Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Pdb	52	61	32	0.00%	Show methods

Class Pdb

Class Pdb	Line # 52	Total Statements 61	Complexity 32	TOTAL Coverage 0.00%
Pdb()   Pdb()	6262	1.01	1.01	0.0 0.00%
getAccessionSeparator() : String   getAccessionSeparator() : String	7272	1.01	1.01	0.0 0.00%
getAccessionValidator() : Regex   getAccessionValidator() : Regex	8383	3.03	2.02	0.0 0.00%
getDbSource() : String   getDbSource() : String	9999	1.01	1.01	0.0 0.00%
getDbVersion() : String   getDbVersion() : String	110110	1.01	1.01	0.0 0.00%
getSequenceRecords(String) : AlignmentI   getSequenceRecords(String) : AlignmentI	121121	48.048	21.021	0.0 0.00%
isValidReference(String) : boolean   isValidReference(String) : boolean	264264	2.02	1.01	0.0 0.00%
getTestQuery() : String   getTestQuery() : String	274274	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	280280	1.01	1.01	0.0 0.00%
getTier() : int   getTier() : int	286286	1.01	1.01	0.0 0.00%
getFeatureColourScheme() : FeatureSettingsModelI   getFeatureColourScheme() : FeatureSettingsModelI	301301	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.util.Platform;
40		import jalview.ws.ebi.EBIFetchClient;
41
42		import java.io.File;
43		import java.util.ArrayList;
44		import java.util.List;
45
46		import com.stevesoft.pat.Regex;
47
48		/**
49		* @author JimP
50		*
51		*/
		0% Uncovered Elements: 98 (98) Complexity: 32 Complexity Density: 0.52
52		public class Pdb extends EbiFileRetrievedProxy
53		{
54		private static final String SEPARATOR = "|";
55
56		private static final String COLON = ":";
57
58		private static final int PDB_ID_LENGTH = 4;
59
60		private static Regex ACCESSION_REGEX;
61
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
62	0	public Pdb()...
63		{
64	0	super();
65		}
66
67		/*
68		* (non-Javadoc)
69		*
70		* @see jalview.ws.DbSourceProxy#getAccessionSeparator()
71		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
72	0	@Override...
73		public String getAccessionSeparator()
74		{
75	0	return null;
76		}
77
78		/*
79		* (non-Javadoc)
80		*
81		* @see jalview.ws.DbSourceProxy#getAccessionValidator()
82		*/
		0% Uncovered Elements: 5 (5) Complexity: 2 Complexity Density: 0.67
83	0	@Override...
84		public Regex getAccessionValidator()
85		{
86	0	if (ACCESSION_REGEX == null)
87		{
88	0	ACCESSION_REGEX = Platform
89		.newRegex("([1-9][0-9A-Za-z]{3}):?([ _A-Za-z0-9]?)");
90		}
91	0	return ACCESSION_REGEX;
92		}
93
94		/*
95		* (non-Javadoc)
96		*
97		* @see jalview.ws.DbSourceProxy#getDbSource()
98		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
99	0	@Override...
100		public String getDbSource()
101		{
102	0	return DBRefSource.PDB;
103		}
104
105		/*
106		* (non-Javadoc)
107		*
108		* @see jalview.ws.DbSourceProxy#getDbVersion()
109		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
110	0	@Override...
111		public String getDbVersion()
112		{
113	0	return "0";
114		}
115
116		/*
117		* (non-Javadoc)
118		*
119		* @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
120		*/
		0% Uncovered Elements: 72 (72) Complexity: 21 Complexity Density: 0.44
121	0	@Override...
122		public AlignmentI getSequenceRecords(String queries) throws Exception
123		{
124	0	AlignmentI pdbAlignment = null;
125	0	String chain = null;
126	0	String id = null;
127	0	if (queries.indexOf(COLON) > -1)
128		{
129	0	chain = queries.substring(queries.indexOf(COLON) + 1);
130	0	id = queries.substring(0, queries.indexOf(COLON));
131		}
132		else
133		{
134	0	id = queries;
135		}
136
137		/*
138		* extract chain code if it is appended to the id and we
139		* don't already have one
140		*/
141	0	if (queries.length() > PDB_ID_LENGTH && chain == null)
142		{
143	0	chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
144	0	id = queries.substring(0, PDB_ID_LENGTH);
145		}
146
147	0	if (!isValidReference(id))
148		{
149	0	jalview.bin.Console
150		.errPrintln("Ignoring invalid pdb query: '" + id + "'");
151	0	stopQuery();
152	0	return null;
153		}
154
155		/*
156		* ensure that an mmCIF format structure file is saved with extension.cif,
157		* because the Chimera "open" command recognises this extension
158		*/
159	0	Type pdbFileFormat = StructureImportSettings
160		.getDefaultStructureFileFormat();
161	0	String ext = pdbFileFormat.getExtension();
162	0	String fetchFormat = pdbFileFormat.getFormat();
163
164	0	EBIFetchClient ebi = new EBIFetchClient();
165	0	File tmpFile = ebi.fetchDataAsFile("pdb:" + id, fetchFormat, ext);
166	0	file = tmpFile.getAbsolutePath();
167	0	stopQuery();
168	0	if (file == null)
169		{
170	0	return null;
171		}
172	0	try
173		{
174		// todo get rid of Type and use FileFormatI instead?
