2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 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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21 import jalview.datamodel.*;
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25 import jalview.schemes.UserColourScheme;
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32 * @version $Revision$
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34 public class FeaturesFile extends AlignFile
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37 * Creates a new FeaturesFile object.
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39 public FeaturesFile()
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44 * Creates a new FeaturesFile object.
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46 * @param inStr DOCUMENT ME!
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48 public FeaturesFile(String inStr)
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54 * Creates a new FeaturesFile object.
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56 * @param inFile DOCUMENT ME!
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57 * @param type DOCUMENT ME!
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59 * @throws IOException DOCUMENT ME!
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61 public FeaturesFile(String inFile, String type)
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64 super(inFile, type);
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70 * @throws IOException DOCUMENT ME!
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72 public boolean parse(AlignmentI align, Hashtable colours)
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78 SequenceI seq = null;
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79 String type, desc, token=null;
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81 int index, start, end;
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85 String featureGroup = null;
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87 boolean GFFFile = true;
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89 while ( (line = nextLine()) != null)
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91 if(line.startsWith("#"))
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94 st = new StringTokenizer(line, "\t");
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95 if (st.countTokens()>1 && st.countTokens() < 4 )
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98 type = st.nextToken();
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99 if (type.equalsIgnoreCase("startgroup"))
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101 featureGroup = st.nextToken();
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103 else if (type.equalsIgnoreCase("endgroup"))
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105 //We should check whether this is the current group,
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106 //but at present theres no way of showing more than 1 group
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108 featureGroup = null;
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112 UserColourScheme ucs = new UserColourScheme(st.nextToken());
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113 colours.put(type, ucs.findColour("A"));
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118 while (st.hasMoreElements())
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123 // Still possible this is an old Jalview file,
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124 // which does not have type colours at the beginning
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125 token = st.nextToken();
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126 seq = align.findName(token);
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129 desc = st.nextToken();
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130 type = st.nextToken();
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131 start = Integer.parseInt(st.nextToken());
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132 end = Integer.parseInt(st.nextToken());
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135 score = Float.parseFloat(st.nextToken());
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137 catch (NumberFormatException ex)
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142 sf = new SequenceFeature(type, desc, start, end, score, null);
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146 sf.setValue("STRAND", st.nextToken());
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147 sf.setValue("FRAME", st.nextToken());
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149 catch (Exception ex)
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152 seq.getDatasetSequence().addSequenceFeature(sf);
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158 if(GFFFile && seq==null)
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163 desc = st.nextToken();
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166 token = st.nextToken();
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167 if (!token.equals("ID_NOT_SPECIFIED"))
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169 seq = align.findName(token);
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175 index = Integer.parseInt(st.nextToken());
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176 seq = align.getSequenceAt(index);
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178 catch(NumberFormatException ex)
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186 System.out.println("Sequence not found: "+line);
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190 start = Integer.parseInt(st.nextToken());
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191 end = Integer.parseInt(st.nextToken());
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193 type = st.nextToken();
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195 if (!colours.containsKey(type))
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197 // Probably the old style groups file
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198 UserColourScheme ucs = new UserColourScheme(type);
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199 colours.put(type, ucs.findColour("A"));
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202 sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
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204 seq.getDatasetSequence().addSequenceFeature(sf);
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206 //If we got here, its not a GFFFile
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211 catch (Exception ex)
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213 System.out.println(line);
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214 ex.printStackTrace();
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215 System.out.println("Error parsing groups file: " + ex +"\n"+line);
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227 * @param s DOCUMENT ME!
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228 * @param len DOCUMENT ME!
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229 * @param gaps DOCUMENT ME!
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230 * @param displayId DOCUMENT ME!
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232 * @return DOCUMENT ME!
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234 public String printJalviewFormat(SequenceI [] seqs,
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237 StringBuffer out = new StringBuffer();
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238 SequenceFeature [] next;
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240 if(visible==null || visible.size()<1)
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241 return "No Features Visible";
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243 Enumeration en = visible.keys();
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246 while( en.hasMoreElements() )
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248 type = en.nextElement().toString();
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249 color = Integer.parseInt( visible.get(type).toString() );
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250 out.append(type + "\t"
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251 + jalview.util.Format.getHexString(
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252 new java.awt.Color(color) )
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256 //Work out which groups are both present and visible
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257 Vector groups = new Vector();
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258 int groupIndex = 0;
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260 for(int i=0; i<seqs.length; i++)
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262 next = seqs[i].getSequenceFeatures();
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265 for(int j=0; j<next.length; j++)
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267 if (!visible.containsKey(next[j].type))
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270 if ( next[j].featureGroup != null
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271 && !groups.contains(next[j].featureGroup))
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272 groups.addElement(next[j].featureGroup);
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277 String group = null;
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281 if (groups.size() > 0)
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283 group = groups.elementAt(groupIndex).toString();
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284 out.append("\nSTARTGROUP\t" + group + "\n");
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288 for (int i = 0; i < seqs.length; i++)
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290 next = seqs[i].getSequenceFeatures();
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293 for (int j = 0; j < next.length; j++)
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295 if (!visible.containsKey(next[j].type))
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298 if (group != null && !next[j].featureGroup.equals(group))
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301 if(next[j].description==null || next[j].description.equals(""))
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302 out.append(next[j].type+"\t");
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304 out.append(next[j].description + "\t");
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306 out.append( seqs[i].getName() + "\t-1\t"
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307 + next[j].begin + "\t"
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308 + next[j].end + "\t"
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309 + next[j].type + "\n"
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315 if(groups.size()>0)
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317 out.append("ENDGROUP\t"+group+"\n");
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322 while(groupIndex < groups.size());
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325 return out.toString();
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328 public String printGFFFormat(SequenceI [] seqs, Hashtable visible)
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330 StringBuffer out = new StringBuffer();
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331 SequenceFeature [] next;
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333 for(int i=0; i<seqs.length; i++)
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335 if(seqs[i].getSequenceFeatures()!=null)
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337 next = seqs[i].getSequenceFeatures();
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338 for(int j=0; j<next.length; j++)
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340 if(!visible.containsKey(next[j].type))
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343 out.append(seqs[i].getName() + "\t"
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344 + next[j].description + "\t"
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345 + next[j].type + "\t"
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346 + next[j].begin + "\t"
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347 + next[j].end + "\t"
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348 + next[j].score + "\t"
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351 if(next[j].getValue("STRAND")!=null)
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352 out.append(next[j].getValue("STRAND")+"\t");
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355 if(next[j].getValue("FRAME")!=null)
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356 out.append(next[j].getValue("FRAME")+"\n");
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364 return out.toString();
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367 public void parse()
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375 * @return DOCUMENT ME!
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377 public String print()
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379 return "USE printGFFFormat() or printJalviewFormat()";
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