3 import jalview.analysis.AlignSeq;
4 import jalview.api.FeatureSettingsModelI;
5 import jalview.datamodel.Alignment;
6 import jalview.datamodel.AlignmentAnnotation;
7 import jalview.datamodel.AlignmentI;
8 import jalview.datamodel.DBRefEntry;
9 import jalview.datamodel.DBRefSource;
10 import jalview.datamodel.PDBEntry;
11 import jalview.datamodel.PDBEntry.Type;
12 import jalview.datamodel.SequenceI;
13 import jalview.structure.StructureImportSettings;
15 import java.awt.Color;
16 import java.io.IOException;
17 import java.lang.reflect.Constructor;
18 import java.util.Hashtable;
19 import java.util.List;
20 import java.util.Vector;
22 import MCview.PDBChain;
24 public abstract class StructureFile extends AlignFile
29 private PDBEntry.Type dbRefType;
32 * set to true to add derived sequence annotations (temp factor read from
33 * file, or computed secondary structure) to the alignment
35 protected boolean visibleChainAnnotation = false;
38 * Set true to predict secondary structure (using JMol for protein, Annotate3D
41 protected boolean predictSecondaryStructure = false;
44 * Set true (with predictSecondaryStructure=true) to predict secondary
45 * structure using an external service (currently Annotate3D for RNA only)
47 protected boolean externalSecondaryStructure = false;
49 private Vector<PDBChain> chains;
51 public StructureFile(String inFile, String type) throws IOException
56 public StructureFile(FileParse fp) throws IOException
61 public void addSettings(boolean addAlignmentAnnotations,
62 boolean predictSecondaryStructure, boolean externalSecStr)
64 this.visibleChainAnnotation = addAlignmentAnnotations;
65 this.predictSecondaryStructure = predictSecondaryStructure;
66 this.externalSecondaryStructure = externalSecStr;
69 public void xferSettings()
71 this.visibleChainAnnotation = StructureImportSettings
72 .isVisibleChainAnnotation();
73 this.predictSecondaryStructure = StructureImportSettings
74 .isProcessSecondaryStructure();
75 this.externalSecondaryStructure = StructureImportSettings
76 .isExternalSecondaryStructure();
80 public StructureFile(boolean parseImmediately, String dataObject, String type)
83 super(parseImmediately, dataObject, type);
86 public StructureFile(boolean a, FileParse fp) throws IOException
91 public StructureFile()
95 @SuppressWarnings("rawtypes")
96 protected SequenceI postProcessChain(PDBChain chain)
98 SequenceI pdbSequence = chain.sequence;
99 pdbSequence.setName(getId() + "|" + pdbSequence.getName());
100 PDBEntry entry = new PDBEntry();
101 entry.setId(getId());
102 entry.setType(this.dbRefType);
103 entry.setProperty(new Hashtable());
104 if (chain.id != null)
106 entry.setChainCode(String.valueOf(chain.id));
110 entry.setFile(inFile.getAbsolutePath());
114 entry.setFile(getDataName());
117 DBRefEntry sourceDBRef = new DBRefEntry();
118 sourceDBRef.setAccessionId(getId());
119 sourceDBRef.setSource(DBRefSource.PDB);
120 pdbSequence.setSourceDBRef(sourceDBRef);
121 pdbSequence.addPDBId(entry);
122 pdbSequence.addDBRef(sourceDBRef);
123 SequenceI chainseq = pdbSequence;
124 seqs.addElement(chainseq);
125 AlignmentAnnotation[] chainannot = chainseq.getAnnotation();
127 if (chainannot != null && visibleChainAnnotation)
129 for (int ai = 0; ai < chainannot.length; ai++)
131 chainannot[ai].visible = visibleChainAnnotation;
132 annotations.addElement(chainannot[ai]);
138 @SuppressWarnings({ "unchecked", "rawtypes" })
139 protected void processPdbFileWithAnnotate3d(List<SequenceI> rna)
142 // System.out.println("this is a PDB format and RNA sequence");
143 // note: we use reflection here so that the applet can compile and run
144 // without the HTTPClient bits and pieces needed for accessing Annotate3D
148 Class cl = Class.forName("jalview.ws.jws1.Annotate3D");
151 // TODO: use the PDB ID of the structure if one is available, to save
152 // bandwidth and avoid uploading the whole structure to the service
153 Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(
155 AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor",
156 new Class[] { FileParse.class }).invoke(annotate3d,
157 new Object[] { new FileParse(getDataName(), type) }));
158 for (SequenceI sq : al.getSequences())
160 if (sq.getDatasetSequence() != null)
162 if (sq.getDatasetSequence().getAllPDBEntries() != null)
164 sq.getDatasetSequence().getAllPDBEntries().clear();
169 if (sq.getAllPDBEntries() != null)
171 sq.getAllPDBEntries().clear();
175 replaceAndUpdateChains(rna, al, AlignSeq.DNA, false);
177 } catch (ClassNotFoundException x)
179 // ignore classnotfounds - occurs in applet
183 @SuppressWarnings("unchecked")
