Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
TDBeaconsFTSPanel	44	86	28	0.1694915316.9%	Show methods

Class TDBeaconsFTSPanel

Class TDBeaconsFTSPanel	Line # 44	Total Statements 86	Complexity 28	TOTAL Coverage 0.1694915316.9%
TDBeaconsFTSPanel(SequenceFetcher)   TDBeaconsFTSPanel(SequenceFetcher)	5757	4.04	2.02	0.8333333 0.833333383.3%
run() : void   run() : void	7878	40.040	9.09	0.0 0.00%
searchAction(boolean) : void   searchAction(boolean) : void	6868	4.04	2.02	0.0 0.00%
run() : void   run() : void	198198	11.011	4.04	0.0 0.00%
okAction() : void   okAction() : void	161161	18.018	2.02	0.0 0.00%
getFTSRestClient() : FTSRestClientI   getFTSRestClient() : FTSRestClientI	241241	1.01	1.01	1.0 1.0100%
getFTSFrameTitle() : String   getFTSFrameTitle() : String	247247	1.01	1.01	1.0 1.0100%
isPaginationEnabled() : boolean   isPaginationEnabled() : boolean	253253	1.01	1.01	1.0 1.0100%
getTempUserPrefs() : Map<String, Integer>   getTempUserPrefs() : Map<String, Integer>	259259	1.01	1.01	1.0 1.0100%
getCacheKey() : String   getCacheKey() : String	265265	1.01	1.01	1.0 1.0100%
getAutosearchPreference() : String   getAutosearchPreference() : String	271271	1.01	1.01	1.0 1.0100%
showHelp() : void   showHelp() : void	277277	1.01	1.01	0.0 0.00%
decodeSearchTerm(String) : String   decodeSearchTerm(String) : String	284284	1.01	1.01	0.0 0.00%
getDbName() : String   getDbName() : String	290290	1.01	1.01	1.0 1.0100%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.16949153	jalview.fts.threedbeacons.TDBeaconsPanelTest.populateCmbSearchTargetOptionsTestjalview.fts.threedbeacons.TDBeaconsPanelTest.populateCmbSearchTargetOptionsTest	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.fts.service.threedbeacons;
22
23		import java.net.HttpURLConnection;
24		import java.util.HashMap;
25		import java.util.HashSet;
26		import java.util.Map;
27
28		import javax.swing.SwingUtilities;
29
30		import jalview.bin.Console;
31		import jalview.datamodel.AlignmentI;
32		import jalview.fts.api.FTSDataColumnI;
33		import jalview.fts.api.FTSRestClientI;
34		import jalview.fts.core.FTSRestRequest;
35		import jalview.fts.core.FTSRestResponse;
36		import jalview.fts.core.GFTSPanel;
37		import jalview.gui.SequenceFetcher;
38		import jalview.io.DataSourceType;
39		import jalview.io.FileFormat;
40		import jalview.io.FormatAdapter;
41		import jalview.util.MessageManager;
42
43		@SuppressWarnings("serial")
		16.9% Uncovered Elements: 98 (118) Complexity: 28 Complexity Density: 0.33
44		public class TDBeaconsFTSPanel extends GFTSPanel
45		{
46		private static String defaultFTSFrameTitle = MessageManager
47		.getString("label.pdb_sequence_fetcher");
48
49		private static Map<String, Integer> tempUserPrefs = new HashMap<>();
50
51		private static final String THREEDB_FTS_CACHE_KEY = "CACHE.THREEDB_FTS";
52
53		private static final String THREEDB_AUTOSEARCH = "FTS.THREEDB.AUTOSEARCH";
54
55		private static HttpURLConnection connection;
56
		83.3% Uncovered Elements: 1 (6) Complexity: 2 Complexity Density: 0.5
57	1	public TDBeaconsFTSPanel(SequenceFetcher fetcher)...
