Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Jws2InstanceFactory	32	12	7	0.00%	Show methods

Class Jws2InstanceFactory

Class Jws2InstanceFactory	Line # 32	Total Statements 12	Complexity 7	TOTAL Coverage 0.00%
category_rewrite(String) : String   category_rewrite(String) : String	3838	1.01	3.03	0.0 0.00%
init() : void   init() : void	4545	5.05	2.02	0.0 0.00%
ignoreService(String) : boolean   ignoreService(String) : boolean	6666	2.02	1.01	0.0 0.00%
newJws2Instance(String,String,String,String,JABAService) : Jws2Instance   newJws2Instance(String,String,String,String,JABAService) : Jws2Instance	8383	4.04	1.01	0.0 0.00%

 

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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.ws.jws2.jabaws2;
22
23		import jalview.ws.jws2.AAConClient;
24		import jalview.ws.jws2.RNAalifoldClient;
25		import jalview.ws.uimodel.AlignAnalysisUIText;
26
27		import java.util.HashMap;
28		import java.util.HashSet;
29
30		import compbio.data.msa.JABAService;
31
		0% Uncovered Elements: 20 (20) Complexity: 7 Complexity Density: 0.58
32		public class Jws2InstanceFactory
33		{
34		private static HashMap<String, AlignAnalysisUIText> aaConGUI;
35
36		private static HashSet<String> ignoreGUI;
37
		0% Uncovered Elements: 3 (3) Complexity: 3 Complexity Density: 3
38	0	private static String category_rewrite(String cat_name)...
39		{
40	0	return (cat_name != null && cat_name.equals("Prediction"))
41		? "Secondary Structure Prediction"
42		: cat_name;
43		}
44
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
45	0	private static void init()...
46		{
47	0	if (aaConGUI == null)
48		{
49	0	aaConGUI = new HashMap<String, AlignAnalysisUIText>();
50	0	aaConGUI.put(compbio.ws.client.Services.AAConWS.toString(),
51		AAConClient.getAlignAnalysisUITest());
52	0	aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
53		RNAalifoldClient.getAlignAnalysisUITest());
54		// ignore list for JABAWS services not supported in jalview ...
55	0	ignoreGUI = new HashSet<String>();
56		}
57		}
58
59		/**
60		* exclusion list to avoid creating GUI elements for services we don't fully
61		* support
62		*
63		* @param serviceType
64		* @return
65		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
66	0	public static boolean ignoreService(String serviceType)...
67		{
68	0	init();
69	0	return (ignoreGUI.contains(serviceType.toString()));
70		}
71
72		/**
73		* construct a service instance and configure it with any additional
74		* properties needed so Jalview can access it correctly
75		*
76		* @param jwsservers
77		* @param serviceType
78		* @param name
79		* @param description
80		* @param service
81		* @return
82		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
83	0	public static Jws2Instance newJws2Instance(String jwsservers,...
84		String serviceType, String name, String description,
85		JABAService service)
86		{
87	0	init();
88	0	Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
89		category_rewrite(name), description, service);
90	0	svc.aaui = aaConGUI.get(serviceType.toString());
91	0	return svc;
92		}
93
94		}