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jalviewX

  1. Project Clover database Wed Oct 31 2018 15:13:58 GMT
  2. Package mc_view

File PDBfile.java

 
testFileParser: Problem opening 1GAQ.txt : FILE CANNOT BE OPENED FOR READING
 

Coverage histogram

../img/srcFileCovDistChart8.png
19% of files have more coverage

Code metrics

36
86
9
1
257
203
34
0.4
9.56
9
3.78

Classes

Class Line # Actions
PDBfile 37 86 34 34
0.74045874%
 

Contributing tests

This file is covered by 15 tests. .

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 jalview.datamodel.AlignmentAnnotation;
24    import jalview.datamodel.DBRefSource;
25    import jalview.datamodel.SequenceI;
26    import jalview.io.DataSourceType;
27    import jalview.io.FileParse;
28    import jalview.io.StructureFile;
29    import jalview.util.MessageManager;
30   
31    import java.io.IOException;
32    import java.util.ArrayList;
33    import java.util.Hashtable;
34    import java.util.List;
35    import java.util.Vector;
36   
 
37    public class PDBfile extends StructureFile
38    {
39    private static String CALC_ID_PREFIX = "JalviewPDB";
40   
 
41  0 toggle public PDBfile(boolean addAlignmentAnnotations,
42    boolean predictSecondaryStructure, boolean externalSecStr)
43    {
44  0 super();
45  0 addSettings(addAlignmentAnnotations, predictSecondaryStructure,
46    externalSecStr);
47    }
48   
 
49  7 toggle public PDBfile(boolean addAlignmentAnnotations, boolean predictSecStr,
50    boolean externalSecStr, String dataObject,
51    DataSourceType sourceType) throws IOException
52    {
53  7 Test failure here super(false, dataObject, sourceType);
54  7 addSettings(addAlignmentAnnotations, predictSecStr, externalSecStr);
55  7 doParse();
56    }
57   
 
58  0 toggle 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   
 
66  0 toggle @Override
67    public String print(SequenceI[] seqs, boolean jvSuffix)
68    {
69  0 return null;
70    }
71   
 
