Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PDBFTSPanel	41	104	32	0.3724137837.2%	Show methods

Class PDBFTSPanel

Class PDBFTSPanel	Line # 41	Total Statements 104	Complexity 32	TOTAL Coverage 0.3724137837.2%
PDBFTSPanel(SequenceFetcher)   PDBFTSPanel(SequenceFetcher)	5252	4.04	2.02	0.8333333 0.833333383.3%
run() : void   run() : void	7171	41.041	9.09	0.0 0.00%
searchAction(boolean) : void   searchAction(boolean) : void	6161	4.04	2.02	0.0 0.00%
decodeSearchTerm(String,String) : String   decodeSearchTerm(String,String) : String	153153	15.015	5.05	0.8695652 0.869565287%
okAction() : void   okAction() : void	189189	21.021	2.02	0.0 0.00%
getPDBIdwithSpecifiedChain(String,String) : String   getPDBIdwithSpecifiedChain(String,String) : String	231231	10.010	4.04	0.875 0.87587.5%
getFTSRestClient() : FTSRestClientI   getFTSRestClient() : FTSRestClientI	257257	1.01	1.01	1.0 1.0100%
getFTSFrameTitle() : String   getFTSFrameTitle() : String	263263	1.01	1.01	1.0 1.0100%
isPaginationEnabled() : boolean   isPaginationEnabled() : boolean	269269	1.01	1.01	1.0 1.0100%
getTempUserPrefs() : Map<String, Integer>   getTempUserPrefs() : Map<String, Integer>	275275	1.01	1.01	1.0 1.0100%
getCacheKey() : String   getCacheKey() : String	281281	1.01	1.01	1.0 1.0100%
getAutosearchPreference() : String   getAutosearchPreference() : String	287287	1.01	1.01	1.0 1.0100%
showHelp() : void   showHelp() : void	293293	3.03	2.02	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.14482759	jalview.fts.service.pdb.PDBFTSPanelTest.testDecodeSearchTermjalview.fts.service.pdb.PDBFTSPanelTest.testDecodeSearchTerm	1PASS
	0.12413793	jalview.fts.service.pdb.PDBFTSPanelTest.populateCmbSearchTargetOptionsTestjalview.fts.service.pdb.PDBFTSPanelTest.populateCmbSearchTargetOptionsTest	1PASS
	0.10344828	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.Help;
30		import jalview.gui.Help.HelpId;
31		import jalview.gui.SequenceFetcher;
32		import jalview.util.MessageManager;
33
34		import java.util.HashMap;
35		import java.util.HashSet;
36		import java.util.Map;
37
38		import javax.help.HelpSetException;
39
40		@SuppressWarnings("serial")
		37.2% Uncovered Elements: 91 (145) Complexity: 32 Complexity Density: 0.31
41		public class PDBFTSPanel extends GFTSPanel
42		{
43		private static String defaultFTSFrameTitle = MessageManager
44		.getString("label.pdb_sequence_fetcher");
45
46		private static Map<String, Integer> tempUserPrefs = new HashMap<>();
47
48		private static final String PDB_FTS_CACHE_KEY = "CACHE.PDB_FTS";
49
50		private static final String PDB_AUTOSEARCH = "FTS.PDB.AUTOSEARCH";
51
		83.3% Uncovered Elements: 1 (6) Complexity: 2 Complexity Density: 0.5
52	1	public PDBFTSPanel(SequenceFetcher fetcher)...
53		{
54	1	super(fetcher);
55	1	pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
56	1	this.seqFetcher = fetcher;
57	1	this.progressIndicator = (fetcher == null) ? null
58		: fetcher.getProgressIndicator();
59		}
60
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
61	0	@Override...
62		public void searchAction(boolean isFreshSearch)
63		{
64	0	mainFrame.requestFocusInWindow();
65	0	if (isFreshSearch)
66		{
67	0	offSet = 0;
68		}
69	0	new Thread()
70		{
		0% Uncovered Elements: 51 (51) Complexity: 9 Complexity Density: 0.22
71	0	@Override...
