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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21 import jalview.datamodel.*;
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23 public class ModellerDescription
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26 * Translates between a String containing a set of colon-separated values
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27 * on a single line, and sequence start/end and other properties.
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28 * See PIRFile IO for its use.
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30 final String[] seqTypes =
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32 "sequence", "structure", "structureX", "structureN"};
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33 final String[] Fields =
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35 "objectType", "objectId",
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36 "startField", "startCode",
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37 "endField", "endCode",
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38 "description1", "description2",
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39 "resolutionField", "tailField"};
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41 final int LOCALID = 1;
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42 final int START = 2;
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43 final int START_CHAIN = 3;
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45 final int END_CHAIN = 5;
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46 final int DESCRIPTION1 = 6;
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47 final int DESCRIPTION2 = 7;
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48 final int RESOLUTION = 8;
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52 * 0 is free text or empty
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53 * 1 is something that parses to an integer, or \@
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57 0, 0, 1, 0, 1, 0, 0, 0, 0, 0
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59 final char Padding[] =
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61 ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.', '.'
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64 java.util.Hashtable fields = new java.util.Hashtable();
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65 ModellerDescription()
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67 fields.put(Fields[TAIL], "");
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74 resCode(String f, Integer v)
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82 val = new Integer(v);
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83 field = val.toString();
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87 private resCode validResidueCode(String field)
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90 com.stevesoft.pat.Regex r = new com.stevesoft.pat.Regex(
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91 "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
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93 if (!r.search(field))
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95 return null; // invalid
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97 String value = r.stringMatched(3);
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100 value = r.stringMatched(1);
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102 // jalview.bin.Cache.log.debug("from '" + field + "' matched '" + value +
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106 val = Integer.valueOf(value);
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107 return new resCode(field, val); // successful numeric extraction
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109 catch (Exception e)
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112 return new resCode(field, null);
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115 private java.util.Hashtable parseDescription(String desc)
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117 java.util.Hashtable fields = new java.util.Hashtable();
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118 java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":");
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121 if (st.countTokens() > 0)
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123 // parse colon-fields
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125 field = st.nextToken(":");
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128 if (seqTypes[i].equalsIgnoreCase(field))
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133 while (++i < seqTypes.length);
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135 if (i < seqTypes.length)
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137 // valid seqType for modeller
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139 i = 1; // continue parsing fields
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140 while (i < TAIL && st.hasMoreTokens())
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142 if ( (field = st.nextToken(":")) != null)
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144 // validate residue field value
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147 resCode val = validResidueCode(field);
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150 fields.put(new String(Fields[i] + "num"), val);
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154 // jalview.bin.Cache.log.debug(
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155 // "Ignoring non-Modeller description: invalid integer-like field '" + field + "'");
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156 type = -1; /* invalid field! - throw the FieldSet away */
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160 fields.put(Fields[i++], field);
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165 // slurp remaining fields
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166 while (st.hasMoreTokens())
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168 field += ":" + st.nextToken(":");
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170 fields.put(Fields[TAIL], field);
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176 // object is not a proper ModellerPIR object
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177 fields = new java.util.Hashtable();
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178 fields.put(Fields[TAIL], new String(desc));
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182 fields.put(Fields[TYPE], seqTypes[type]);
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187 ModellerDescription(String desc)
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193 fields = parseDescription(desc);
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196 void setStartCode(int v)
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199 fields.put(Fields[START] + "num", r = new resCode(v));
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200 fields.put(Fields[START], r.field);
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203 void setEndCode(int v)
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206 fields.put(Fields[END] + "num", r = new resCode(v));
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207 fields.put(Fields[END], r.field);
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211 * make a possibly updated modeller field line for the sequence object
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212 * @param seq SequenceI
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214 ModellerDescription(SequenceI seq)
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217 if (seq.getDescription() != null)
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219 fields = parseDescription(seq.getDescription());
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222 if (isModellerFieldset())
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224 // Set start and end before we update the type (in the case of a synthesized field set)
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225 if (getStartNum() != seq.getStart() && getStartCode().val != null)
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227 setStartCode(seq.getStart());
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230 if (getEndNum() != seq.getEnd() && getStartCode().val != null)
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232 setEndCode(seq.getEnd());
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237 // synthesize fields
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238 setStartCode(seq.getStart());
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239 setEndCode(seq.getEnd());
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240 fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten below...
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241 // type - decide based on evidence of PDB database references - this also sets the local reference field
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242 int t = 0; // sequence
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243 if (seq.getDatasetSequence() != null &&
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244 seq.getDatasetSequence().getDBRef() != null)
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246 jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence().getDBRef();
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248 for (i = 0, j = dbr.length; i < j; i++)
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250 if (dbr[i] != null)
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252 // JBPNote PDB dbRefEntry needs properties to propagate onto ModellerField
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253 // 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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254 if (dbr[i].getSource().equals(jalview.datamodel.DBRefSource.PDB))
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256 fields.put(Fields[LOCALID], dbr[i].getAccessionId());
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263 fields.put(Fields[TYPE], seqTypes[t]);
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269 * Indicate if fields parsed to a modeller-like colon-separated value line
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272 boolean isModellerFieldset()
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274 return (fields.containsKey(Fields[TYPE]));
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277 String getDescriptionLine()
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280 int lastfield = Fields.length - 1;
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282 if (isModellerFieldset())
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285 // try to write a minimal modeller field set, so..
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287 // find the last valid field in the entry
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289 for (; lastfield > 6; lastfield--)
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291 if (fields.containsKey(Fields[lastfield]))
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297 for (int i = 0; i < lastfield; i++)
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299 value = (String) fields.get(Fields[i]);
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300 if (value != null && value.length() > 0)
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302 desc += ( (String) fields.get(Fields[i])) + ":";
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306 desc += Padding[i] + ":";
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310 // just return the last field if no others were defined.
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311 if (fields.containsKey(Fields[lastfield]))
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313 desc += (String) fields.get(Fields[lastfield]);
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325 resCode val = getStartCode();
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326 if (val.val != null)
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328 return val.val.intValue();
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333 resCode getStartCode()
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335 if (isModellerFieldset() && fields.containsKey(Fields[START] + "num"))
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337 return (resCode) fields.get(Fields[START] + "num");
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342 resCode getEndCode()
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344 if (isModellerFieldset() && fields.containsKey(Fields[END] + "num"))
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346 return (resCode) fields.get(Fields[END] + "num");
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354 resCode val = getEndCode();
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355 if (val.val != null)
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357 return val.val.intValue();
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363 * returns true if sequence object was modifed with a valid modellerField set
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364 * @param newSeq SequenceI
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367 boolean updateSequenceI(SequenceI newSeq)
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369 if (isModellerFieldset())
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371 if (getStartCode().val != null)
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373 newSeq.setStart(getStartNum());
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377 newSeq.setStart(1);
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379 if (getEndCode().val != null)
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381 newSeq.setEnd(getEndNum());
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385 newSeq.setEnd(newSeq.getStart() + newSeq.getLength());
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