Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AssociatePdbFileWithSeq	38	24	9	0.00%	Show methods

Class AssociatePdbFileWithSeq

Class AssociatePdbFileWithSeq	Line # 38	Total Statements 24	Complexity 9	TOTAL Coverage 0.00%
associatePdbWithSeq(String,DataSourceType,SequenceI,boolean,StructureSelectionManagerProvider) : PDBEntry   associatePdbWithSeq(String,DataSourceType,SequenceI,boolean,StructureSelectionManagerProvider) : PDBEntry	4747	1.01	1.01	0.0 0.00%
associatePdbWithSeq(String,DataSourceType,SequenceI,boolean,StructureSelectionManagerProvider,TFType,String,boolean) : PDBEntry   associatePdbWithSeq(String,DataSourceType,SequenceI,boolean,StructureSelectionManagerProvider,TFType,String,boolean) : PDBEntry	5555	23.023	8.08	0.0 0.00%

 

Contributing 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 jalview.gui;
22
23		import jalview.api.StructureSelectionManagerProvider;
24		import jalview.datamodel.PDBEntry;
25		import jalview.datamodel.SequenceI;
26		import jalview.io.DataSourceType;
27		import jalview.io.StructureFile;
28		import jalview.structure.StructureImportSettings.TFType;
29		import jalview.structure.StructureSelectionManager;
30		import jalview.util.MessageManager;
31
32		/**
33		* GUI related routines for associating PDB files with sequences
34		*
35		* @author JimP
36		*
37		*/
		0% Uncovered Elements: 40 (40) Complexity: 9 Complexity Density: 0.38
38		public class AssociatePdbFileWithSeq
39		{
40
41		/**
42		* assocate the given PDB file with
43		*
44		* @param choice
45		* @param sequence
46		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
47	0	public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,...
48		SequenceI sequence, boolean prompt,
49		StructureSelectionManagerProvider ssmp)
50		{
51	0	return associatePdbWithSeq(choice, file, sequence, prompt, ssmp,
52		TFType.DEFAULT, null, false);
53		}
54
		0% Uncovered Elements: 37 (37) Complexity: 8 Complexity Density: 0.35
55	0	public PDBEntry associatePdbWithSeq(String choice, DataSourceType file,...
56		SequenceI sequence, boolean prompt,
57		StructureSelectionManagerProvider ssmp, TFType tft,
58		String paeFilename, boolean doXferSettings)
59		{
60	0	PDBEntry entry = new PDBEntry();
61	0	StructureFile pdbfile = StructureSelectionManager
62		.getStructureSelectionManager(ssmp)
63		.setMapping(false, new SequenceI[]
64		{ sequence }, null, choice, file, tft, paeFilename,
65		doXferSettings);
66	0	if (pdbfile == null)
67		{
68		// stacktrace already thrown so just return
69	0	return null;
70		}
71	0	if (pdbfile.getId() == null)
72		{
73	0	String reply = null;
74
75	0	if (prompt)
76		{
77	0	reply = JvOptionPane.showInternalInputDialog(Desktop.desktop,
78		MessageManager
79		.getString("label.couldnt_find_pdb_id_in_file"),
80		MessageManager.getString("label.no_pdb_id_in_file"),
81		JvOptionPane.QUESTION_MESSAGE);
82		}
83	0	if (reply == null)
84		{
85	0	return null;
86		}
87
88	0	entry.setId(reply);
89		}
90		else
91		{
92	0	entry.setId(pdbfile.getId());
93		}
94	0	entry.setType(PDBEntry.Type.FILE);
95
96	0	if (pdbfile != null)
97		{
98	0	entry.setFile(choice);
99	0	sequence.getDatasetSequence().addPDBId(entry);
100	0	entry.setStructureFile(pdbfile);
101	0	StructureSelectionManager.getStructureSelectionManager(ssmp)
102		.registerPDBEntry(entry);
103		}
104	0	if (tft != null)
105	0	entry.setProperty("TFType", tft.name());
106	0	if (paeFilename != null)
107	0	entry.setProperty("PAEFile", paeFilename);
108	0	return entry;
109		}
110		}