72		public void run()
73		{
74	0	reset();
75	0	boolean allowEmptySequence = false;
76	0	if (getTypedText().length() > 0)
77		{
78	0	setSearchInProgress(true);
79	0	long startTime = System.currentTimeMillis();
80
81	0	String searchTarget = ((FTSDataColumnI) cmb_searchTarget
82		.getSelectedItem()).getCode();
83	0	wantedFields = PDBFTSRestClient.getInstance()
84		.getAllDefaultDisplayedFTSDataColumns();
85	0	String searchTerm = decodeSearchTerm(getTypedText(),
86		searchTarget);
87
88	0	FTSRestRequest request = new FTSRestRequest();
89	0	request.setAllowEmptySeq(allowEmptySequence);
90	0	request.setResponseSize(100);
91	0	request.setFieldToSearchBy("(" + searchTarget + ":");
92	0	request.setSearchTerm(searchTerm + ")");
93	0	request.setOffSet(offSet);
94	0	request.setWantedFields(wantedFields);
95	0	FTSRestClientI pdbRestClient = PDBFTSRestClient.getInstance();
96	0	FTSRestResponse resultList;
97	0	try
98		{
99	0	resultList = pdbRestClient.executeRequest(request);
100		} catch (Exception e)
101		{
102	0	setErrorMessage(e.getMessage());
103	0	checkForErrors();
104	0	setSearchInProgress(false);
105	0	return;
106		}
107
108	0	if (resultList.getSearchSummary() != null
109		&& resultList.getSearchSummary().size() > 0)
110		{
111	0	getResultTable().setModel(FTSRestResponse.getTableModel(request,
112		resultList.getSearchSummary()));
113	0	FTSRestResponse.configureTableColumn(getResultTable(),
114		wantedFields, tempUserPrefs);
115	0	getResultTable().setVisible(true);
116		}
117
118	0	long endTime = System.currentTimeMillis();
119	0	totalResultSetCount = resultList.getNumberOfItemsFound();
120	0	resultSetCount = resultList.getSearchSummary() == null ? 0
121		: resultList.getSearchSummary().size();
122	0	String result = (resultSetCount > 0)
123		? MessageManager.getString("label.results")
124		: MessageManager.getString("label.result");
125
126	0	if (isPaginationEnabled() && resultSetCount > 0)
127		{
128	0	String f1 = totalNumberformatter.format(Integer.valueOf(offSet + 1));
129	0	String f2 = totalNumberformatter
130		.format(Integer.valueOf(offSet + resultSetCount));
131	0	String f3 = totalNumberformatter
132		.format(Integer.valueOf(totalResultSetCount));
133	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
134		+ " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
135		+ (endTime - startTime) + " milli secs)");
136		}
137		else
138		{
139	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - "
140		+ resultSetCount + " " + result + " ("
141		+ (endTime - startTime) + " milli secs)");
142		}
143
144	0	setSearchInProgress(false);
145	0	refreshPaginatorState();
146	0	updateSummaryTableSelections();
147		}
148	0	txt_search.updateCache();
149		}
150		}.start();
151		}
152
		87% Uncovered Elements: 3 (23) Complexity: 5 Complexity Density: 0.33
153	2	public static String decodeSearchTerm(String enteredText,...
154		String targetField)
155		{
156	2	String foundSearchTerms = enteredText;
157	2	StringBuilder foundSearchTermsBuilder = new StringBuilder();
158	2	if (enteredText.contains(";"))
159		{
160	1	String[] searchTerms = enteredText.split(";");
161	1	for (String searchTerm : searchTerms)
162		{
163	3	if (searchTerm.contains(":"))
164		{
165	1	foundSearchTermsBuilder.append(targetField).append(":")
166		.append(searchTerm.split(":")[0]).append(" OR ");
167		}
168		else
169		{
170	2	foundSearchTermsBuilder.append(targetField).append(":")
171		.append(searchTerm).append(" OR ");
172		}
173		}
174	1	int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
175	1	foundSearchTerms = foundSearchTermsBuilder.toString();
176	1	if (foundSearchTerms.contains(" OR "))
177		{
178	1	foundSearchTerms = foundSearchTerms
179		.substring(targetField.length() + 1, endIndex);
180		}
181		}
182	1	else if (enteredText.contains(":"))
183		{
184	0	foundSearchTerms = foundSearchTerms.split(":")[0];
185		}
186	2	return foundSearchTerms;
187		}
188
		0% Uncovered Elements: 21 (21) Complexity: 2 Complexity Density: 0.1
189	0	@Override...
