2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.bin.Cache;
24 import jalview.datamodel.DBRefEntry;
25 import jalview.datamodel.SequenceI;
27 import java.util.List;
29 import com.stevesoft.pat.Regex;
31 public class ModellerDescription
34 * Translates between a String containing a set of colon-separated values on a
35 * single line, and sequence start/end and other properties. See PIRFile IO
38 final String[] seqTypes = { "sequence", "structure", "structureX",
41 final String[] Fields = { "objectType", "objectId", "startField",
42 "startCode", "endField", "endCode", "description1", "description2",
43 "resolutionField", "tailField" };
47 final int LOCALID = 1;
51 final int START_CHAIN = 3;
55 final int END_CHAIN = 5;
57 final int DESCRIPTION1 = 6;
59 final int DESCRIPTION2 = 7;
61 final int RESOLUTION = 8;
66 * 0 is free text or empty 1 is something that parses to an integer, or \@
68 final int Types[] = { 0, 0, 1, 0, 1, 0, 0, 0, 0, 0 };
70 final char Padding[] = { ' ', ' ', ' ', '.', ' ', '.', '.', '.', '.',
73 java.util.Hashtable fields = new java.util.Hashtable();
77 fields.put(Fields[TAIL], "");
86 resCode(String f, Integer v)
94 val = Integer.valueOf(v);
95 field = val.toString();
99 private resCode validResidueCode(String field)
103 "\\s*((([-0-9]+).?)|FIRST|LAST|@)");
105 if (!r.search(field))
107 return null; // invalid
109 String value = r.stringMatched(3);
112 value = r.stringMatched(1);
114 // Cache.debug("from '" + field + "' matched '" + value +
118 val = Integer.valueOf(value);
119 return new resCode(field, val); // successful numeric extraction
120 } catch (Exception e)
123 return new resCode(field, null);
126 private java.util.Hashtable parseDescription(String desc)
128 java.util.Hashtable fields = new java.util.Hashtable();
129 java.util.StringTokenizer st = new java.util.StringTokenizer(desc, ":",
134 if (st.countTokens() > 0)
136 // parse colon-fields
138 field = st.nextToken(":");
141 if (seqTypes[i].equalsIgnoreCase(field))
145 } while (++i < seqTypes.length);
147 if (i < seqTypes.length)
149 st.nextToken(); // skip ':'
150 // valid seqType for modeller
152 i = 1; // continue parsing fields
153 while (i < TAIL && st.hasMoreTokens())
155 if ((field = st.nextToken(":")) != null)
157 if (!field.equals(":"))
159 // validate residue field value
162 resCode val = validResidueCode(field);
165 fields.put(new String(Fields[i] + "num"), val);
170 // "Ignoring non-Modeller description: invalid integer-like
171 // field '" + field + "'");
172 type = -1; /* invalid field! - throw the FieldSet away */
176 fields.put(Fields[i++], field);
177 if (st.hasMoreTokens())
179 st.nextToken(); // skip token sep.
190 // slurp remaining fields
191 while (st.hasMoreTokens())
193 String tl = st.nextToken(":");
194 field += tl.equals(":") ? tl : (":" + tl);
196 fields.put(Fields[TAIL], field);
202 // object is not a proper ModellerPIR object
203 fields = new java.util.Hashtable();
204 fields.put(Fields[TAIL], new String(desc));
208 fields.put(Fields[TYPE], seqTypes[type]);
213 ModellerDescription(String desc)
219 fields = parseDescription(desc);
222 void setStartCode(int v)
225 fields.put(Fields[START] + "num", r = new resCode(v));
226 fields.put(Fields[START], r.field);
229 void setEndCode(int v)
232 fields.put(Fields[END] + "num", r = new resCode(v));
233 fields.put(Fields[END], r.field);
237 * make a possibly updated modeller field line for the sequence object
242 ModellerDescription(SequenceI seq)
245 if (seq.getDescription() != null)
247 fields = parseDescription(seq.getDescription());
250 if (isModellerFieldset())
252 // Set start and end before we update the type (in the case of a
253 // synthesized field set)
254 if (getStartCode() == null || (getStartNum() != seq.getStart()
255 && getStartCode().val != null))
257 // unset or user updated sequence start position
258 setStartCode(seq.getStart());
261 if (getEndCode() == null || (getEndNum() != seq.getEnd()
262 && getStartCode() != null && getStartCode().val != null))
264 setEndCode(seq.getEnd());
270 setStartCode(seq.getStart());
271 setEndCode(seq.getEnd());
272 fields.put(Fields[LOCALID], seq.getName()); // this may be overwritten
274 // type - decide based on evidence of PDB database references - this also
275 // sets the local reference field
276 int t = 0; // sequence
277 if (seq.getDatasetSequence() != null
278 && seq.getDatasetSequence().getDBRefs() != null)
280 List<DBRefEntry> dbr = seq.getDatasetSequence().getDBRefs();
281 for (int i = 0, ni = dbr.size(); i < ni; i++)
283 DBRefEntry dbri = dbr.get(i);
286 // JBPNote PDB dbRefEntry needs properties to propagate onto
288 // JBPNote Need to get info from the user about whether the sequence
289 // is the one being modelled, or if it is a template.
291 .equals(jalview.datamodel.DBRefSource.PDB))
293 fields.put(Fields[LOCALID], dbri.getAccessionId());
300 fields.put(Fields[TYPE], seqTypes[t]);
306 * Indicate if fields parsed to a modeller-like colon-separated value line
310 boolean isModellerFieldset()
312 return (fields.containsKey(Fields[TYPE]));
315 String getDescriptionLine()
318 int lastfield = Fields.length - 1;
320 if (isModellerFieldset())
323 // try to write a minimal modeller field set, so..
325 // find the last valid field in the entry
327 for (; lastfield > 6; lastfield--)
329 if (fields.containsKey(Fields[lastfield]))
335 for (int i = 0; i < lastfield; i++)
337 value = (String) fields.get(Fields[i]);
338 if (value != null && value.length() > 0)
340 desc += ((String) fields.get(Fields[i])) + ":";
344 desc += Padding[i] + ":";
348 // just return the last field if no others were defined.
349 if (fields.containsKey(Fields[lastfield]))
351 desc += (String) fields.get(Fields[lastfield]);
363 resCode val = getStartCode();
364 if (val != null && val.val != null)
366 return val.val.intValue();
371 resCode getStartCode()
373 if (isModellerFieldset() && fields.containsKey(Fields[START] + "num"))
375 return (resCode) fields.get(Fields[START] + "num");
382 if (isModellerFieldset() && fields.containsKey(Fields[END] + "num"))
384 return (resCode) fields.get(Fields[END] + "num");
392 resCode val = getEndCode();
393 if (val != null && val.val != null)
395 return val.val.intValue();
401 * returns true if sequence object was modifed with a valid modellerField set
407 boolean updateSequenceI(SequenceI newSeq)
409 if (isModellerFieldset())
411 resCode rc = getStartCode();
412 if (rc != null && rc.val != null)
414 newSeq.setStart(getStartNum());
421 if (rc != null && rc.val != null)
423 newSeq.setEnd(getEndNum());
427 newSeq.setEnd(newSeq.getStart() + newSeq.getLength());