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 java.awt.Color;
24 import java.io.IOException;
25 import java.lang.reflect.Constructor;
26 import java.net.MalformedURLException;
27 import java.util.List;
28 import java.util.Vector;
30 import jalview.analysis.AlignSeq;
31 import jalview.api.FeatureSettingsModelI;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentAnnotation;
34 import jalview.datamodel.AlignmentI;
35 import jalview.datamodel.DBRefEntry;
36 import jalview.datamodel.DBRefSource;
37 import jalview.datamodel.PDBEntry;
38 import jalview.datamodel.PDBEntry.Type;
39 import jalview.datamodel.SequenceI;
40 import jalview.ext.jmol.JmolParser;
41 import jalview.structure.StructureImportSettings;
42 import jalview.structure.StructureImportSettings.TFType;
43 import mc_view.PDBChain;
45 public abstract class StructureFile extends AlignFile
49 private PDBEntry.Type dbRefType;
52 * set to true to add derived sequence annotations (temp factor read from
53 * file, or computed secondary structure) to the alignment
55 protected boolean visibleChainAnnotation = false;
58 * Set true to predict secondary structure (using JMol for protein, Annotate3D
61 protected boolean predictSecondaryStructure = false;
64 * Set true (with predictSecondaryStructure=true) to predict secondary
65 * structure using an external service (currently Annotate3D for RNA only)
67 protected boolean externalSecondaryStructure = false;
69 private Vector<PDBChain> chains;
71 private boolean pdbIdAvailable;
73 private TFType temperatureFactorType = TFType.DEFAULT;
75 private String paeMatrix = null;
77 private boolean alphaFoldModel;
79 public void setPAEMatrix(String paeFilename)
81 paeMatrix = paeFilename;
84 public String getPAEMatrix()
89 public boolean hasPAEMatrix()
91 return paeMatrix != null;
94 public void setTemperatureFactorType(TFType t)
96 this.temperatureFactorType = t;
99 public TFType getTemperatureFactorType()
101 return temperatureFactorType;
104 public void setAlphafoldModel(boolean afm)
106 alphaFoldModel = afm;
109 public boolean isAlphafoldModel()
111 return alphaFoldModel;
114 public StructureFile(Object inFile, DataSourceType sourceType)
117 this(inFile, sourceType, null);
120 public StructureFile(Object inFile, DataSourceType sourceType,
121 TFType tempfacType) throws IOException
123 super(false, inFile, sourceType);
124 this.setTemperatureFactorType(tempfacType);
128 public StructureFile(FileParse fp) throws IOException
133 public StructureFile(FileParse fp, boolean doXferSettings)
136 super(fp, doXferSettings);
139 public void addSettings(boolean addAlignmentAnnotations,
140 boolean predictSecondaryStructure, boolean externalSecStr)
142 this.visibleChainAnnotation = addAlignmentAnnotations;
143 this.predictSecondaryStructure = predictSecondaryStructure;
144 this.externalSecondaryStructure = externalSecStr;
147 public void xferSettings()
149 if (this.getDoXferSettings())
151 this.visibleChainAnnotation = StructureImportSettings
152 .isVisibleChainAnnotation();
153 this.predictSecondaryStructure = StructureImportSettings
154 .isProcessSecondaryStructure();
155 this.externalSecondaryStructure = StructureImportSettings
156 .isExternalSecondaryStructure();
157 this.temperatureFactorType = StructureImportSettings
158 .getTemperatureFactorType();
162 public StructureFile(boolean parseImmediately, Object dataObject,
163 DataSourceType sourceType) throws IOException
165 super(parseImmediately, dataObject, sourceType);
168 public StructureFile(boolean a, FileParse fp) throws IOException
173 public StructureFile()
177 protected SequenceI postProcessChain(PDBChain chain)
179 SequenceI pdbSequence = chain.sequence;
180 pdbSequence.setName(getId() + "|" + pdbSequence.getName());
181 PDBEntry entry = new PDBEntry();
182 entry.setId(getId());
183 entry.setFakedPDBId(!isPPDBIdAvailable());
184 entry.setType(getStructureFileType());
185 if (chain.id != null)
187 entry.setChainCode(chain.id);
191 entry.setFile(inFile.getAbsolutePath());
195 entry.setFile(getDataName());
198 DBRefEntry sourceDBRef = new DBRefEntry();
199 sourceDBRef.setAccessionId(getId());
200 sourceDBRef.setSource(DBRefSource.PDB);
201 // TODO: specify version for 'PDB' database ref if it is read from a file.
202 // TODO: decide if jalview.io should be creating primary refs!
