Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PDBfile	37	86	34	0.729323372.9%	Show methods

Class PDBfile

Class PDBfile	Line # 37	Total Statements 86	Complexity 34	TOTAL Coverage 0.729323372.9%
PDBfile(boolean,boolean,boolean)   PDBfile(boolean,boolean,boolean)	4141	2.02	1.01	0.0 0.00%
PDBfile(boolean,boolean,boolean,String,DataSourceType)   PDBfile(boolean,boolean,boolean,String,DataSourceType)	4949	3.03	1.01	1.0 1.0100%
PDBfile(boolean,boolean,boolean,FileParse)   PDBfile(boolean,boolean,boolean,FileParse)	5858	3.03	1.01	0.0 0.00%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	6666	1.01	1.01	0.0 0.00%
parse() : void   parse() : void	7272	63.063	24.024	0.8041237 0.804123780.4%
isCalcIdHandled(String) : boolean   isCalcIdHandled(String) : boolean	215215	1.01	1.01	0.0 0.00%
isCalcIdForFile(AlignmentAnnotation,String) : boolean   isCalcIdForFile(AlignmentAnnotation,String) : boolean	220220	1.01	1.01	1.0 1.0100%
relocateCalcId(String,Hashtable<String, String>) : String   relocateCalcId(String,Hashtable<String, String>) : String	228228	3.03	1.01	0.0 0.00%
markCalcIds() : void   markCalcIds() : void	238238	9.09	3.03	0.84615386 0.8461538684.6%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.69924814	jalview.ext.jmol.JmolParserTest.testAlignmentLoaderjalview.ext.jmol.JmolParserTest.testAlignmentLoader	1PASS
	0.66917294	mc_view.PDBfileTest.testParse_withJmolAddAlignmentAnnotationsmc_view.PDBfileTest.testParse_withJmolAddAlignmentAnnotations	1PASS
	0.66917294	mc_view.PDBfileTest.testParse_withJmol_noAnnotationsmc_view.PDBfileTest.testParse_withJmol_noAnnotations	1PASS
	0.6616541	mc_view.PDBfileTest.testParse_withAnnotations_noSSmc_view.PDBfileTest.testParse_withAnnotations_noSS	1PASS
	0.63909775	jalview.ext.jmol.JmolParserTest.testFileParserjalview.ext.jmol.JmolParserTest.testFileParser	1PASS
	0.60902256	mc_view.PDBfileTest.testParsemc_view.PDBfileTest.testParse	1PASS
	0.57894737	jalview.ext.jmol.JmolParserTest.testParse_alternativeResiduesjalview.ext.jmol.JmolParserTest.testParse_alternativeResidues	1PASS
	0.56390977	jalview.ext.jmol.JmolParserTest.testParse_missingResiduesjalview.ext.jmol.JmolParserTest.testParse_missingResidues	1PASS
	0.015037594	jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol	1PASS
	0.015037594	jalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMol	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
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.
11		*
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.
16		*
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.
20		*/
21		package mc_view;
22
23		import java.io.IOException;
24		import java.util.ArrayList;
25		import java.util.Hashtable;
26		import java.util.List;
27		import java.util.Vector;
28
29		import jalview.datamodel.AlignmentAnnotation;
30		import jalview.datamodel.DBRefSource;
31		import jalview.datamodel.SequenceI;
32		import jalview.io.DataSourceType;
33		import jalview.io.FileParse;
34		import jalview.io.StructureFile;
35		import jalview.util.MessageManager;
36
		72.9% Uncovered Elements: 36 (133) Complexity: 34 Complexity Density: 0.4
37		public class PDBfile extends StructureFile
38		{
39		private static String CALC_ID_PREFIX = "JalviewPDB";
40
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
41	0	public PDBfile(boolean addAlignmentAnnotations,...
42		boolean predictSecondaryStructure, boolean externalSecStr)
43		{
44	0	super();
45	0	addSettings(addAlignmentAnnotations, predictSecondaryStructure,
46		externalSecStr);
47		}
48
		100% Uncovered Elements: 0 (3) Complexity: 1 Complexity Density: 0.33
49	13	public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,...
50		boolean externalSecStr, String dataObject,
51		DataSourceType sourceType) throws IOException
52		{
53	13	super(false, dataObject, sourceType);
54	13	addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
55	13	doParse();
56		}
57
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
58	0	public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,...
59		boolean externalSecStr, FileParse source) throws IOException
60		{
61	0	super(false, source);
62	0	addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
63	0	doParse();
64		}
65
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
66	0	@Override...
67		public String print(SequenceI[] seqs, boolean jvSuffix)
68		{
69	0	return null;
70		}
71
		80.4% Uncovered Elements: 19 (97) Complexity: 24 Complexity Density: 0.38
72	13	@Override...
73		public void parse() throws IOException
74		{
75	13	setDbRefType(DBRefSource.PDB);
76		// TODO set the filename sensibly - try using data source name.
