].type + "\t"
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564 + next[j].begin + "\t"
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565 + next[j].end + "\t"
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566 + next[j].score + "\t"
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569 if (next[j].getValue("STRAND") != null)
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571 out.append(next[j].getValue("STRAND") + "\t");
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578 if (next[j].getValue("FRAME") != null)
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580 out.append(next[j].getValue("FRAME"));
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587 if (next[j].getValue("ATTRIBUTES") != null)
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589 out.append(next[j].getValue("ATTRIBUTES"));
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598 return out.toString();
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601 public void parse()
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609 * @return DOCUMENT ME!
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611 public String print()
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613 return "USE printGFFFormat() or printJalviewFormat()";
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