203 sourceDBRef.setVersion("");
204 pdbSequence.addPDBId(entry);
205 pdbSequence.addDBRef(sourceDBRef);
206 SequenceI chainseq = pdbSequence;
207 seqs.addElement(chainseq);
208 AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
210 if (chainannot != null && visibleChainAnnotation)
212 for (int ai = 0; ai < chainannot.length; ai++)
214 chainannot[ai].visible = visibleChainAnnotation;
215 annotations.addElement(chainannot[ai]);
222 * filetype of structure file - default is PDB
224 String structureFileType = PDBEntry.Type.PDB.toString();
226 protected void setStructureFileType(String structureFileType)
228 this.structureFileType = structureFileType;
232 * filetype of last file processed
236 public String getStructureFileType()
238 return structureFileType;
241 @SuppressWarnings({ "unchecked", "rawtypes" })
242 protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
245 // System.out.println("this is a PDB format and RNA sequence");
246 // note: we use reflection here so that the applet can compile and run
247 // without the HTTPClient bits and pieces needed for accessing Annotate3D
251 Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
254 // TODO: use the PDB ID of the structure if one is available, to save
255 // bandwidth and avoid uploading the whole structure to the service
256 Object annotate3d = cl.getConstructor(new Class[] {})
257 .newInstance(new Object[] {});
258 AlignmentI al = ((AlignmentI) cl
259 .getMethod("getRNAMLFor", new Class[]
261 .invoke(annotate3d, new Object[]
262 { new FileParse(getDataName(), dataSourceType) }));
263 for (SequenceI sq : al.getSequences())
265 if (sq.getDatasetSequence() != null)
267 if (sq.getDatasetSequence().getAllPDBEntries() != null)
269 sq.getDatasetSequence().getAllPDBEntries().clear();
274 if (sq.getAllPDBEntries() != null)
276 sq.getAllPDBEntries().clear();
280 replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
282 } catch (ClassNotFoundException x)
284 // ignore classnotfounds - occurs in applet
288 @SuppressWarnings("unchecked")
289 protected void replaceAndUpdateChains(List<SequenceI> prot, AlignmentI al,
290 String pep, boolean b)
292 List<List<? extends Object>> replaced = AlignSeq
293 .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
295 for (PDBChain ch : getChains())
298 for (SequenceI sq : (List<SequenceI>) replaced.get(0))
301 if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
310 // set shadow entry for chains
311 ch.shadow = (SequenceI) replaced.get(1).get(p);
312 ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
313 .getMappingFromS1(false);
319 * Predict secondary structure for RNA and/or protein sequences and add as
322 * @param rnaSequences
323 * @param proteinSequences
325 protected void addSecondaryStructure(List<SequenceI> rnaSequences,
326 List<SequenceI> proteinSequences)
329 * Currently using Annotate3D for RNA, but only if the 'use external
330 * prediction' flag is set
332 if (externalSecondaryStructure && rnaSequences.size() > 0)
336 processPdbFileWithAnnotate3d(rnaSequences);
337 } catch (Exception x)
339 System.err.println("Exceptions when dealing with RNA in pdb file");
346 * Currently using JMol PDB parser for peptide
348 if (proteinSequences.size() > 0)
352 processWithJmolParser(proteinSequences, true);
353 } catch (Exception x)
356 "Exceptions from Jmol when processing data in pdb file");
362 private void processWithJmolParser(List<SequenceI> prot,
363 boolean doXferSettings) throws MalformedURLException, IOException
365 FileParse fp = new FileParse(getDataName(), dataSourceType);
367 StructureImportSettings.setShowSeqFeatures(false);
368 StructureImportSettings.setVisibleChainAnnotation(false);
369 StructureImportSettings
370 .setProcessSecondaryStructure(predictSecondaryStructure);
371 StructureImportSettings
372 .setExternalSecondaryStructure(externalSecondaryStructure);
373 StructureImportSettings.setTemperatureFactorType(temperatureFactorType);
374 JmolParser jmf = new JmolParser(fp, doXferSettings);
375 AlignmentI al = new Alignment((SequenceI[]) jmf.getSeqsAsArray());
376 jmf.addAnnotations(al);
377 for (SequenceI sq : al.getSequences())
379 if (sq.getDatasetSequence() != null)
381 sq.getDatasetSequence().getAllPDBEntries().clear();
385 sq.getAllPDBEntries().clear();
388 replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
389 StructureImportSettings.setShowSeqFeatures(true);
393 * Answers the first PDBChain found matching the given id, or null if none is
399 public PDBChain findChain(String id)
401 for (PDBChain chain : getChains())
403 if (chain.id.equals(id))
411 public void makeResidueList()
413 for (PDBChain chain : getChains())
415 chain.makeResidueList(visibleChainAnnotation);
419 public void makeCaBondList()
421 for (PDBChain chain : getChains())
423 chain.makeCaBondList();
427 public void setChargeColours()
429 for (PDBChain chain : getChains())
431 chain.setChargeColours();
435 public void setColours(jalview.schemes.ColourSchemeI cs)
437 for (PDBChain chain : getChains())
439 chain.setChainColours(cs);
443 public void setChainColours()
446 for (PDBChain chain : getChains())
448 chain.setChainColours(Color.getHSBColor(1.0f / i++, .4f, 1.0f));
452 public static boolean isRNA(SequenceI seq)
454 int length = seq.getLength();
455 for (int i = 0; i < length; i++)
457 char c = seq.getCharAt(i);
458 if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
467 * make a friendly ID string.
470 * @return truncated dataName to after last '/' and pruned .extension if
473 protected String safeName(String dataName)
476 while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
478 dataName = dataName.substring(p + 1);
480 if (dataName.indexOf(".") > -1)
482 dataName = dataName.substring(0, dataName.lastIndexOf("."));
487 public String getId()
492 public void setId(String id)
497 public Vector<PDBChain> getChains()
502 public void setChains(Vector<PDBChain> chains)
504 this.chains = chains;
507 public Type getDbRefType()
512 public void setDbRefType(String dbRefType)
514 this.dbRefType = Type.getType(dbRefType);
517 public void setDbRefType(Type dbRefType)
519 this.dbRefType = dbRefType;
523 * Returns a descriptor for suitable feature display settings with
525 * <li>ResNums or insertions features visible</li>
526 * <li>insertions features coloured red</li>
527 * <li>ResNum features coloured by label</li>
528 * <li>Insertions displayed above (on top of) ResNums</li>
532 public FeatureSettingsModelI getFeatureColourScheme()
534 return new PDBFeatureSettings();
538 * Answers true if the structure file has a PDBId
542 public boolean isPPDBIdAvailable()
544 return pdbIdAvailable;
547 public void setPDBIdAvailable(boolean pdbIdAvailable)
549 this.pdbIdAvailable = pdbIdAvailable;