58		{
59		// no ID retrieval option for TD Beacons just now
60	1	super(null);
61	1	pageLimit = TDBeaconsFTSRestClient.getInstance()
62		.getDefaultResponsePageSize();
63	1	this.seqFetcher = fetcher;
64	1	this.progressIndicator = (fetcher == null) ? null
65		: fetcher.getProgressIndicator();
66		}
67
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
68	0	@Override...
69		public void searchAction(boolean isFreshSearch)
70		{
71	0	mainFrame.requestFocusInWindow();
72	0	if (isFreshSearch)
73		{
74	0	offSet = 0;
75		}
76	0	new Thread()
77		{
		0% Uncovered Elements: 50 (50) Complexity: 9 Complexity Density: 0.22
78	0	@Override...
79		public void run()
80		{
81	0	reset();
82	0	boolean allowEmptySequence = false;
83	0	if (getTypedText().length() > 0)
84		{
85	0	setSearchInProgress(true);
86	0	long startTime = System.currentTimeMillis();
87
88	0	String searchTarget = ((FTSDataColumnI) cmb_searchTarget
89		.getSelectedItem()).getCode();
90	0	wantedFields = TDBeaconsFTSRestClient.getInstance()
91		.getAllDefaultDisplayedFTSDataColumns();
92	0	String searchTerm = getTypedText(); // to add : decodeSearchTerm
93
94	0	FTSRestRequest request = new FTSRestRequest();
95	0	request.setAllowEmptySeq(allowEmptySequence);
96	0	request.setResponseSize(100);
97		// expect it to be uniprot accesssion
98	0	request.setSearchTerm(searchTerm + ".json");
99	0	request.setOffSet(offSet);
100	0	request.setWantedFields(wantedFields);
101	0	FTSRestClientI tdbRestClient = TDBeaconsFTSRestClient
102		.getInstance();
103	0	FTSRestResponse resultList;
104	0	try
105		{
106	0	resultList = tdbRestClient.executeRequest(request);
107		} catch (Exception e)
108		{
109	0	setErrorMessage(e.getMessage());
110	0	checkForErrors();
111	0	setSearchInProgress(false);
112	0	return;
113		}
114
115	0	if (resultList.getSearchSummary() != null
116		&& resultList.getSearchSummary().size() > 0)
117		{
118	0	getResultTable().setModel(FTSRestResponse.getTableModel(request,
119		resultList.getSearchSummary()));
120	0	FTSRestResponse.configureTableColumn(getResultTable(),
121		wantedFields, tempUserPrefs);
122	0	getResultTable().setVisible(true);
123		}
124
125	0	long endTime = System.currentTimeMillis();
126	0	totalResultSetCount = resultList.getNumberOfItemsFound();
127	0	resultSetCount = resultList.getSearchSummary() == null ? 0
128		: resultList.getSearchSummary().size();
129	0	String result = (resultSetCount > 0)
130		? MessageManager.getString("label.results")
131		: MessageManager.getString("label.result");
132
133	0	if (isPaginationEnabled() && resultSetCount > 0)
134		{
135	0	String f1 = totalNumberformatter
136		.format(Integer.valueOf(offSet + 1));
137	0	String f2 = totalNumberformatter
138		.format(Integer.valueOf(offSet + resultSetCount));
139	0	String f3 = totalNumberformatter
140		.format(Integer.valueOf(totalResultSetCount));
141	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
142		+ " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
143		+ (endTime - startTime) + " milli secs)");
144		}
145		else
146		{
147	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - "
148		+ resultSetCount + " " + result + " ("
149		+ (endTime - startTime) + " milli secs)");
150		}
151
152	0	setSearchInProgress(false);
153	0	refreshPaginatorState();
154	0	updateSummaryTableSelections();
155		}
156	0	txt_search.updateCache();
157		}
158		}.start();
159		}
160
		0% Uncovered Elements: 18 (18) Complexity: 2 Complexity Density: 0.11
161	0	@Override...
