Clover icon

Coverage Report

  1. Project Clover database Thu Dec 11 2025 10:57:44 GMT
  2. Package jalview.ws.uimodel

File AlignAnalysisUIText.java

 

Coverage histogram

../../../img/srcFileCovDistChart6.png
37% of files have more coverage

Code metrics

0
31
19
1
181
108
19
0.61
1.63
19
1

Classes

Class Line # Actions
AlignAnalysisUIText 29 31 19
0.5252%
 

Contributing tests

This file is covered by 103 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.uimodel;
22   
23    /**
24    * configures annotation worker style web service clients
25    *
26    * @author jprocter
27    *
28    */
 
29    public class AlignAnalysisUIText
30    {
31   
32    private String serviceType;
33   
 
34  0 toggle public String getServiceType()
35    {
36  0 return serviceType;
37    }
38   
39    private Class client;
40   
41    private String calcId;
42   
 
43  0 toggle public String getCalcId()
44    {
45  0 return calcId;
46    }
47   
48    private String AAconToggle, AAconToggleTooltip, AAeditSettings,
49    AAeditSettingsTooltip;
50   
51    private boolean isNa;
52   
 
53  0 toggle public boolean isNa()
54    {
55  0 return isNa;
56    }
57   
 
58  0 toggle public boolean isPr()
59    {
60  0 return isPr;
61    }
62   
63    /**
64    * @return true if service can accept sequences with gaps
65    */
 
66  1775 toggle public boolean isAA()
67    {
68  1775 return isAA;
69    }
70   
71    private boolean isPr;
72   
73    private boolean isAA;
74   
75    private boolean filterSymbols;
76   
77   
78    private boolean needsAlignedSeqs;
79   
80    private int min_valid_seqs;
81   
82   
 
83  8 toggle public AlignAnalysisUIText(String serviceType, Class<?> client,
84    String calcId, boolean acceptNucl, boolean acceptProt,
85    boolean acceptGaps, boolean alignedSeq,
86    boolean filterNonStandardSymbols, int minSeq, String toggle,
87    String toggleTooltip,
88    String settings, String settingsTooltip)
89    {
90  8 this.serviceType = serviceType;
91  8 this.calcId = calcId;
92  8 isNa = acceptNucl;
93  8 isPr = acceptProt;
94  8 isAA = acceptGaps;
95  8 this.needsAlignedSeqs = alignedSeq;
96  8 this.filterSymbols = filterNonStandardSymbols;
97  8 this.client = client;
98  8 this.AAconToggle = toggle;
99  8 this.AAconToggleTooltip = toggleTooltip;
100  8 this.AAeditSettings = settings;
101  8 this.AAeditSettingsTooltip = settingsTooltip;
102  8 this.min_valid_seqs = minSeq;
103    }
104   
105    /**
106    *
107    * @return true if non-standard nucleotides and amino acids should be replaced
108    * or omitted
109    *
110    */
 
111  0 toggle public boolean isFilterSymbols()
112    {
113  0 return filterSymbols;
114    }
115   
116    /**
117    *
118    * @return true if service needs sequences all the same length (ie padded with
119    * gaps if necessary)
120    */
 
121  0 toggle public boolean isNeedsAlignedSeqs()
122    {
123  0 return needsAlignedSeqs;
124    }
125   
 
126  1757 toggle public Class getClient()
127    {
128  1757 return client;
129    }
130   
 
131  0 toggle public void setClient(Class client)
132    {
133  0 this.client = client;
134    }
135   
 
136  1775 toggle public String getAAconToggle()
137    {
138  1775 return AAconToggle;
139    }
140   
 
141  0 toggle public void setAAconToggle(String aAconToggle)
142    {
143  0 AAconToggle = aAconToggle;
144    }
145   
 
146  1775 toggle public String getAAconToggleTooltip()
147    {
148  1775 return AAconToggleTooltip;
149    }
150   
 
151  0 toggle public void setAAconToggleTooltip(String aAconToggleTooltip)
152    {
153  0 AAconToggleTooltip = aAconToggleTooltip;
154    }
155   
 
156  1775 toggle public String getAAeditSettings()
157    {
158  1775 return AAeditSettings;
159    }
160   
 
161  0 toggle public void setAAeditSettings(String aAeditSettings)
162    {
163  0 AAeditSettings = aAeditSettings;
164    }
165   
 
166  1775 toggle public String getAAeditSettingsTooltip()
167    {
168  1775 return AAeditSettingsTooltip;
169    }
170   
 
171  0 toggle public void setAAeditSettingsTooltip(String aAeditSettingsTooltip)
172    {
173  0 AAeditSettingsTooltip = aAeditSettingsTooltip;
174    }
175   
 
176  0 toggle public int getMinimumSequences()
177    {
178  0 return min_valid_seqs;
179    }
180   
181    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 11 2025 11:05:58 GMT using coverage data from Thu Dec 11 2025 11:05:47 GMT.
  • OpenClover is free and open-source software.