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Coverage Report

  1. Project Clover database Wed Dec 3 2025 15:58:31 GMT
  2. Package jalview.bin.argparser

File ArgValues.java

 

Coverage histogram

../../../img/srcFileCovDistChart5.png
44% of files have more coverage

Code metrics

32
71
23
1
256
188
49
0.69
3.09
23
2.13

Classes

Class Line # Actions
ArgValues 33 71 49
0.4285714342.9%
 

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.bin.argparser;
22   
23    import java.util.ArrayList;
24    import java.util.HashMap;
25    import java.util.List;
26    import java.util.Map;
27    import java.util.stream.Collectors;
28   
29    import jalview.bin.Console;
30    import jalview.bin.argparser.Arg.Opt;
31    import jalview.bin.argparser.Arg.Type;
32   
 
33    public class ArgValues
34    {
35    public static final String ID = "id";
36   
37    private Arg arg;
38   
39    private int argCount = 0;
40   
41    private boolean boolValue = false;
42   
43    private boolean negated = false;
44   
45    private boolean setByWildcard = false;
46   
47    private String givenLinkedId = null;
48   
49    private int boolIndex = -1;
50   
51    private List<Integer> argsIndexes;
52   
53    private List<ArgValue> argValueList;
54   
55    private Map<String, ArgValue> idMap = new HashMap<>();
56   
57    private ArgValuesMap avm;
58   
59    /*
60    * Type type is only really used by --help-type
61    */
62    private Type type = null;
63   
 
64  1258 toggle protected ArgValues(Arg a, ArgValuesMap avm)
65    {
66  1258 this.arg = a;
67  1258 this.argValueList = new ArrayList<ArgValue>();
68  1258 this.boolValue = arg.getDefaultBoolValue();
69  1258 this.avm = avm;
70    }
71   
 
72  0 toggle protected boolean setByWildcard()
73    {
74  0 return setByWildcard;
75    }
76   
 
77  1096 toggle protected void setSetByWildcard(boolean b)
78    {
79  1096 setByWildcard = b;
80    }
81   
 
82  4476 toggle public Arg arg()
83    {
84  4476 return arg;
85    }
86   
 
87  397 toggle protected void setType(Type t)
88    {
89  397 if (this.arg().hasOption(Opt.HASTYPE))
90  0 this.type = t;
91    }
92   
 
93  0 toggle public Type getType()
94    {
95  0 return type;
96    }
97   
 
98  0 toggle protected int getCount()
99    {
100  0 return argCount;
101    }
102   
 
103  1096 toggle protected void incrementCount()
104    {
105  1096 argCount++;
106    }
107   
 
108  198 toggle protected void setNegated(boolean b, boolean beingSetByWildcard)
109    {
110    // don't overwrite a wildcard set boolean with a non-wildcard set boolean
111  198 if (boolIndex >= 0 && !this.setByWildcard && beingSetByWildcard)
112  0 return;
113  198 this.negated = b;
114    }
115   
 
116  0 toggle protected boolean isNegated()
117    {
118  0 return this.negated;
119    }
120   
 
121  397 toggle protected void setBoolean(Type t, boolean b, int i,
122    boolean beingSetByWildcard, String givenLinkedId)
123    {
124  397 this.setType(t);
125    // don't overwrite a wildcard set boolean with a non-wildcard set boolean
126  397 if (boolIndex >= 0 && !this.setByWildcard && beingSetByWildcard)
127  0 return;
128  397 this.boolValue = b;
129  397 this.boolIndex = i;
130  397 this.setSetByWildcard(beingSetByWildcard);
131  397 this.givenLinkedId = givenLinkedId;
132    }
133   
 
134  140 toggle protected boolean getBoolean()
135    {
136  140 return this.boolValue;
137    }
138   
 