190		public void okAction()
191		{
192		// mainFrame.dispose();
193	0	disableActionButtons();
194	0	StringBuilder selectedIds = new StringBuilder();
195	0	HashSet<String> selectedIdsSet = new HashSet<>();
196	0	int primaryKeyColIndex = 0;
197	0	try
198		{
199	0	primaryKeyColIndex = getFTSRestClient()
200		.getPrimaryKeyColumIndex(wantedFields, false);
201		} catch (Exception e)
202		{
203	0	e.printStackTrace();
204		}
205	0	int[] selectedRows = getResultTable().getSelectedRows();
206	0	String searchTerm = getTypedText();
207	0	for (int summaryRow : selectedRows)
208		{
209	0	String idStr = getResultTable()
210		.getValueAt(summaryRow, primaryKeyColIndex).toString();
211	0	selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
212		}
213
214	0	for (String idStr : paginatorCart)
215		{
216	0	selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
217		}
218
219	0	for (String selectedId : selectedIdsSet)
220		{
221	0	selectedIds.append(selectedId).append(";");
222		}
223
224	0	String ids = selectedIds.toString();
225	0	seqFetcher.setQuery(ids);
226	0	Thread worker = new Thread(seqFetcher);
227	0	worker.start();
228	0	delayAndEnableActionButtons();
229		}
230
		87.5% Uncovered Elements: 2 (16) Complexity: 4 Complexity Density: 0.4
231	3	public static String getPDBIdwithSpecifiedChain(String pdbId,...
232		String searchTerm)
233		{
234	3	String pdbIdWithChainCode = "";
235	3	if (searchTerm.contains(";"))
236		{
237	2	String[] foundTerms = searchTerm.split(";");
238	2	for (String foundTerm : foundTerms)
239		{
240	6	if (foundTerm.contains(pdbId))
241		{
242	2	pdbIdWithChainCode = foundTerm;
243		}
244		}
245		}
246	1	else if (searchTerm.contains(pdbId))
247		{
248	1	pdbIdWithChainCode = searchTerm;
249		}
250		else
251		{
252	0	pdbIdWithChainCode = pdbId;
253		}
254	3	return pdbIdWithChainCode;
255		}
256
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
257	3	@Override...
258		public FTSRestClientI getFTSRestClient()
259		{
260	3	return PDBFTSRestClient.getInstance();
261		}
262
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
263	2	@Override...
264		public String getFTSFrameTitle()
265		{
266	2	return defaultFTSFrameTitle;
267		}
268
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
269	1	@Override...
270		public boolean isPaginationEnabled()
271		{
272	1	return true;
273		}
274
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
275	4	@Override...
276		public Map<String, Integer> getTempUserPrefs()
277		{
278	4	return tempUserPrefs;
279		}
280
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
281	1	@Override...
282		public String getCacheKey()
283		{
284	1	return PDB_FTS_CACHE_KEY;
285		}
286
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
287	1	@Override...
288		public String getAutosearchPreference()
289		{
290	1	return PDB_AUTOSEARCH;
291		}
292
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
293	0	@Override...
294		protected void showHelp()
295		{
296	0	try
297		{
298	0	Help.showHelpWindow(HelpId.PdbFts);
299		} catch (HelpSetException e1)
300		{
301	0	e1.printStackTrace();
302		}
303		}
304		}