Clover icon

Coverage Report

  1. Project Clover database Mon Nov 11 2024 15:14:12 GMT
  2. Package jalview.io

File HtmlFile.java

 

Coverage histogram

../../img/srcFileCovDistChart0.png
60% of files have more coverage

Code metrics

8
43
15
1
194
134
21
0.49
2.87
15
1.4

Classes

Class Line # Actions
HtmlFile 37 43 21
0.00%
 

Contributing tests

No tests hitting this source file were found.

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   
22    package jalview.io;
23   
24    import jalview.api.ComplexAlignFile;
25    import jalview.api.FeatureSettingsModelI;
26    import jalview.api.FeaturesDisplayedI;
27    import jalview.datamodel.HiddenColumns;
28    import jalview.datamodel.SequenceI;
29   
30    import java.io.IOException;
31    import java.io.StringReader;
32   
33    import org.jsoup.Jsoup;
34    import org.jsoup.nodes.Document;
35    import org.jsoup.nodes.Element;
36   
 
37    public class HtmlFile extends AlignFile implements ComplexAlignFile
38    {
39    public static final String FILE_EXT = "html";
40   
41    public static final String FILE_DESC = "HTML";
42   
43    private String globalColourScheme;
44   
45    private boolean showSeqFeatures;
46   
47    private HiddenColumns hiddenColumns;
48   
49    private SequenceI[] hiddenSequences;
50   
51    private FeaturesDisplayedI displayedFeatures;
52   
 
53  0 toggle public HtmlFile()
54    {
55  0 super();
56    }
57   
 
58  0 toggle public HtmlFile(FileParse source) throws IOException
59    {
60  0 super(source);
61    }
62   
 
63  0 toggle public HtmlFile(String inFile, DataSourceType sourceType)
64    throws IOException
65    {
66  0 super(inFile, sourceType);
67    }
68   
 
69  0 toggle @Override
70    public void parse() throws IOException
71    {
72  0 Element content = null;
73  0 Document doc = null;
74  0 try
75    {
76  0 StringBuilder htmlData = new StringBuilder();
77  0 String currentLine;
78  0 while ((currentLine = nextLine()) != null)
79    {
80  0 htmlData.append(currentLine);
81    }
82  0 doc = Jsoup.parse(htmlData.toString());
83    } catch (OutOfMemoryError oom)
84    {
85  0 errormessage = "Not enough memory to process HTML document";
86  0 throw new IOException(errormessage);
87    }
88   
89  0 try
90    {
91  0 boolean contentFromDiv = true;
92    // search for BioJSON data in div element with id seqData
93  0 content = doc.select("div[id=seqData]").first();
94  0 if (content == null)
95    {
96  0 contentFromDiv = false;
97    // search for BioJSON data in input element with id seqData
98  0 content = doc.getElementById("seqData");
99    }
100   
101  0 if (content == null)
102    {
103  0 errormessage = "The html document is not embedded with BioJSON data";
104  0 throw new IOException(errormessage);
105    }
106  0 JSONFile jsonFile = new JSONFile().parse(new StringReader(
107  0 contentFromDiv ? content.text() : content.val()));
108  0 this.seqs = jsonFile.getSeqs();
109  0 this.seqGroups = jsonFile.getSeqGroups();
110  0 this.annotations = jsonFile.getAnnotations();
111  0 this.showSeqFeatures = jsonFile.isShowSeqFeatures();
112  0 this.globalColourScheme = jsonFile.getGlobalColourScheme();
113  0 this.hiddenSequences = jsonFile.getHiddenSequences();
114  0 this.hiddenColumns = jsonFile.getHiddenColumns();
115  0 this.displayedFeatures = jsonFile.getDisplayedFeatures();
116    } catch (Exception e)
117    {
118  0 throw e;
119    }
120    }
121   
 
122  0 toggle @Override
123    public String print(SequenceI[] sqs, boolean jvsuffix)
124    {
125  0 throw new UnsupportedOperationException(
126    "Print method of HtmlFile is not supported!");
127    }
128   
 
129  0 toggle @Override
130    public boolean isShowSeqFeatures()
131    {
132  0 return showSeqFeatures;
133    }
134   
 
135  0 toggle public void setShowSeqFeatures(boolean showSeqFeatures)
136    {
137  0 this.showSeqFeatures = showSeqFeatures;
138    }
139   
 
140  0 toggle @Override
141    public String getGlobalColourScheme()
142    {
143  0 return globalColourScheme;
144    }
145   
 
146  0 toggle public void setColourScheme(String globalColourScheme)
147    {
148  0 this.globalColourScheme = globalColourScheme;
149    }
150   
 
151  0 toggle @Override
152    public HiddenColumns getHiddenColumns()
153    {
154  0 return hiddenColumns;
155    }
156   
 
157  0 toggle public void setHiddenColumns(HiddenColumns hidden)
158    {
159  0 this.hiddenColumns = hidden;
160    }
161   
 
162  0 toggle @Override
163    public SequenceI[] getHiddenSequences()
164    {
165  0 return hiddenSequences;
166    }
167   
 
168  0 toggle public void setHiddenSequences(SequenceI[] hiddenSequences)
169    {
170  0 this.hiddenSequences = hiddenSequences;
171    }
172   
 
173  0 toggle @Override
174    public FeaturesDisplayedI getDisplayedFeatures()
175    {
176  0 return displayedFeatures;
177    }
178   
179    /**
180    * Returns a descriptor for suitable feature display settings with
181    * <ul>
182    * <li>ResNums or insertions features visible</li>
183    * <li>insertions features coloured red</li>
184    * <li>ResNum features coloured by label</li>
185    * <li>Insertions displayed above (on top of) ResNums</li>
186    * </ul>
187    */
 
188  0 toggle @Override
189    public FeatureSettingsModelI getFeatureColourScheme()
190    {
191  0 return new PDBFeatureSettings();
192    }
193   
194    }