Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
BioJsHTMLOutput	41	85	35	53	0.57657.6%	Show methods

Class BioJsHTMLOutput

Class BioJsHTMLOutput	Line # 41	Total Statements 85	Complexity 35	Uncovered Elements 53	TOTAL Coverage 0.57657.6%
BioJsHTMLOutput(AlignmentPanel)   BioJsHTMLOutput(AlignmentPanel)	5757	1.01	1.01	1.01	0.0 0.00%
refreshVersionInfo(String) : void   refreshVersionInfo(String) : void	6262	16.016	6.06	4.04	0.8333333 0.833333383.3%
run() : void   run() : void	9999	7.07	3.03	2.02	0.7777778 0.777777877.8%
updateBioJS() : void   updateBioJS() : void	9595	2.02	1.01	0.00	1.0 1.0100%
syncUpdates(String,BioJSRepositoryPojo) : void   syncUpdates(String,BioJSRepositoryPojo) : void	123123	21.021	7.07	17.017	0.4516129 0.451612945.2%
getURLContentAsString(String) : String   getURLContentAsString(String) : String	171171	17.017	7.07	7.07	0.6956522 0.695652269.6%
getCurrentBJSTemplateFile() : File   getCurrentBJSTemplateFile() : File	211211	1.01	1.01	0.00	1.0 1.0100%
setCurrentBJSTemplateFile(File) : void   setCurrentBJSTemplateFile(File) : void	216216	1.01	1.01	0.00	1.0 1.0100%
getBioJsMSAVersions() : TreeMap<String, File>   getBioJsMSAVersions() : TreeMap<String, File>	221221	1.01	1.01	0.00	1.0 1.0100%
setBioJsMSAVersions(TreeMap<String, File>) : void   setBioJsMSAVersions(TreeMap<String, File>) : void	226226	1.01	1.01	0.00	1.0 1.0100%
isEmbedData() : boolean   isEmbedData() : boolean	232232	1.01	1.01	1.01	0.0 0.00%
isLaunchInBrowserAfterExport() : boolean   isLaunchInBrowserAfterExport() : boolean	238238	1.01	1.01	1.01	0.0 0.00%
run() : void   run() : void	244244	14.014	3.03	14.014	0.0 0.00%
getDescription() : String   getDescription() : String	278278	1.01	1.01	1.01	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.56	jalview.io.BioJsHTMLOutputTest.getJalviewAlignmentAsJsonStringjalview.io.BioJsHTMLOutputTest.getJalviewAlignmentAsJsonString	1PASS
	0.536	jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol	1PASS
	0.464	jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView	1PASS
	0.464	jalview.io.JalviewExportPropertiesTests.testImportExportPeriodGapsjalview.io.JalviewExportPropertiesTests.testImportExportPeriodGaps	1PASS
	0.232	jalview.io.BioJsHTMLOutputTest.getBioJsMSAVersionsjalview.io.BioJsHTMLOutputTest.getBioJsMSAVersions	1PASS
	0.072	jalview.datamodel.SequenceTest.testAddDBRefjalview.datamodel.SequenceTest.testAddDBRef	1PASS
	0.024	jalview.io.BioJsHTMLOutputTest.expectedNullPointerExceptionjalview.io.BioJsHTMLOutputTest.expectedNullPointerException	1PASS

 

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.io;
22
23		import jalview.gui.AlignmentPanel;
24		import jalview.gui.OOMWarning;
25		import jalview.json.binding.biojs.BioJSReleasePojo;
26		import jalview.json.binding.biojs.BioJSRepositoryPojo;
27		import jalview.util.MessageManager;
28
29		import java.io.BufferedInputStream;
30		import java.io.BufferedReader;
31		import java.io.File;
32		import java.io.IOException;
33		import java.io.InputStream;
34		import java.io.InputStreamReader;
35		import java.io.PrintWriter;
36		import java.net.URISyntaxException;
37		import java.net.URL;
38		import java.util.Objects;
39		import java.util.TreeMap;
40
		57.6% Uncovered Elements: 53 (125) Complexity: 35 Complexity Density: 0.41
41		public class BioJsHTMLOutput extends HTMLOutput
42		{
43		private static File currentBJSTemplateFile;
44
45		private static TreeMap<String, File> bioJsMSAVersions;
46
47		public static final String DEFAULT_DIR = System.getProperty("user.home")
48		+ File.separatorChar + ".biojs_templates" + File.separatorChar;
49
50		public static final String BJS_TEMPLATES_LOCAL_DIRECTORY = jalview.bin.Cache
51		.getDefault("biojs_template_directory", DEFAULT_DIR);
52
53		public static final String BJS_TEMPLATE_GIT_REPO = jalview.bin.Cache
54		.getDefault("biojs_template_git_repo",
55		"https://raw.githubusercontent.com/jalview/exporter-templates/master/biojs/package.json");
56
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
57	0	public BioJsHTMLOutput(AlignmentPanel ap)...