162		public void okAction()
163		{
164		// mainFrame.dispose();
165	0	disableActionButtons();
166	0	StringBuilder selectedIds = new StringBuilder();
167	0	final HashSet<String> selectedIdsSet = new HashSet<>();
168	0	int primaryKeyColIndex = 0;
169	0	try
170		{
171	0	primaryKeyColIndex = getFTSRestClient()
172		.getPrimaryKeyColumIndex(wantedFields, false);
173		} catch (Exception e)
174		{
175	0	e.printStackTrace();
176		}
177	0	int[] selectedRows = getResultTable().getSelectedRows();
178	0	String searchTerm = getTypedText();
179	0	for (int summaryRow : selectedRows)
180		{
181	0	String idStr = getResultTable()
182		.getValueAt(summaryRow, primaryKeyColIndex).toString();
183	0	selectedIdsSet.add(idStr);
184		}
185
186	0	for (String idStr : paginatorCart)
187		{
188	0	selectedIdsSet.add(idStr);
189		}
190
191	0	for (String selectedId : selectedIdsSet)
192		{
193	0	selectedIds.append(selectedId).append(";");
194		}
195
196	0	SwingUtilities.invokeLater(new Runnable()
197		{
		0% Uncovered Elements: 15 (15) Complexity: 4 Complexity Density: 0.36
198	0	@Override...
199		public void run()
200		{
201	0	AlignmentI allSeqs = null;
202	0	FormatAdapter fl = new jalview.io.FormatAdapter();
203	0	for (String tdbURL : selectedIdsSet)
204		{
205	0	try
206		{
207		// retrieve the structure via its URL
208	0	AlignmentI tdbAl = fl.readFile(tdbURL, DataSourceType.URL,
209		FileFormat.MMCif);
210
211		// TODO: pad structure according to its Uniprot Start so all line up
212		// w.r.t. the Uniprot reference sequence
213		// TODO: give the structure a sensible name (not the giant URL *:o)
214		// )
215	0	if (tdbAl != null)
216		{
217	0	if (allSeqs != null)
218		{
219	0	allSeqs.append(tdbAl);
220		}
221		else
222		{
223	0	allSeqs = tdbAl;
224		}
225		}
226		} catch (Exception x)
227		{
228	0	Console.warn("Couldn't retrieve 3d-beacons model for uniprot id"
229		+ searchTerm + " : " + tdbURL, x);
230		}
231		}
232	0	seqFetcher.parseResult(allSeqs,
233		"3D-Beacons models for " + searchTerm, FileFormat.MMCif,
234		null);
235
236		}
237		});
238	0	delayAndEnableActionButtons();
239		}
240
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
241	3	@Override...
242		public FTSRestClientI getFTSRestClient()
243		{
244	3	return TDBeaconsFTSRestClient.getInstance();
245		}
246
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
247	2	@Override...
248		public String getFTSFrameTitle()
249		{
250	2	return defaultFTSFrameTitle;
251		}
252
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
253	1	@Override...
254		public boolean isPaginationEnabled()
255		{
256	1	return true;
257		}
258
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
259	4	@Override...
260		public Map<String, Integer> getTempUserPrefs()
261		{
262	4	return tempUserPrefs;
263		}
264
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
265	1	@Override...
266		public String getCacheKey()
267		{
268	1	return THREEDB_FTS_CACHE_KEY;
269		}
270
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
271	1	@Override...
272		public String getAutosearchPreference()
273		{
274	1	return THREEDB_AUTOSEARCH;
275		}
276
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
277	0	@Override...
278		protected void showHelp()
279		{
280	0	jalview.bin.Console.outPrintln("No help implemented yet.");
281
282		}
283
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
284	0	public static String decodeSearchTerm(String enteredText)...
285		{
286		// no multiple query support yet
287	0	return enteredText;
288		}
289
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
290	1	public String getDbName()...
291		{
292	1	return "3D-Beacons";
293		}
294		}