139  0 toggle @Override
140    public String toString()
141    {
142  0 if (argValueList == null)
143  0 return null;
144  0 StringBuilder sb = new StringBuilder();
145  0 sb.append(arg.toLongString());
146  0 if (arg.hasOption(Opt.BOOLEAN) || arg.hasOption(Opt.UNARY))
147  0 sb.append("Boolean: ").append(boolValue).append("; Default: ")
148    .append(arg.getDefaultBoolValue()).append("; Negated: ")
149    .append(negated).append("\n");
150  0 if (arg.hasOption(Opt.STRING))
151    {
152  0 sb.append("Values:");
153  0 sb.append("'")
154    .append(String
155    .join("',\n '",
156    argValueList.stream().map(av -> av.getValue())
157    .collect(Collectors.toList())))
158    .append("'");
159  0 sb.append("\n");
160    }
161  0 sb.append("Count: ").append(argCount).append("\n");
162  0 return sb.toString();
163    }
164   
 
165  440 toggle protected void addValue(Type type, String val, int argIndex,
166    boolean wildcard, String givenLinkedId)
167    {
168  440 addArgValue(new ArgValue(arg(), type, val, argIndex, wildcard,
169    givenLinkedId, avm.getLinkedId()), wildcard);
170    }
171   
 
172  259 toggle protected void addValue(SubVals sv, Type type, String content,
173    int argIndex, boolean wildcard, String givenLinkedId)
174    {
175  259 addArgValue(new ArgValue(arg(), sv, type, content, argIndex, wildcard,
176    givenLinkedId, avm.getLinkedId()), wildcard);
177    }
178   
 
179  699 toggle protected void addArgValue(ArgValue av, boolean beingSetByWildcard)
180    {
181    // allow a non-wildcard value to overwrite a wildcard set single value
182  699 boolean overwrite = !arg.hasOption(Opt.MULTIVALUE) && setByWildcard
183    && !beingSetByWildcard;
184  699 if ((!arg.hasOption(Opt.MULTIVALUE) && argValueList.size() > 0)
185    && !overwrite)
186  0 return;
187  699 if (arg.hasOption(Opt.NODUPLICATEVALUES)
188    && this.containsValue(av.getValue()))
189  0 return;
190    // new or overwrite if single valued
191  699 if (argValueList == null || overwrite)
192    {
193  0 argValueList = new ArrayList<ArgValue>();
194    }
195  699 SubVals sv = new SubVals(av.getValue());
196  699 if (sv.has(ID))
197    {
198  0 String id = sv.get(ID);
199  0 av.setId(id);
200  0 idMap.put(id, av);
201    }
202  699 argValueList.add(av);
203  699 this.setSetByWildcard(beingSetByWildcard);
204    }
205   
 
206  0 toggle protected boolean hasValue(String val)
207    {
208  0 return argValueList.contains(val);
209    }
210   
 
211  6 toggle protected ArgValue getArgValue()
212    {
213  6 if (arg.hasOption(Opt.MULTIVALUE))
214  3 Console.warn("Requesting single value for multi value argument");
215  6 return argValueList.size() > 0 ? argValueList.get(0) : null;
216    }
217   
 
218  2147 toggle protected List<ArgValue> getArgValueList()
219    {
220  2147 return argValueList;
221    }
222   
 
223  0 toggle protected boolean hasId(String id)
224    {
225  0 return idMap.containsKey(id);
226    }
227   
 
228  0 toggle protected ArgValue getId(String id)
229    {
230  0 return idMap.get(id);
231    }
232   
 
233  0 toggle private boolean containsValue(String v)
234    {
235  0 if (argValueList == null)
236  0 return false;
237  0 for (ArgValue av : argValueList)
238    {
239  0 String val = av.getValue();
240  0 if (v == null && val == null)
241  0 return true;
242  0 if (v == null)
243  0 continue;
244  0 if (v.equals(val))
245  0 return true;
246    }
247  0 return false;
248    }
249   
 
250  0 toggle public boolean setByWildcardLinkedId()
251    {
252    // looking for deliberately user set wildcard
253  0 return this.setByWildcard && this.givenLinkedId != null;
254    }
255   
256    }
  • Report generated by OpenClover v 4.4.1 on Wed Dec 3 2025 16:08:47 GMT using coverage data from Wed Dec 3 2025 16:08:32 GMT.
  • OpenClover is free and open-source software.