58		{
59	0	super(ap);
60		}
61
		83.3% Uncovered Elements: 4 (24) Complexity: 6 Complexity Density: 0.38
62	14	public static void refreshVersionInfo(String dirName)...
63		throws URISyntaxException
64		{
65	14	File directory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
66	14	Objects.requireNonNull(dirName, "dirName MUST not be null!");
67	13	Objects.requireNonNull(directory, "directory MUST not be null!");
68	13	TreeMap<String, File> versionFileMap = new TreeMap<String, File>();
69
70	13	for (File file : directory.listFiles())
71		{
72	39	if (file.isFile())
73		{
74	39	String fileName = file.getName().substring(0,
75		file.getName().lastIndexOf("."));
76	39	String fileMeta[] = fileName.split("_");
77	39	if (fileMeta.length > 2)
78		{
79	13	setCurrentBJSTemplateFile(file);
80	13	versionFileMap.put(fileMeta[2], file);
81		}
82	26	else if (fileMeta.length > 1)
83		{
84	26	versionFileMap.put(fileMeta[1], file);
85		}
86		}
87		}
88	13	if (getCurrentBJSTemplateFile() == null && versionFileMap.size() > 0)
89		{
90	0	setCurrentBJSTemplateFile(versionFileMap.lastEntry().getValue());
91		}
92	13	setBioJsMSAVersions(versionFileMap);
93		}
94
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
95	12	public static void updateBioJS()...
96		{
97	12	Thread updateThread = new Thread()
98		{
		77.8% Uncovered Elements: 2 (9) Complexity: 3 Complexity Density: 0.43
99	12	@Override...
100		public void run()
101		{
102	12	try
103		{
104	12	String gitRepoPkgJson = getURLContentAsString(
105		BJS_TEMPLATE_GIT_REPO);
106	12	if (gitRepoPkgJson != null)
107		{
108	12	BioJSRepositoryPojo release = new BioJSRepositoryPojo(
109		gitRepoPkgJson);
110	12	syncUpdates(BJS_TEMPLATES_LOCAL_DIRECTORY, release);
111	12	refreshVersionInfo(BJS_TEMPLATES_LOCAL_DIRECTORY);
112		}
113		} catch (URISyntaxException e)
114		{
115	0	e.printStackTrace();
116		}
117		}
118		};
119	12	updateThread.start();
120
121		}
122
		45.2% Uncovered Elements: 17 (31) Complexity: 7 Complexity Density: 0.33
123	12	public static void syncUpdates(String localDir, BioJSRepositoryPojo repo)...
124		{
125	12	for (BioJSReleasePojo bjsRelease : repo.getReleases())
126		{
127	36	String releaseUrl = bjsRelease.getUrl();
128	36	String releaseVersion = bjsRelease.getVersion();
129	36	String releaseFile = "BioJsMSA_" + releaseVersion + ".txt";
130	36	if (releaseVersion.equals(repo.getLatestReleaseVersion()))
131		{
132	12	releaseFile = "Latest_BioJsMSA_" + releaseVersion + ".txt";
133		}
134
135	36	File biojsDirectory = new File(BJS_TEMPLATES_LOCAL_DIRECTORY);
136	36	if (!biojsDirectory.exists())
137		{
138	0	if (!biojsDirectory.mkdirs())
139		{
140	0	System.out.println("Couldn't create local directory : "
141		+ BJS_TEMPLATES_LOCAL_DIRECTORY);
142	0	return;
143		}
144		}
145
146	36	File file = new File(BJS_TEMPLATES_LOCAL_DIRECTORY + releaseFile);
147	36	if (!file.exists())
148		{
149
150	0	PrintWriter out = null;
151	0	try
152		{
153	0	out = new java.io.PrintWriter(new java.io.FileWriter(file));
154	0	out.print(getURLContentAsString(releaseUrl));
155		} catch (IOException e)
156		{
157	0	e.printStackTrace();
158		} finally
159		{
160	0	if (out != null)
161		{
162	0	out.flush();
163	0	out.close();
164		}
165		}
166		}
167		}
168
169		}
170
		69.6% Uncovered Elements: 7 (23) Complexity: 7 Complexity Density: 0.41
171	12	public static String getURLContentAsString(String url)...
