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.analysis.AlignSeq;
24 import jalview.api.FeatureSettingsModelI;
25 import jalview.datamodel.Alignment;
26 import jalview.datamodel.AlignmentAnnotation;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.DBRefEntry;
29 import jalview.datamodel.DBRefSource;
30 import jalview.datamodel.PDBEntry;
31 import jalview.datamodel.PDBEntry.Type;
32 import jalview.datamodel.SequenceI;
33 import jalview.structure.StructureImportSettings;
35 import java.awt.Color;
36 import java.io.IOException;
37 import java.lang.reflect.Constructor;
38 import java.util.List;
39 import java.util.Vector;
41 import mc_view.PDBChain;
43 public abstract class StructureFile extends AlignFile
47 private PDBEntry.Type dbRefType;
50 * set to true to add derived sequence annotations (temp factor read from
51 * file, or computed secondary structure) to the alignment
53 protected boolean visibleChainAnnotation = false;
56 * Set true to predict secondary structure (using JMol for protein, Annotate3D
59 protected boolean predictSecondaryStructure = false;
62 * Set true (with predictSecondaryStructure=true) to predict secondary
63 * structure using an external service (currently Annotate3D for RNA only)
65 protected boolean externalSecondaryStructure = false;
67 private Vector<PDBChain> chains;
69 private boolean pdbIdAvailable;
71 public StructureFile(Object inFile, DataSourceType sourceType)
74 super(inFile, sourceType);
77 public StructureFile(FileParse fp) throws IOException
82 public void addSettings(boolean addAlignmentAnnotations,
83 boolean predictSecondaryStructure, boolean externalSecStr)
85 this.visibleChainAnnotation = addAlignmentAnnotations;
86 this.predictSecondaryStructure = predictSecondaryStructure;
87 this.externalSecondaryStructure = externalSecStr;
90 public void xferSettings()
92 this.visibleChainAnnotation = StructureImportSettings
93 .isVisibleChainAnnotation();
94 this.predictSecondaryStructure = StructureImportSettings
95 .isProcessSecondaryStructure();
96 this.externalSecondaryStructure = StructureImportSettings
97 .isExternalSecondaryStructure();
101 public StructureFile(boolean parseImmediately, Object dataObject,
102 DataSourceType sourceType) throws IOException
104 super(parseImmediately, dataObject, sourceType);
107 public StructureFile(boolean a, FileParse fp) throws IOException
112 public StructureFile()
116 protected SequenceI postProcessChain(PDBChain chain)
118 SequenceI pdbSequence = chain.sequence;
119 pdbSequence.setName(getId() + "|" + pdbSequence.getName());
120 PDBEntry entry = new PDBEntry();
121 entry.setId(getId());
122 entry.setFakedPDBId(!isPPDBIdAvailable());
123 entry.setType(getStructureFileType());
124 if (chain.id != null)
126 entry.setChainCode(chain.id);
130 entry.setFile(inFile.getAbsolutePath());
134 entry.setFile(getDataName());
137 DBRefEntry sourceDBRef = new DBRefEntry();
138 sourceDBRef.setAccessionId(getId());
139 sourceDBRef.setSource(DBRefSource.PDB);
140 // TODO: specify version for 'PDB' database ref if it is read from a file.
141 // TODO: decide if jalview.io should be creating primary refs!
142 sourceDBRef.setVersion("");
143 pdbSequence.addPDBId(entry);
144 pdbSequence.addDBRef(sourceDBRef);
145 SequenceI chainseq = pdbSequence;
146 seqs.addElement(chainseq);
147 AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
149 if (chainannot != null && visibleChainAnnotation)
151 for (int ai = 0; ai < chainannot.length; ai++)
153 chainannot[ai].visible = visibleChainAnnotation;
154 annotations.addElement(chainannot[ai]);
161 * filetype of structure file - default is PDB
163 String structureFileType = PDBEntry.Type.PDB.toString();
165 protected void setStructureFileType(String structureFileType)
167 this.structureFileType = structureFileType;
171 * filetype of last file processed
175 public String getStructureFileType()
177 return structureFileType;
180 @SuppressWarnings({ "unchecked", "rawtypes" })
181 protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
184 // System.out.println("this is a PDB format and RNA sequence");
185 // note: we use reflection here so that the applet can compile and run
186 // without the HTTPClient bits and pieces needed for accessing Annotate3D
190 Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
193 // TODO: use the PDB ID of the structure if one is available, to save
194 // bandwidth and avoid uploading the whole structure to the service
195 Object annotate3d = cl.getConstructor(new Class[] {})
196 .newInstance(new Object[] {});
197 AlignmentI al = ((AlignmentI) cl
198 .getMethod("getRNAMLFor", new Class[]
200 .invoke(annotate3d, new Object[]
201 { new FileParse(getDataName(), dataSourceType) }));
202 for (SequenceI sq : al.getSequences())
204 if (sq.getDatasetSequence() != null)
206 if (sq.getDatasetSequence().getAllPDBEntries() != null)
208 sq.getDatasetSequence().getAllPDBEntries().clear();
213 if (sq.getAllPDBEntries() != null)
215 sq.getAllPDBEntries().clear();
219 replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
