Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
PDBFTSPanel	37	98	30	84	0.3913043439.1%	Show methods

Class PDBFTSPanel

Class PDBFTSPanel	Line # 37	Total Statements 98	Complexity 30	Uncovered Elements 84	TOTAL Coverage 0.3913043439.1%
PDBFTSPanel(SequenceFetcher)   PDBFTSPanel(SequenceFetcher)	4848	4.04	2.02	1.01	0.8333333 0.833333383.3%
run() : void   run() : void	6767	38.038	9.09	48.048	0.0 0.00%
searchAction(boolean) : void   searchAction(boolean) : void	5757	4.04	2.02	6.06	0.0 0.00%
decodeSearchTerm(String,String) : String   decodeSearchTerm(String,String) : String	151151	15.015	5.05	3.03	0.8695652 0.869565287%
okAction() : void   okAction() : void	187187	21.021	2.02	21.021	0.0 0.00%
getPDBIdwithSpecifiedChain(String,String) : String   getPDBIdwithSpecifiedChain(String,String) : String	230230	10.010	4.04	2.02	0.875 0.87587.5%
getFTSRestClient() : FTSRestClientI   getFTSRestClient() : FTSRestClientI	256256	1.01	1.01	0.00	1.0 1.0100%
getFTSFrameTitle() : String   getFTSFrameTitle() : String	262262	1.01	1.01	0.00	1.0 1.0100%
isPaginationEnabled() : boolean   isPaginationEnabled() : boolean	268268	1.01	1.01	0.00	1.0 1.0100%
getTempUserPrefs() : Map<String, Integer>   getTempUserPrefs() : Map<String, Integer>	274274	1.01	1.01	0.00	1.0 1.0100%
getCacheKey() : String   getCacheKey() : String	280280	1.01	1.01	0.00	1.0 1.0100%
getAutosearchPreference() : String   getAutosearchPreference() : String	286286	1.01	1.01	0.00	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.1521739	jalview.fts.service.pdb.PDBFTSPanelTest.testDecodeSearchTermjalview.fts.service.pdb.PDBFTSPanelTest.testDecodeSearchTerm	1PASS
	0.13043478	jalview.fts.service.pdb.PDBFTSPanelTest.populateCmbSearchTargetOptionsTestjalview.fts.service.pdb.PDBFTSPanelTest.populateCmbSearchTargetOptionsTest	1PASS
	0.10869565	jalview.fts.service.pdb.PDBFTSPanelTest.testgetPDBIdwithSpecifiedChainjalview.fts.service.pdb.PDBFTSPanelTest.testgetPDBIdwithSpecifiedChain	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
22		package jalview.fts.service.pdb;
23
24		import jalview.fts.api.FTSDataColumnI;
25		import jalview.fts.api.FTSRestClientI;
26		import jalview.fts.core.FTSRestRequest;
27		import jalview.fts.core.FTSRestResponse;
28		import jalview.fts.core.GFTSPanel;
29		import jalview.gui.SequenceFetcher;
30		import jalview.util.MessageManager;
31
32		import java.util.HashMap;
33		import java.util.HashSet;
34		import java.util.Map;
35
36		@SuppressWarnings("serial")
		39.1% Uncovered Elements: 84 (138) Complexity: 30 Complexity Density: 0.31
37		public class PDBFTSPanel extends GFTSPanel
38		{
39		private static String defaultFTSFrameTitle = MessageManager
40		.getString("label.pdb_sequence_fetcher");
41
42		private static Map<String, Integer> tempUserPrefs = new HashMap<String, Integer>();
43
44		private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
45
46		private static final String PDB_AUTOSEARCH = "FTS.PDB.AUTOSEARCH";
47
		83.3% Uncovered Elements: 1 (6) Complexity: 2 Complexity Density: 0.5
48	1	public PDBFTSPanel(SequenceFetcher fetcher)...
49		{
50	1	super(fetcher);
51	1	pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
52	1	this.seqFetcher = fetcher;
53	1	this.progressIndicator = (fetcher == null) ? null
54		: fetcher.getProgressIndicator();
55		}
56
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
57	0	@Override...