77	13	setId(safeName(getDataName()));
78
79	13	setChains(new Vector<PDBChain>());
80	13	List<SequenceI> rna = new ArrayList<SequenceI>();
81	13	List<SequenceI> prot = new ArrayList<SequenceI>();
82	13	PDBChain tmpchain;
83	13	String line = null;
84	13	boolean modelFlag = false;
85	13	boolean terFlag = false;
86	13	String lastID = "";
87
88	13	int indexx = 0;
89	13	String atomnam = null;
90	13	try
91		{
92	?	while ((line = nextLine()) != null)
93		{
94	52002	if (line.indexOf("HEADER") == 0)
95		{
96	13	if (line.length() > 62)
97		{
98	13	String tid;
99	13	if (line.length() > 67)
100		{
101	9	tid = line.substring(62, 67).trim();
102		}
103		else
104		{
105	4	tid = line.substring(62).trim();
106		}
107	13	if (tid.length() > 0)
108		{
109	13	setId(tid);
110		}
111	13	continue;
112		}
113		}
114		// Were we to do anything with SEQRES - we start it here
115	51989	if (line.indexOf("SEQRES") == 0)
116		{
117		}
118
119	51989	if (line.indexOf("MODEL") == 0)
120		{
121	0	modelFlag = true;
122		}
123
124	51989	if (line.indexOf("TER") == 0)
125		{
126	23	terFlag = true;
127		}
128
129	51989	if (modelFlag && line.indexOf("ENDMDL") == 0)
130		{
131	0	break;
132		}
133	51989	if (line.indexOf("ATOM") == 0
134		|| (line.indexOf("HETATM") == 0 && !terFlag))
135		{
136	44406	terFlag = false;
137
138		// Jalview is only interested in CA bonds????
139	44406	atomnam = line.substring(12, 15).trim();
140	44406	if (!atomnam.equals("CA") && !atomnam.equals("P"))
141		{
142	37593	continue;
143		}
144
145	6813	Atom tmpatom = new Atom(line);
146	6813	if (tmpatom.resNumIns.trim().equals(lastID))
147		{
148		// phosphorylated protein - seen both CA and P..
149	3	continue;
150		}
151	6810	tmpchain = findChain(tmpatom.chain);
152	6810	if (tmpchain != null)
153		{
154	6778	tmpchain.atoms.addElement(tmpatom);
155		}
156		else
157		{
158		// PDBfile never handles alphafold models
159	32	tmpchain = new PDBChain(getId(), tmpatom.chain);
160	32	getChains().add(tmpchain);
161	32	tmpchain.atoms.addElement(tmpatom);
162		}
163	6810	lastID = tmpatom.resNumIns.trim();
164		}
165	14393	index++;
166		}
167
168	13	makeResidueList();
169	13	makeCaBondList();
170
171	13	if (getId() == null)
172		{
173	0	setId(inFile.getName());
174		}
175	13	for (PDBChain chain : getChains())
176		{
177	32	SequenceI chainseq = postProcessChain(chain);
178	32	if (isRNA(chainseq))
179		{
180	0	rna.add(chainseq);
181		}
182		else
183		{
184	32	prot.add(chainseq);
185		}
186		}
187	13	if (predictSecondaryStructure)
188		{
189	5	addSecondaryStructure(rna, prot);
190		}
191		} catch (OutOfMemoryError er)
192		{
193	0	System.out.println("OUT OF MEMORY LOADING PDB FILE");
194	0	throw new IOException(MessageManager
195		.getString("exception.outofmemory_loading_pdb_file"));
196		} catch (NumberFormatException ex)
197		{
198	0	if (line != null)
199		{
200	0	System.err.println("Couldn't read number from line:");
201	0	System.err.println(line);
202		}
203		}
204	13	markCalcIds();
205		}
206
207		/**
208		* Process a parsed chain to construct and return a Sequence, and add it to
209		* the list of sequences parsed.
210		*
211		* @param chain
212		* @return
213		*/
214
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
215	0	public static boolean isCalcIdHandled(String calcId)...
216		{
217	0	return calcId != null && (CALC_ID_PREFIX.equals(calcId));
218		}
219
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
220	8	public static boolean isCalcIdForFile(AlignmentAnnotation alan,...
221		String pdbFile)
222		{
223	8	return alan.getCalcId() != null
224		&& CALC_ID_PREFIX.equals(alan.getCalcId())
225		&& pdbFile.equals(alan.getProperty("PDBID"));
226		}
227
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
228	0	public static String relocateCalcId(String calcId,...
229		Hashtable<String, String> alreadyLoadedPDB) throws Exception
230		{
231	0	int s = CALC_ID_PREFIX.length(),
232		end = calcId.indexOf(CALC_ID_PREFIX, s);
233	0	String between = calcId.substring(s, end - 1);
234	0	return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
235		+ calcId.substring(end);
236		}
237
		84.6% Uncovered Elements: 2 (13) Complexity: 3 Complexity Density: 0.33
238	13	private void markCalcIds()...
239		{
240	13	for (SequenceI sq : seqs)
241		{
242	32	if (sq.getAnnotation() != null)
243		{
244	18	for (AlignmentAnnotation aa : sq.getAnnotation())
245		{
246	22	String oldId = aa.getCalcId();
247	22	if (oldId == null)
248		{
249	0	oldId = "";
250		}
251	22	aa.setCalcId(CALC_ID_PREFIX);
252	22	aa.setProperty("PDBID", getId());
253	22	aa.setProperty("oldCalcId", oldId);
254		}
255		}
256		}
257		}
258
259		}