221 } catch (ClassNotFoundException x)
223 // ignore classnotfounds - occurs in applet
227 @SuppressWarnings("unchecked")
228 protected void replaceAndUpdateChains(List<SequenceI> prot, AlignmentI al,
229 String pep, boolean b)
231 List<List<? extends Object>> replaced = AlignSeq
232 .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
234 for (PDBChain ch : getChains())
237 for (SequenceI sq : (List<SequenceI>) replaced.get(0))
240 if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
249 // set shadow entry for chains
250 ch.shadow = (SequenceI) replaced.get(1).get(p);
251 ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
252 .getMappingFromS1(false);
258 * Predict secondary structure for RNA and/or protein sequences and add as
261 * @param rnaSequences
262 * @param proteinSequences
264 protected void addSecondaryStructure(List<SequenceI> rnaSequences,
265 List<SequenceI> proteinSequences)
268 * Currently using Annotate3D for RNA, but only if the 'use external
269 * prediction' flag is set
271 if (externalSecondaryStructure && rnaSequences.size() > 0)
275 processPdbFileWithAnnotate3d(rnaSequences);
276 } catch (Exception x)
278 System.err.println("Exceptions when dealing with RNA in pdb file");
285 * Currently using JMol PDB parser for peptide
287 if (proteinSequences.size() > 0)
291 processWithJmolParser(proteinSequences);
292 } catch (Exception x)
295 "Exceptions from Jmol when processing data in pdb file");
301 @SuppressWarnings({ "unchecked", "rawtypes" })
302 private void processWithJmolParser(List<SequenceI> prot) throws Exception
307 Class cl = Class.forName("jalview.ext.jmol.JmolParser");
310 final Constructor constructor = cl
311 .getConstructor(new Class[]
312 { FileParse.class });
313 final Object[] args = new Object[] {
314 new FileParse(getDataName(), dataSourceType) };
316 StructureImportSettings.setShowSeqFeatures(false);
317 StructureImportSettings.setVisibleChainAnnotation(false);
318 StructureImportSettings
319 .setProcessSecondaryStructure(predictSecondaryStructure);
320 StructureImportSettings
321 .setExternalSecondaryStructure(externalSecondaryStructure);
322 Object jmf = constructor.newInstance(args);
323 AlignmentI al = new Alignment((SequenceI[]) cl
324 .getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
325 cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
327 for (SequenceI sq : al.getSequences())
329 if (sq.getDatasetSequence() != null)
331 sq.getDatasetSequence().getAllPDBEntries().clear();
335 sq.getAllPDBEntries().clear();
338 replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
340 } catch (ClassNotFoundException q)
343 StructureImportSettings.setShowSeqFeatures(true);
347 * Answers the first PDBChain found matching the given id, or null if none is
353 public PDBChain findChain(String id)
355 for (PDBChain chain : getChains())
357 if (chain.id.equals(id))
365 public void makeResidueList()
367 for (PDBChain chain : getChains())
369 chain.makeResidueList(visibleChainAnnotation);
373 public void makeCaBondList()
375 for (PDBChain chain : getChains())
377 chain.makeCaBondList();
381 public void setChargeColours()
383 for (PDBChain chain : getChains())
385 chain.setChargeColours();
389 public void setColours(jalview.schemes.ColourSchemeI cs)
391 for (PDBChain chain : getChains())
393 chain.setChainColours(cs);
397 public void setChainColours()
400 for (PDBChain chain : getChains())
402 chain.setChainColours(Color.getHSBColor(1.0f / i++, .4f, 1.0f));
406 public static boolean isRNA(SequenceI seq)
408 int length = seq.getLength();
409 for (int i = 0; i < length; i++)
411 char c = seq.getCharAt(i);
412 if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
421 * make a friendly ID string.
424 * @return truncated dataName to after last '/' and pruned .extension if
427 protected String safeName(String dataName)
430 while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
432 dataName = dataName.substring(p + 1);
434 if (dataName.indexOf(".") > -1)
436 dataName = dataName.substring(0, dataName.lastIndexOf("."));
441 public String getId()
446 public void setId(String id)
451 public Vector<PDBChain> getChains()
456 public void setChains(Vector<PDBChain> chains)
458 this.chains = chains;
461 public Type getDbRefType()
466 public void setDbRefType(String dbRefType)
468 this.dbRefType = Type.getType(dbRefType);
471 public void setDbRefType(Type dbRefType)
473 this.dbRefType = dbRefType;
477 * Returns a descriptor for suitable feature display settings with
479 * <li>ResNums or insertions features visible</li>
480 * <li>insertions features coloured red</li>
481 * <li>ResNum features coloured by label</li>
482 * <li>Insertions displayed above (on top of) ResNums</li>
486 public FeatureSettingsModelI getFeatureColourScheme()
488 return new PDBFeatureSettings();
492 * Answers true if the structure file has a PDBId
496 public boolean isPPDBIdAvailable()
498 return pdbIdAvailable;
501 public void setPDBIdAvailable(boolean pdbIdAvailable)
503 this.pdbIdAvailable = pdbIdAvailable;