3 import jalview.datamodel.SequenceI;
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4 import java.util.Vector;
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5 import com.stevesoft.pat.Regex;
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6 public class ModellerDescription
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9 * Translates between a String containing a set of colon-separated values
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10 * on a single line, and sequence start/end and other properties.
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11 * See PIRFile IO for its use.
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13 final String[] seqTypes =
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15 "sequence", "structure", "structureX", "structureN"};
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16 final String[] Fields =
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18 "objectType", "objectId",
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19 "startField", "startCode",
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20 "endField", "endCode",
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21 "description1", "description2",
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22 "resolutionField", "tailField"};
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24 final int LOCALID = 1;
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25 final int START = 2;
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26 final int START_CHAIN = 3;
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28 final int END_CHAIN = 5;
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29 final int DESCRIPTION1 = 6;
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30 final int DESCRIPTION2 = 7;
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31 final int RESOLUTION = 8;
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35 * 0 is free text or empty
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36 * 1 is something that parses to an integer, or \@
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40 0, 0, 1, 0, 1, 0, 0, 0, 0, 0
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42 final char Padding[] =
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44 ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.'
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47 java.util.Hashtable fields = new java.util.Hashtable();
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48 ModellerDescription()
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50 fields.put(Fields[TAIL], "");
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57 resCode(String f, Integer v)
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65 val = new Integer(v);
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66 field = val.toString();
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70 private resCode validResidueCode(String field)
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73 com.stevesoft.pat.Regex r = new Regex("\\s*((([-0-9]+).?)|FIRST|LAST|@)");
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75 if (!r.search(field))
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77 return null; // invalid
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79 String value = r.stringMatched(3);
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82 value = r.stringMatched(1);
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84 // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
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88 val = Integer.valueOf(value);
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89 return new resCode(field, val); // successful numeric extraction
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94 return new resCode(field, null);
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97 private java.util.Hashtable parseDescription(String desc)
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99 java.util.Hashtable fields = new java.util.Hashtable();
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100 java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":");
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103 if (st.countTokens() > 0)
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105 // parse colon-fields
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107 field = st.nextToken(":");
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110 if (seqTypes[i].equalsIgnoreCase(field) )
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115 while (++i < seqTypes.length);
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117 if (i < seqTypes.length)
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119 // valid seqType for modeller
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121 i = 1; // continue parsing fields
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122 while (i < TAIL && st.hasMoreTokens())
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124 if ( (field = st.nextToken(":")) != null)
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126 // validate residue field value
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129 resCode val = validResidueCode(field);
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132 fields.put(new String(Fields[i] + "num"), val);
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136 // jalview.bin.Cache.log.debug(
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137 // "Ignoring non-Modeller description: invalid integer-like field '" + field + "'");
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138 type = -1; /* invalid field! - throw the FieldSet away */
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142 fields.put(Fields[i++], field);
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147 // slurp remaining fields
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148 while (st.hasMoreTokens())
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150 field += ":" + st.nextToken(":");
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152 fields.put(Fields[TAIL], field);
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158 // object is not a proper ModellerPIR object
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159 fields = new java.util.Hashtable();
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160 fields.put(Fields[TAIL], new String(desc));
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164 fields.put(Fields[TYPE], seqTypes[type]);
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169 ModellerDescription(String desc)
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175 fields = parseDescription(desc);
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178 void setStartCode(int v)
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181 fields.put(Fields[START] + "num", r = new resCode(v));
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182 fields.put(Fields[START], r.field);
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185 void setEndCode(int v)
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188 fields.put(Fields[END] + "num", r = new resCode(v));
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189 fields.put(Fields[END], r.field);
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193 * make a possibly updated modeller field line for the sequence object
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194 * @param seq SequenceI
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196 ModellerDescription(SequenceI seq)
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199 if (seq.getDescription() != null)
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201 fields = parseDescription(seq.getDescription());
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204 if (isModellerFieldset())
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206 // Set start and end before we update the type (in the case of a synthesized field set)
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207 if (getStartNum() != seq.getStart() && getStartCode().val != null)
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209 setStartCode(seq.getStart());
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212 if (getEndNum() != seq.getEnd() && getStartCode().val != null)
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214 setEndCode(seq.getEnd());
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219 // synthesize fields
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220 setStartCode(seq.getStart());
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221 setEndCode(seq.getEnd());
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222 fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten below...
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223 // type - decide based on evidence of PDB database references - this also sets the local reference field
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224 int t = 0; // sequence
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225 if (seq.getDatasetSequence() != null &&
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226 seq.getDatasetSequence().getDBRef() != null)
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228 Vector dbr = seq.getDatasetSequence().getDBRef();
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230 for (i = 0, j = dbr.size(); i < j; i++)
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232 jalview.datamodel.DBRefEntry dref = (jalview.datamodel.DBRefEntry)
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236 // JBPNote PDB dbRefEntry needs properties to propagate onto ModellerField
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237 // JBPNote Need to get info from the user about whether the sequence is the one being modelled, or if it is a template.
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238 if (dref.getSource().equals("PDB"))
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240 fields.put(Fields[LOCALID], dref.getAccessionId());
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247 fields.put(Fields[TYPE], seqTypes[t]);
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253 * Indicate if fields parsed to a modeller-like colon-separated value line
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256 boolean isModellerFieldset()
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258 return (fields.containsKey(Fields[TYPE]));
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261 String getDescriptionLine()
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264 int lastfield = Fields.length - 1;
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266 if (isModellerFieldset())
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269 // try to write a minimal modeller field set, so..
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271 // find the last valid field in the entry
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273 for (; lastfield > 6; lastfield--)
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275 if (fields.containsKey(Fields[lastfield]))
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281 for (int i = 0; i < lastfield; i++)
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283 value = (String) fields.get(Fields[i]);
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284 if (value != null && value.length() > 0)
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286 desc += ( (String) fields.get(Fields[i])) + ":";
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290 desc += Padding[i] + ":";
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294 // just return the last field if no others were defined.
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295 if (fields.containsKey(Fields[lastfield]))
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297 desc += (String) fields.get(Fields[lastfield]);
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309 resCode val = getStartCode();
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310 if (val.val != null)
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312 return val.val.intValue();
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317 resCode getStartCode()
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319 if (isModellerFieldset() && fields.containsKey(Fields[START] + "num"))
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321 return (resCode) fields.get(Fields[START] + "num");
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326 resCode getEndCode()
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328 if (isModellerFieldset() && fields.containsKey(Fields[END] + "num"))
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330 return (resCode) fields.get(Fields[END] + "num");
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338 resCode val = getEndCode();
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339 if (val.val != null)
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341 return val.val.intValue();
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347 * returns true if sequence object was modifed with a valid modellerField set
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348 * @param newSeq SequenceI
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351 boolean updateSequenceI(SequenceI newSeq)
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353 if (isModellerFieldset())
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355 if (getStartCode().val != null)
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357 newSeq.setStart(getStartNum());
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361 newSeq.setStart(1);
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363 if (getEndCode().val != null)
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365 newSeq.setEnd(getEndNum());
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369 newSeq.setEnd(newSeq.getStart() + newSeq.getLength());
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