Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Pdb	51	59	31	0.00%	Show methods

Class Pdb

Class Pdb	Line # 51	Total Statements 59	Complexity 31	TOTAL Coverage 0.00%
Pdb()   Pdb()	5959	1.01	1.01	0.0 0.00%
getAccessionSeparator() : String   getAccessionSeparator() : String	6969	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	8080	1.01	1.01	0.0 0.00%
getDbSource() : String   getDbSource() : String	9191	1.01	1.01	0.0 0.00%
getDbVersion() : String   getDbVersion() : String	102102	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	113113	48.048	21.021	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	256256	2.02	1.01	0.0 0.00%
getTestQuery() : String   getTestQuery() : String	266266	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	272272	1.01	1.01	0.0 0.00%
getTier() : int   getTier() : int	278278	1.01	1.01	0.0 0.00%
getFeatureColourScheme() : FeatureSettingsModelI   getFeatureColourScheme() : FeatureSettingsModelI	293293	1.01	1.01	0.0 0.00%

 

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1
2		/*
3		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4		* Copyright (C) $$Year-Rel$$ The Jalview Authors
5		*
6		* This file is part of Jalview.
7		*
8		* Jalview is free software: you can redistribute it and/or
9		* modify it under the terms of the GNU General Public License
10		* as published by the Free Software Foundation, either version 3
11		* of the License, or (at your option) any later version.
12		*
13		* Jalview is distributed in the hope that it will be useful, but
14		* WITHOUT ANY WARRANTY; without even the implied warranty
15		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16		* PURPOSE. See the GNU General Public License for more details.
17		*
18		* You should have received a copy of the GNU General Public License
19		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20		* The Jalview Authors are detailed in the 'AUTHORS' file.
21		*/
22		package jalview.ws.dbsources;
23
24		import jalview.api.FeatureSettingsModelI;
25		import jalview.datamodel.AlignmentAnnotation;
26		import jalview.datamodel.AlignmentI;
27		import jalview.datamodel.DBRefEntry;
28		import jalview.datamodel.DBRefSource;
29		import jalview.datamodel.PDBEntry;
30		import jalview.datamodel.PDBEntry.Type;
31		import jalview.datamodel.SequenceI;
32		import jalview.io.DataSourceType;
33		import jalview.io.FileFormat;
34		import jalview.io.FileFormatI;
35		import jalview.io.FormatAdapter;
36		import jalview.io.PDBFeatureSettings;
37		import jalview.structure.StructureImportSettings;
38		import jalview.util.MessageManager;
39		import jalview.ws.ebi.EBIFetchClient;
40
41		import java.io.File;
42		import java.util.ArrayList;
43		import java.util.List;
44
45		import com.stevesoft.pat.Regex;
46
47		/**
48		* @author JimP
49		*
50		*/
		0% Uncovered Elements: 94 (94) Complexity: 31 Complexity Density: 0.53
51		public class Pdb extends EbiFileRetrievedProxy
52		{
53		private static final String SEPARATOR = "|";
54
55		private static final String COLON = ":";
56
57		private static final int PDB_ID_LENGTH = 4;
58
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
59	0	public Pdb()...
60		{
61	0	super();
62		}
63
64		/*
65		* (non-Javadoc)
66		*
67		* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
68		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
69	0	@Override...
70		public String getAccessionSeparator()
71		{
72	0	return null;
73		}
74
75		/*
76		* (non-Javadoc)
77		*
78		* @see jalview.ws.DbSourceProxy#getAccessionValidator()
79		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
80	0	@Override...
81		public Regex getAccessionValidator()
82		{
83	0	return new Regex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
84		}
85
86		/*
87		* (non-Javadoc)
88		*
89		* @see jalview.ws.DbSourceProxy#getDbSource()
90		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
91	0	@Override...
92		public String getDbSource()
93		{
94	0	return DBRefSource.PDB;
95		}
96
97		/*
98		* (non-Javadoc)
99		*
100		* @see jalview.ws.DbSourceProxy#getDbVersion()
101		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
102	0	@Override...
103		public String getDbVersion()
104		{
105	0	return "0";
106		}
107
108		/*
109		* (non-Javadoc)
110		*
111		* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
112		*/
		0% Uncovered Elements: 72 (72) Complexity: 21 Complexity Density: 0.44
113	0	@Override...
114		public AlignmentI getSequenceRecords(String queries) throws Exception
115		{
116	0	AlignmentI pdbAlignment = null;
117	0	String chain = null;
118	0	String id = null;
119	0	if (queries.indexOf(COLON) > -1)
120		{
121	0	chain = queries.substring(queries.indexOf(COLON) + 1);
122	0	id = queries.substring(0, queries.indexOf(COLON));
123		}
124		else
125		{
126	0	id = queries;
127		}
128
129		/*
130		* extract chain code if it is appended to the id and we
131		* don't already have one
132		*/
133	0	if (queries.length() > PDB_ID_LENGTH && chain == null)