58		public void searchAction(boolean isFreshSearch)
59		{
60	0	mainFrame.requestFocusInWindow();
61	0	if (isFreshSearch)
62		{
63	0	offSet = 0;
64		}
65	0	new Thread()
66		{
		0% Uncovered Elements: 48 (48) Complexity: 9 Complexity Density: 0.24
67	0	@Override...
68		public void run()
69		{
70	0	reset();
71	0	boolean allowEmptySequence = false;
72	0	if (getTypedText().length() > 0)
73		{
74	0	setSearchInProgress(true);
75	0	long startTime = System.currentTimeMillis();
76
77	0	String searchTarget = ((FTSDataColumnI) cmb_searchTarget
78		.getSelectedItem()).getCode();
79	0	wantedFields = PDBFTSRestClient.getInstance()
80		.getAllDefaultDisplayedFTSDataColumns();
81	0	String searchTerm = decodeSearchTerm(getTypedText(),
82		searchTarget);
83
84	0	FTSRestRequest request = new FTSRestRequest();
85	0	request.setAllowEmptySeq(allowEmptySequence);
86	0	request.setResponseSize(100);
87	0	request.setFieldToSearchBy("(" + searchTarget + ":");
88	0	request.setSearchTerm(searchTerm + ")");
89	0	request.setOffSet(offSet);
90	0	request.setWantedFields(wantedFields);
91	0	FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
92	0	FTSRestResponse resultList;
93	0	try
94		{
95	0	resultList = pdbRestClient.executeRequest(request);
96		} catch (Exception e)
97		{
98	0	setErrorMessage(e.getMessage());
99	0	checkForErrors();
100	0	setSearchInProgress(false);
101	0	return;
102		}
103
104	0	if (resultList.getSearchSummary() != null
105		&& resultList.getSearchSummary().size() > 0)
106		{
107	0	getResultTable().setModel(FTSRestResponse.getTableModel(request,
108		resultList.getSearchSummary()));
109	0	FTSRestResponse.configureTableColumn(getResultTable(),
110		wantedFields, tempUserPrefs);
111	0	getResultTable().setVisible(true);
112		}
113
114	0	long endTime = System.currentTimeMillis();
115	0	totalResultSetCount = resultList.getNumberOfItemsFound();
116	0	resultSetCount = resultList.getSearchSummary() == null ? 0
117		: resultList.getSearchSummary().size();
118	0	String result = (resultSetCount > 0)
119		? MessageManager.getString("label.results")
120		: MessageManager.getString("label.result");
121
122	0	if (isPaginationEnabled() && resultSetCount > 0)
123		{
124	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
125		+ " "
126		+ totalNumberformatter.format((Number) (offSet + 1))
127		+ " to "
128		+ totalNumberformatter
129		.format((Number) (offSet + resultSetCount))
130		+ " of "
131		+ totalNumberformatter
132		.format((Number) totalResultSetCount)
133		+ " " + " (" + (endTime - startTime) + " milli secs)");
134		}
135		else
136		{
137	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - "
138		+ resultSetCount + " " + result + " ("
139		+ (endTime - startTime) + " milli secs)");
140		}
141
142	0	setSearchInProgress(false);
143	0	refreshPaginatorState();
144	0	updateSummaryTableSelections();
145		}
146	0	txt_search.updateCache();
147		}
148		}.start();
149		}
150
		87% Uncovered Elements: 3 (23) Complexity: 5 Complexity Density: 0.33
151	2	public static String decodeSearchTerm(String enteredText,...
