Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
HtmlFile	37	43	21	66	0.00%	Show methods

Class HtmlFile

Class HtmlFile	Line # 37	Total Statements 43	Complexity 21	Uncovered Elements 66	TOTAL Coverage 0.00%
HtmlFile()   HtmlFile()	5353	1.01	1.01	1.01	0.0 0.00%
HtmlFile(FileParse)   HtmlFile(FileParse)	5858	1.01	1.01	1.01	0.0 0.00%
HtmlFile(String,DataSourceType)   HtmlFile(String,DataSourceType)	6363	1.01	1.01	1.01	0.0 0.00%
parse() : void   parse() : void	6969	29.029	7.07	37.037	0.0 0.00%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	122122	1.01	1.01	1.01	0.0 0.00%
isShowSeqFeatures() : boolean   isShowSeqFeatures() : boolean	129129	1.01	1.01	1.01	0.0 0.00%
setShowSeqFeatures(boolean) : void   setShowSeqFeatures(boolean) : void	135135	1.01	1.01	1.01	0.0 0.00%
getGlobalColourScheme() : String   getGlobalColourScheme() : String	140140	1.01	1.01	1.01	0.0 0.00%
setColourScheme(String) : void   setColourScheme(String) : void	146146	1.01	1.01	1.01	0.0 0.00%
getHiddenColumns() : HiddenColumns   getHiddenColumns() : HiddenColumns	151151	1.01	1.01	1.01	0.0 0.00%
setHiddenColumns(HiddenColumns) : void   setHiddenColumns(HiddenColumns) : void	157157	1.01	1.01	1.01	0.0 0.00%
getHiddenSequences() : SequenceI[]   getHiddenSequences() : SequenceI[]	162162	1.01	1.01	1.01	0.0 0.00%
setHiddenSequences(SequenceI[]) : void   setHiddenSequences(SequenceI[]) : void	168168	1.01	1.01	1.01	0.0 0.00%
getDisplayedFeatures() : FeaturesDisplayedI   getDisplayedFeatures() : FeaturesDisplayedI	173173	1.01	1.01	1.01	0.0 0.00%
getFeatureColourScheme() : FeatureSettingsModelI   getFeatureColourScheme() : FeatureSettingsModelI	188188	1.01	1.01	1.01	0.0 0.00%

 

Contributing tests

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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
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
		0% Uncovered Elements: 66 (66) Complexity: 21 Complexity Density: 0.49
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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
53	0	public HtmlFile()...
54		{
55	0	super();
56		}
57
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
58	0	public HtmlFile(FileParse source) throws IOException...
59		{
60	0	super(source);
61		}
62
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
63	0	public HtmlFile(String inFile, DataSourceType sourceType)...
64		throws IOException
65		{
66	0	super(inFile, sourceType);
67		}
68
		0% Uncovered Elements: 37 (37) Complexity: 7 Complexity Density: 0.24
69	0	@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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
122	0	@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
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
129	0	@Override...
130		public boolean isShowSeqFeatures()
131		{
132	0	return showSeqFeatures;
133		}
134
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
135	0	public void setShowSeqFeatures(boolean showSeqFeatures)...
136		{
137	0	this.showSeqFeatures = showSeqFeatures;
138		}
139
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
140	0	@Override...
141		public String getGlobalColourScheme()
142		{
143	0	return globalColourScheme;
144		}
145
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
146	0	public void setColourScheme(String globalColourScheme)...
147		{
148	0	this.globalColourScheme = globalColourScheme;
149		}
150
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
151	0	@Override...
152		public HiddenColumns getHiddenColumns()
153		{
154	0	return hiddenColumns;
155		}
156
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
157	0	public void setHiddenColumns(HiddenColumns hidden)...
158		{
159	0	this.hiddenColumns = hidden;
160		}
161
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
162	0	@Override...
163		public SequenceI[] getHiddenSequences()
164		{
165	0	return hiddenSequences;
166		}
167
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
168	0	public void setHiddenSequences(SequenceI[] hiddenSequences)...
169		{
170	0	this.hiddenSequences = hiddenSequences;
171		}
172
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
173	0	@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		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
188	0	@Override...
189		public FeatureSettingsModelI getFeatureColourScheme()
190		{
191	0	return new PDBFeatureSettings();
192		}
193
194		}