134		{
135	0	chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
136	0	id = queries.substring(0, PDB_ID_LENGTH);
137		}
138
139	0	if (!isValidReference(id))
140		{
141	0	jalview.bin.Console
142		.errPrintln("Ignoring invalid pdb query: '" + id + "'");
143	0	stopQuery();
144	0	return null;
145		}
146
147		/*
148		* ensure that an mmCIF format structure file is saved with extension.cif,
149		* because the Chimera "open" command recognises this extension
150		*/
151	0	Type pdbFileFormat = StructureImportSettings
152		.getDefaultStructureFileFormat();
153	0	String ext = pdbFileFormat.getExtension();
154	0	String fetchFormat = pdbFileFormat.getFormat();
155
156	0	EBIFetchClient ebi = new EBIFetchClient();
157	0	File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext);
158	0	file = tmpFile.getAbsolutePath();
159	0	stopQuery();
160	0	if (file == null)
161		{
162	0	return null;
163		}
164	0	try
165		{
166		// todo get rid of Type and use FileFormatI instead?
167	0	FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
168		: FileFormat.MMCif;
169	0	pdbAlignment = new FormatAdapter().readFile(tmpFile,
170		DataSourceType.FILE, fileFormat);
171	0	if (pdbAlignment != null)
172		{
173	0	List<SequenceI> toremove = new ArrayList<SequenceI>();
174	0	for (SequenceI pdbcs : pdbAlignment.getSequences())
175		{
176	0	String chid = null;
177		// Mapping map=null;
178	0	for (PDBEntry pid : pdbcs.getAllPDBEntries())
179		{
180	0	if (pid.getFile() == file)
181		{
182	0	chid = pid.getChainCode();
183
184		}
185		}
186	0	if (chain == null || (chid != null && (chid.equals(chain)
187		|| chid.trim().equals(chain.trim())
188		|| (chain.trim().length() == 0 && chid.equals("_")))))
189		{
190		// FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
191		// TODO: suggest simplify naming to 1qip|A as default name defined
192	0	pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
193		+ SEPARATOR + pdbcs.getName());
194		// Might need to add more metadata to the PDBEntry object
195		// like below
196		/*
197		* PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
198		* entry.setId(id); if (entry.getProperty() == null)
199		* entry.setProperty(new Hashtable());
200		* entry.getProperty().put("chains", pdbchain.id + "=" +
201		* sq.getStart() + "-" + sq.getEnd());
202		* sq.getDatasetSequence().addPDBId(entry);
203		*/
204		// Add PDB DB Refs
205		// We make a DBRefEtntry because we have obtained the PDB file from
206		// a
207		// verifiable source
208		// JBPNote - PDB DBRefEntry should also carry the chain and mapping
209		// information
210	0	DBRefEntry dbentry = new DBRefEntry(getDbSource(),
211	0	getDbVersion(), (chid == null ? id : id + chid));
212		// dbentry.setMap()
213	0	pdbcs.addDBRef(dbentry);
214		}
215		else
216		{
217		// mark this sequence to be removed from the alignment
218		// - since it's not from the right chain
219	0	toremove.add(pdbcs);
220		}
221		}
222		// now remove marked sequences
223	0	for (SequenceI pdbcs : toremove)
224		{
225	0	pdbAlignment.deleteSequence(pdbcs);
226	0	if (pdbcs.getAnnotation() != null)
227		{
228	0	for (AlignmentAnnotation aa : pdbcs.getAnnotation())
229		{
230	0	pdbAlignment.deleteAnnotation(aa);
231		}
232		}
233		}
234		}
235
236	0	if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
237		{
238	0	throw new Exception(MessageManager.formatMessage(
239		"exception.no_pdb_records_for_chain", new String[]
240	0	{ id, ((chain == null) ? "' '" : chain) }));
241		}
242
243		} catch (Exception ex) // Problem parsing PDB file
244		{
245	0	stopQuery();
246	0	throw (ex);
247		}
248	0	return pdbAlignment;
249		}
250
251		/*
252		* (non-Javadoc)
253		*
254		* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
255		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
256	0	@Override...
257		public boolean isValidReference(String accession)
258		{
259	0	Regex r = getAccessionValidator();
260	0	return r.search(accession.trim());
261		}
262
263		/**
264		* human glyoxalase
265		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
266	0	@Override...
267		public String getTestQuery()
268		{
269	0	return "1QIP";
270		}
271
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
272	0	@Override...
273		public String getDbName()
274		{
275	0	return "PDB"; // getDbSource();
276		}
277
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
278	0	@Override...
279		public int getTier()
280		{
281	0	return 0;
282		}
283
284		/**
285		* Returns a descriptor for suitable feature display settings with
286		* <ul>
287		* <li>ResNums or insertions features visible</li>
288		* <li>insertions features coloured red</li>
289		* <li>ResNum features coloured by label</li>
290		* <li>Insertions displayed above (on top of) ResNums</li>
291		* </ul>
292		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
293	0	@Override...
294		public FeatureSettingsModelI getFeatureColourScheme()
295		{
296	0	return new PDBFeatureSettings();
297		}
298		}