172		throws OutOfMemoryError
173		{
174	12	StringBuilder responseStrBuilder = null;
175	12	InputStream is = null;
176	12	try
177		{
178	12	URL resourceUrl = new URL(url);
179	12	is = new BufferedInputStream(resourceUrl.openStream());
180	12	BufferedReader br = new BufferedReader(new InputStreamReader(is));
181	12	responseStrBuilder = new StringBuilder();
182	12	String lineContent;
183
184	?	while ((lineContent = br.readLine()) != null)
185		{
186	252	responseStrBuilder.append(lineContent).append("\n");
187		}
188		} catch (OutOfMemoryError er)
189		{
190	0	er.printStackTrace();
191		} catch (Exception ex)
192		{
193	0	ex.printStackTrace();
194		} finally
195		{
196	12	if (is != null)
197		{
198	12	try
199		{
200	12	is.close();
201		} catch (IOException e)
202		{
203	0	e.printStackTrace();
204		}
205		}
206		}
207	12	return responseStrBuilder == null ? null
208		: responseStrBuilder.toString();
209		}
210
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
211	16	public static File getCurrentBJSTemplateFile()...
212		{
213	16	return currentBJSTemplateFile;
214		}
215
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
216	13	public static void setCurrentBJSTemplateFile(File currentBJSTemplateFile)...
217		{
218	13	BioJsHTMLOutput.currentBJSTemplateFile = currentBJSTemplateFile;
219		}
220
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
221	1	public static TreeMap<String, File> getBioJsMSAVersions()...
222		{
223	1	return bioJsMSAVersions;
224		}
225
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
226	13	public static void setBioJsMSAVersions(...
227		TreeMap<String, File> bioJsMSAVersions)
228		{
229	13	BioJsHTMLOutput.bioJsMSAVersions = bioJsMSAVersions;
230		}
231
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
232	0	@Override...
233		public boolean isEmbedData()
234		{
235	0	return true;
236		}
237
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
238	0	@Override...
239		public boolean isLaunchInBrowserAfterExport()
240		{
241	0	return true;
242		}
243
		0% Uncovered Elements: 14 (14) Complexity: 3 Complexity Density: 0.21
244	0	@Override...
245		public void run()
246		{
247	0	try
248		{
249	0	String bioJSON = getBioJSONData();
250	0	String bioJSTemplateString = HTMLOutput
251		.readFileAsString(getCurrentBJSTemplateFile());
252	0	String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
253		.replaceAll("#sequenceData#", bioJSON).toString();
254
255	0	PrintWriter out = new java.io.PrintWriter(
256		new java.io.FileWriter(generatedFile));
257	0	out.print(generatedBioJsWithJalviewAlignmentAsJson);
258	0	out.flush();
259	0	out.close();
260	0	setProgressMessage(MessageManager
261		.formatMessage("status.export_complete", getDescription()));
262	0	exportCompleted();
263
264		} catch (OutOfMemoryError err)
265		{
266	0	System.out.println("########################\n" + "OUT OF MEMORY "
267		+ generatedFile + "\n" + "########################");
268	0	new OOMWarning("Creating Image for " + generatedFile, err);
269		} catch (Exception e)
270		{
271	0	setProgressMessage(MessageManager
272		.formatMessage("info.error_creating_file", getDescription()));
273	0	e.printStackTrace();
274		}
275
276		}
277
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
278	0	@Override...
279		protected String getDescription()
280		{
281	0	return "BioJS MSA";
282		}
283
284		}