72  7 toggle @Override
73    public void parse() throws IOException
74    {
75  7 setDbRefType(DBRefSource.PDB);
76    // TODO set the filename sensibly - try using data source name.
77  7 setId(safeName(getDataName()));
78   
79  7 setChains(new Vector<PDBChain>());
80  7 List<SequenceI> rna = new ArrayList<SequenceI>();
81  7 List<SequenceI> prot = new ArrayList<SequenceI>();
82  7 PDBChain tmpchain;
83  7 String line = null;
84  7 boolean modelFlag = false;
85  7 boolean terFlag = false;
86  7 String lastID = "";
87   
88  7 int indexx = 0;
89  7 String atomnam = null;
90  7 try
91    {
92  ? while ((line = nextLine()) != null)
93    {
94  29510 if (line.indexOf("HEADER") == 0)
95    {
96  7 if (line.length() > 62)
97    {
98  7 String tid;
99  7 if (line.length() > 67)
100    {
101  5 tid = line.substring(62, 67).trim();
102    }
103    else
104    {
105  2 tid = line.substring(62).trim();
106    }
107  7 if (tid.length() > 0)
108    {
109  7 setId(tid);
110    }
111  7 continue;
112    }
113    }
114    // Were we to do anything with SEQRES - we start it here
115  29503 if (line.indexOf("SEQRES") == 0)
116    {
117    }
118   
119  29503 if (line.indexOf("MODEL") == 0)
120    {
121  0 modelFlag = true;
122    }
123   
124  29503 if (line.indexOf("TER") == 0)
125    {
126  17 terFlag = true;
127    }
128   
129  29503 if (modelFlag && line.indexOf("ENDMDL") == 0)
130    {
131  0 break;
132    }
133  29503 if (line.indexOf("ATOM") == 0
134    || (line.indexOf("HETATM") == 0 && !terFlag))
135    {
136  25446 terFlag = false;
137   
138    // Jalview is only interested in CA bonds????
139  25446 atomnam = line.substring(12, 15).trim();
140  25446 if (!atomnam.equals("CA") && !atomnam.equals("P"))
141    {
142  22195 continue;
143    }
144   
145  3251 Atom tmpatom = new Atom(line);
146  3251 try
147    {
148  3251 tmpchain = findChain(tmpatom.chain);
149  3231 if (tmpatom.resNumIns.trim().equals(lastID))
150    {
151    // phosphorylated protein - seen both CA and P..
152  1 continue;
153    }
154  3230 tmpchain.atoms.addElement(tmpatom);
155    } catch (Exception e)
156    {
157  20 tmpchain = new PDBChain(getId(), tmpatom.chain);
158  20 getChains().add(tmpchain);
159  20 tmpchain.atoms.addElement(tmpatom);
160    }
161  3250 lastID = tmpatom.resNumIns.trim();
162    }
163  7307 index++;
164    }
165   
166  7 makeResidueList();
167  7 makeCaBondList();
168   
169  7 if (getId() == null)
170    {
171  0 setId(inFile.getName());
172    }
173  7 for (PDBChain chain : getChains())
174    {
175  20 SequenceI chainseq = postProcessChain(chain);
176  20 if (isRNA(chainseq))
177    {
178  0 rna.add(chainseq);
179    }
180    else
181    {
182  20 prot.add(chainseq);
183    }
184    }
185  7 if (predictSecondaryStructure)
186    {
187  2 addSecondaryStructure(rna, prot);
188    }
189    } catch (OutOfMemoryError er)
190    {
191  0 System.out.println("OUT OF MEMORY LOADING PDB FILE");
192  0 throw new IOException(MessageManager
193    .getString("exception.outofmemory_loading_pdb_file"));
194    } catch (NumberFormatException ex)
195    {
196  0 if (line != null)
197    {
198  0 System.err.println("Couldn't read number from line:");
199  0 System.err.println(line);
200    }
201    }
202  7 markCalcIds();
203    }
204   
205    /**
206    * Process a parsed chain to construct and return a Sequence, and add it to
207    * the list of sequences parsed.
208    *
209    * @param chain
210    * @return
211    */
212   
 
213  6 toggle public static boolean isCalcIdHandled(String calcId)
214    {
215  6 return calcId != null && (CALC_ID_PREFIX.equals(calcId));
216    }
217   
 
218  192 toggle public static boolean isCalcIdForFile(AlignmentAnnotation alan,
219    String pdbFile)
220    {
221  192 return alan.getCalcId() != null
222    && CALC_ID_PREFIX.equals(alan.getCalcId())
223    && pdbFile.equals(alan.getProperty("PDBID"));
224    }
225   
 
226  0 toggle public static String relocateCalcId(String calcId,
227    Hashtable<String, String> alreadyLoadedPDB) throws Exception
228    {
229  0 int s = CALC_ID_PREFIX.length(),
230    end = calcId.indexOf(CALC_ID_PREFIX, s);
231  0 String between = calcId.substring(s, end - 1);
232  0 return CALC_ID_PREFIX + alreadyLoadedPDB.get(between) + ":"
233    + calcId.substring(end);
234    }
235   
 
236  7 toggle private void markCalcIds()
237    {
238  7 for (SequenceI sq : seqs)
239    {
240  20 if (sq.getAnnotation() != null)
241    {
242  12 for (AlignmentAnnotation aa : sq.getAnnotation())
243    {
244  16 String oldId = aa.getCalcId();
245  16 if (oldId == null)
246    {
247  0 oldId = "";
248    }
249  16 aa.setCalcId(CALC_ID_PREFIX);
250  16 aa.setProperty("PDBID", getId());
251  16 aa.setProperty("oldCalcId", oldId);
252    }
253    }
254    }
255    }
256   
257    }
  • Report generated by OpenClover v 4.2.1 on Wed Oct 31 2018 15:15:54 GMT using coverage data from Wed Oct 31 2018 15:15:47 GMT.
  • Clover free edition.