Clover icon

Coverage Report

  1. Project Clover database Thu Nov 27 2025 17:07:57 GMT
  2. Package jalview.ws.jws2.jabaws2

File Jws2InstanceFactory.java

 

Coverage histogram

../../../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

4
12
4
1
94
45
7
0.58
3
4
1.75

Classes

Class Line # Actions
Jws2InstanceFactory 32 12 7
1.0100%
 

Contributing tests

This file is covered by 86 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.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   
 
32    public class Jws2InstanceFactory
33    {
34    private static HashMap<String, AlignAnalysisUIText> aaConGUI;
35   
36    private static HashSet<String> ignoreGUI;
37   
 
38  620 toggle private static String category_rewrite(String cat_name)
39    {
40  620 return (cat_name != null && cat_name.equals("Prediction"))
41    ? "Secondary Structure Prediction"
42    : cat_name;
43    }
44   
 
45  1240 toggle private static void init()
46    {
47  1240 if (aaConGUI == null)
48    {
49  6 aaConGUI = new HashMap<String, AlignAnalysisUIText>();
50  6 aaConGUI.put(compbio.ws.client.Services.AAConWS.toString(),
51    AAConClient.getAlignAnalysisUITest());
52  6 aaConGUI.put(compbio.ws.client.Services.RNAalifoldWS.toString(),
53    RNAalifoldClient.getAlignAnalysisUITest());
54    // ignore list for JABAWS services not supported in jalview ...
55  6 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    */
 
66  620 toggle public static boolean ignoreService(String serviceType)
67    {
68  620 init();
69  620 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    */
 
83  620 toggle public static Jws2Instance newJws2Instance(String jwsservers,
84    String serviceType, String name, String description,
85    JABAService service)
86    {
87  620 init();
88  620 Jws2Instance svc = new Jws2Instance(jwsservers, serviceType,
89    category_rewrite(name), description, service);
90  620 svc.aaui = aaConGUI.get(serviceType.toString());
91  620 return svc;
92    }
93   
94    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 27 2025 17:17:47 GMT using coverage data from Thu Nov 27 2025 17:17:32 GMT.
  • OpenClover is free and open-source software.