184 protected void replaceAndUpdateChains(List<SequenceI> prot,
185 AlignmentI al, String pep, boolean b)
187 List<List<? extends Object>> replaced = AlignSeq
188 .replaceMatchingSeqsWith(seqs, annotations, prot, al, pep,
190 for (PDBChain ch : getChains())
193 for (SequenceI sq : (List<SequenceI>) replaced.get(0))
196 if (sq == ch.sequence || sq.getDatasetSequence() == ch.sequence)
205 // set shadow entry for chains
206 ch.shadow = (SequenceI) replaced.get(1).get(p);
207 ch.shadowMap = ((AlignSeq) replaced.get(2).get(p))
208 .getMappingFromS1(false);
214 * Predict secondary structure for RNA and/or protein sequences and add as
217 * @param rnaSequences
218 * @param proteinSequences
220 protected void addSecondaryStructure(List<SequenceI> rnaSequences,
221 List<SequenceI> proteinSequences)
224 * Currently using Annotate3D for RNA, but only if the 'use external
225 * prediction' flag is set
227 if (externalSecondaryStructure && rnaSequences.size() > 0)
231 processPdbFileWithAnnotate3d(rnaSequences);
232 } catch (Exception x)
234 System.err.println("Exceptions when dealing with RNA in pdb file");
241 * Currently using JMol PDB parser for peptide
243 if (proteinSequences.size() > 0)
247 processWithJmolParser(proteinSequences);
248 } catch (Exception x)
251 .println("Exceptions from Jmol when processing data in pdb file");
257 @SuppressWarnings({ "unchecked", "rawtypes" })
258 private void processWithJmolParser(List<SequenceI> prot) throws Exception
263 Class cl = Class.forName("jalview.ext.jmol.JmolParser");
266 final Constructor constructor = cl.getConstructor(new Class[] {
267 boolean.class, boolean.class, boolean.class, FileParse.class });
268 final Object[] args = new Object[] { visibleChainAnnotation,
269 predictSecondaryStructure, externalSecondaryStructure,
270 new FileParse(getDataName(), type) };
272 StructureImportSettings.setShowSeqFeatures(false);
273 StructureImportSettings.setVisibleChainAnnotation(false);
274 StructureImportSettings
275 .setProcessSecondaryStructure(predictSecondaryStructure);
276 StructureImportSettings
277 .setExternalSecondaryStructure(externalSecondaryStructure);
278 Object jmf = constructor.newInstance(args);
279 AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
280 "getSeqsAsArray", new Class[] {}).invoke(jmf));
281 cl.getMethod("addAnnotations", new Class[] { AlignmentI.class })
283 for (SequenceI sq : al.getSequences())
285 if (sq.getDatasetSequence() != null)
287 sq.getDatasetSequence().getAllPDBEntries().clear();
291 sq.getAllPDBEntries().clear();
294 replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
296 } catch (ClassNotFoundException q)
299 StructureImportSettings.setShowSeqFeatures(true);
302 public PDBChain findChain(String id) throws Exception
304 for (PDBChain chain : getChains())
306 if (chain.id.equals(id))
311 throw new Exception("PDB chain not Found!");
314 public void makeResidueList()
316 for (PDBChain chain : getChains())
318 chain.makeResidueList(visibleChainAnnotation);
322 public void makeCaBondList()
324 for (PDBChain chain : getChains())
326 chain.makeCaBondList();
330 public void setChargeColours()
332 for (PDBChain chain : getChains())
334 chain.setChargeColours();
338 public void setColours(jalview.schemes.ColourSchemeI cs)
340 for (PDBChain chain : getChains())
342 chain.setChainColours(cs);
346 public void setChainColours()
349 for (PDBChain chain : getChains())
351 chain.setChainColours(Color.getHSBColor(1.0f / i++, .4f, 1.0f));
355 public static boolean isRNA(SequenceI seq)
357 for (char c : seq.getSequence())
359 if ((c != 'A') && (c != 'C') && (c != 'G') && (c != 'U'))
368 * make a friendly ID string.
371 * @return truncated dataName to after last '/'
373 protected String safeName(String dataName)
376 while ((p = dataName.indexOf("/")) > -1 && p < dataName.length())
378 dataName = dataName.substring(p + 1);
383 public String getId()
388 public void setId(String id)
393 public Vector<PDBChain> getChains()
398 public void setChains(Vector<PDBChain> chains)
400 this.chains = chains;
403 public Type getDbRefType()
408 public void setDbRefType(String dbRefType)
410 this.dbRefType = Type.valueOf(dbRefType);
413 public void setDbRefType(Type dbRefType)
415 this.dbRefType = dbRefType;
419 * Returns a descriptor for suitable feature display settings with
421 * <li>ResNums or insertions features visible</li>
422 * <li>insertions features coloured red</li>
423 * <li>ResNum features coloured by label</li>
424 * <li>Insertions displayed above (on top of) ResNums</li>
428 public FeatureSettingsModelI getFeatureColourScheme()
430 return new PDBFeatureSettings();