152		String targetField)
153		{
154	2	String foundSearchTerms = enteredText;
155	2	StringBuilder foundSearchTermsBuilder = new StringBuilder();
156	2	if (enteredText.contains(";"))
157		{
158	1	String[] searchTerms = enteredText.split(";");
159	1	for (String searchTerm : searchTerms)
160		{
161	3	if (searchTerm.contains(":"))
162		{
163	1	foundSearchTermsBuilder.append(targetField).append(":")
164		.append(searchTerm.split(":")[0]).append(" OR ");
165		}
166		else
167		{
168	2	foundSearchTermsBuilder.append(targetField).append(":")
169		.append(searchTerm).append(" OR ");
170		}
171		}
172	1	int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
173	1	foundSearchTerms = foundSearchTermsBuilder.toString();
174	1	if (foundSearchTerms.contains(" OR "))
175		{
176	1	foundSearchTerms = foundSearchTerms
177		.substring(targetField.length() + 1, endIndex);
178		}
179		}
180	1	else if (enteredText.contains(":"))
181		{
182	0	foundSearchTerms = foundSearchTerms.split(":")[0];
183		}
184	2	return foundSearchTerms;
185		}
186
		0% Uncovered Elements: 21 (21) Complexity: 2 Complexity Density: 0.1
187	0	@Override...
188		public void okAction()
189		{
190		// mainFrame.dispose();
191	0	disableActionButtons();
192	0	StringBuilder selectedIds = new StringBuilder();
193	0	HashSet<String> selectedIdsSet = new HashSet<String>();
194	0	int primaryKeyColIndex = 0;
195	0	try
196		{
197	0	primaryKeyColIndex = getFTSRestClient()
198		.getPrimaryKeyColumIndex(wantedFields, false);
199		} catch (Exception e)
200		{
201	0	e.printStackTrace();
202		}
203	0	int[] selectedRows = getResultTable().getSelectedRows();
204	0	String searchTerm = getTypedText();
205	0	for (int summaryRow : selectedRows)
206		{
207	0	String idStr = getResultTable()
208		.getValueAt(summaryRow, primaryKeyColIndex).toString();
209	0	selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
210		}
211
212	0	for (String idStr : paginatorCart)
213		{
214	0	selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
215		}
216
217	0	for (String selectedId : selectedIdsSet)
218		{
219	0	selectedIds.append(selectedId).append(";");
220		}
221
222	0	String ids = selectedIds.toString();
223		// System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
224	0	seqFetcher.getTextArea().setText(ids);
225	0	Thread worker = new Thread(seqFetcher);
226	0	worker.start();
227	0	delayAndEnableActionButtons();
228		}
229
		87.5% Uncovered Elements: 2 (16) Complexity: 4 Complexity Density: 0.4
230	3	public static String getPDBIdwithSpecifiedChain(String pdbId,...
231		String searchTerm)
232		{
233	3	String pdbIdWithChainCode = "";
234	3	if (searchTerm.contains(";"))
235		{
236	2	String[] foundTerms = searchTerm.split(";");
237	2	for (String foundTerm : foundTerms)
238		{
239	6	if (foundTerm.contains(pdbId))
240		{
241	2	pdbIdWithChainCode = foundTerm;
242		}
243		}
244		}
245	1	else if (searchTerm.contains(pdbId))
246		{
247	1	pdbIdWithChainCode = searchTerm;
248		}
249		else
250		{
251	0	pdbIdWithChainCode = pdbId;
252		}
253	3	return pdbIdWithChainCode;
254		}
255
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
256	3	@Override...
257		public FTSRestClientI getFTSRestClient()
258		{
259	3	return PDBFTSRestClient.getInstance();
260		}
261
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
262	2	@Override...
263		public String getFTSFrameTitle()
264		{
265	2	return defaultFTSFrameTitle;
266		}
267
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
268	1	@Override...
269		public boolean isPaginationEnabled()
270		{
271	1	return true;
272		}
273
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
274	4	@Override...
275		public Map<String, Integer> getTempUserPrefs()
276		{
277	4	return tempUserPrefs;
278		}
279
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
280	1	@Override...
281		public String getCacheKey()
282		{
283	1	return PDB_FTS_CACHE_KEY;
284		}
285
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
286	1	@Override...
287		public String getAutosearchPreference()
288		{
289	1	return PDB_AUTOSEARCH;
290		}
291		}