175	0	FileFormatI fileFormat = (pdbFileFormat == Type.PDB) ? FileFormat.PDB
176		: FileFormat.MMCif;
177	0	pdbAlignment = new FormatAdapter().readFile(tmpFile,
178		DataSourceType.FILE, fileFormat);
179	0	if (pdbAlignment != null)
180		{
181	0	List<SequenceI> toremove = new ArrayList<SequenceI>();
182	0	for (SequenceI pdbcs : pdbAlignment.getSequences())
183		{
184	0	String chid = null;
185		// Mapping map=null;
186	0	for (PDBEntry pid : pdbcs.getAllPDBEntries())
187		{
188	0	if (pid.getFile() == file)
189		{
190	0	chid = pid.getChainCode();
191
192		}
193		}
194	0	if (chain == null || (chid != null && (chid.equals(chain)
195		|| chid.trim().equals(chain.trim())
196		|| (chain.trim().length() == 0 && chid.equals("_")))))
197		{
198		// FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
199		// TODO: suggest simplify naming to 1qip|A as default name defined
200	0	pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR + id
201		+ SEPARATOR + pdbcs.getName());
202		// Might need to add more metadata to the PDBEntry object
203		// like below
204		/*
205		* PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
206		* entry.setId(id); if (entry.getProperty() == null)
207		* entry.setProperty(new Hashtable());
208		* entry.getProperty().put("chains", pdbchain.id + "=" +
209		* sq.getStart() + "-" + sq.getEnd());
210		* sq.getDatasetSequence().addPDBId(entry);
211		*/
212		// Add PDB DB Refs
213		// We make a DBRefEtntry because we have obtained the PDB file from
214		// a
215		// verifiable source
216		// JBPNote - PDB DBRefEntry should also carry the chain and mapping
217		// information
218	0	DBRefEntry dbentry = new DBRefEntry(getDbSource(),
219	0	getDbVersion(), (chid == null ? id : id + chid));
220		// dbentry.setMap()
221	0	pdbcs.addDBRef(dbentry);
222		}
223		else
224		{
225		// mark this sequence to be removed from the alignment
226		// - since it's not from the right chain
227	0	toremove.add(pdbcs);
228		}
229		}
230		// now remove marked sequences
231	0	for (SequenceI pdbcs : toremove)
232		{
233	0	pdbAlignment.deleteSequence(pdbcs);
234	0	if (pdbcs.getAnnotation() != null)
235		{
236	0	for (AlignmentAnnotation aa : pdbcs.getAnnotation())
237		{
238	0	pdbAlignment.deleteAnnotation(aa);
239		}
240		}
241		}
242		}
243
244	0	if (pdbAlignment == null || pdbAlignment.getHeight() < 1)
245		{
246	0	throw new Exception(MessageManager.formatMessage(
247		"exception.no_pdb_records_for_chain", new String[]
248	0	{ id, ((chain == null) ? "' '" : chain) }));
249		}
250
251		} catch (Exception ex) // Problem parsing PDB file
252		{
253	0	stopQuery();
254	0	throw (ex);
255		}
256	0	return pdbAlignment;
257		}
258
259		/*
260		* (non-Javadoc)
261		*
262		* @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
263		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
264	0	@Override...
265		public boolean isValidReference(String accession)
266		{
267	0	Regex r = getAccessionValidator();
268	0	return r.search(accession.trim());
269		}
270
271		/**
272		* human glyoxalase
273		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
274	0	@Override...
275		public String getTestQuery()
276		{
277	0	return "1QIP";
278		}
279
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
280	0	@Override...
281		public String getDbName()
282		{
283	0	return "PDB"; // getDbSource();
284		}
285
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
286	0	@Override...
287		public int getTier()
288		{
289	0	return 0;
290		}
291
292		/**
293		* Returns a descriptor for suitable feature display settings with
294		* <ul>
295		* <li>ResNums or insertions features visible</li>
296		* <li>insertions features coloured red</li>
297		* <li>ResNum features coloured by label</li>
298		* <li>Insertions displayed above (on top of) ResNums</li>
299		* </ul>
300		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
301	0	@Override...
302		public FeatureSettingsModelI getFeatureColourScheme()
303		{
304	0	return new PDBFeatureSettings();
305		}
306		}