Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
UniprotFTSPanel	41	86	28	0.00%	Show methods

Class UniprotFTSPanel

Class UniprotFTSPanel	Line # 41	Total Statements 86	Complexity 28	TOTAL Coverage 0.00%
UniprotFTSPanel(SequenceFetcher)   UniprotFTSPanel(SequenceFetcher)	5959	4.04	2.02	0.0 0.00%
run() : void   run() : void	7979	37.037	9.09	0.0 0.00%
searchAction(boolean) : void   searchAction(boolean) : void	6969	4.04	2.02	0.0 0.00%
decodeSearchTerm(String,String) : String   decodeSearchTerm(String,String) : String	162162	13.013	5.05	0.0 0.00%
isPaginationEnabled() : boolean   isPaginationEnabled() : boolean	189189	1.01	1.01	0.0 0.00%
okAction() : void   okAction() : void	195195	19.019	2.02	0.0 0.00%
getFTSRestClient() : FTSRestClientI   getFTSRestClient() : FTSRestClientI	230230	1.01	1.01	0.0 0.00%
getFTSFrameTitle() : String   getFTSFrameTitle() : String	236236	1.01	1.01	0.0 0.00%
getTempUserPrefs() : Map<String, Integer>   getTempUserPrefs() : Map<String, Integer>	242242	1.01	1.01	0.0 0.00%
getCacheKey() : String   getCacheKey() : String	248248	1.01	1.01	0.0 0.00%
getAutosearchPreference() : String   getAutosearchPreference() : String	254254	1.01	1.01	0.0 0.00%
showHelp() : void   showHelp() : void	260260	3.03	2.02	0.0 0.00%

 

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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.fts.service.uniprot;
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")
		0% Uncovered Elements: 120 (120) Complexity: 28 Complexity Density: 0.33
41		public class UniprotFTSPanel extends GFTSPanel
42		{
43
44		private static String defaultFTSFrameTitle = MessageManager
45		.getString("label.uniprot_sequence_fetcher");
46
47		private static Map<String, Integer> tempUserPrefs = new HashMap<>();
48
49		private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
50
51		private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
52
53		/**
54		* Constructor given an (optional) sequence fetcher panel to revert to on
55		* clicking the 'Back' button
56		*
57		* @param fetcher
58		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
59	0	public UniprotFTSPanel(SequenceFetcher fetcher)...
60		{
61	0	super(fetcher);
62	0	pageLimit = UniProtFTSRestClient.getInstance()
63		.getDefaultResponsePageSize();
64	0	this.seqFetcher = fetcher;
65	0	this.progressIndicator = (fetcher == null) ? null
66		: fetcher.getProgressIndicator();
67		}
68
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
69	0	@Override...
70		public void searchAction(boolean isFreshSearch)
71		{
72	0	mainFrame.requestFocusInWindow();
73	0	if (isFreshSearch)
74		{
75	0	offSet = 0;
76		}
77	0	new Thread()
78		{
		0% Uncovered Elements: 47 (47) Complexity: 9 Complexity Density: 0.24
79	0	@Override...
80		public void run()
81		{
82	0	reset();
83	0	String searchInput = getTypedText();
84	0	if (searchInput.length() > 0)
85		{
86	0	setSearchInProgress(true);
87	0	long startTime = System.currentTimeMillis();
88	0	searchInput = getTypedText();
89	0	String searchTarget = ((FTSDataColumnI) cmb_searchTarget
90		.getSelectedItem()).getAltCode();
91	0	wantedFields = UniProtFTSRestClient.getInstance()
92		.getAllDefaultDisplayedFTSDataColumns();
93	0	String searchTerm = decodeSearchTerm(searchInput, searchTarget);
94
95	0	FTSRestRequest request = new FTSRestRequest();
96	0	request.setFieldToSearchBy(searchTarget);
97	0	request.setSearchTerm(searchTerm);
98	0	request.setOffSet(offSet);
99	0	request.setWantedFields(wantedFields);
100	0	FTSRestClientI uniProtRestClient = UniProtFTSRestClient
101		.getInstance();
102	0	FTSRestResponse resultList;
103	0	try
104		{
105	0	resultList = uniProtRestClient.executeRequest(request);
106		} catch (Exception e)
107		{
108	0	setErrorMessage(e.getMessage());
109	0	checkForErrors();
110	0	setSearchInProgress(false);
111	0	return;
112		}
113
114	0	if (resultList.getSearchSummary() != null
115		&& resultList.getSearchSummary().size() > 0)
116		{
117	0	getResultTable().setModel(FTSRestResponse.getTableModel(request,
118		resultList.getSearchSummary()));
119	0	FTSRestResponse.configureTableColumn(getResultTable(),
120		wantedFields, tempUserPrefs);
121	0	getResultTable().setVisible(true);
122		}
123
124	0	long endTime = System.currentTimeMillis();
125	0	totalResultSetCount = resultList.getNumberOfItemsFound();
126	0	resultSetCount = resultList.getSearchSummary() == null ? 0
127		: resultList.getSearchSummary().size();
128	0	String result = (resultSetCount > 0)
129		? MessageManager.getString("label.results")
130		: MessageManager.getString("label.result");
131	0	if (isPaginationEnabled() && resultSetCount > 0)
132		{
133	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
134		+ " "
135		+ totalNumberformatter
136		.format(Integer.valueOf(offSet + 1))
137		+ " to "
138		+ totalNumberformatter
139		.format(Integer
140		.valueOf(offSet + resultSetCount))
141		+ " of "
142		+ totalNumberformatter
143		.format(Integer.valueOf(totalResultSetCount))
144		+ " " + " (" + (endTime - startTime) + " milli secs)");
145		}
146		else
147		{
148	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - "
149		+ resultSetCount + " " + result + " ("
150		+ (endTime - startTime) + " milli secs)");
151		}
152	0	setSearchInProgress(false);
153	0	refreshPaginatorState();
154	0	updateSummaryTableSelections();
155		}
156	0	txt_search.updateCache();
157		}
158		}.start();
159
160		}
161
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.38
162	0	public String decodeSearchTerm(String enteredText, String targetField)...
163		{
164	0	int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
165		: targetField.length() + 1;
166	0	String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
167		: targetField + ":";
168	0	String foundSearchTerms = enteredText;
169	0	StringBuilder foundSearchTermsBuilder = new StringBuilder();
170	0	if (enteredText.contains(";"))
171		{
172	0	String[] searchTerms = enteredText.split(";");
173	0	for (String searchTerm : searchTerms)
174		{
175	0	foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
176		.append(" OR ");
177		}
178	0	int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
179	0	foundSearchTerms = foundSearchTermsBuilder.toString();
180	0	if (foundSearchTerms.contains(" OR "))
181		{
182	0	foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
183		endIndex);
184		}
185		}
186	0	return foundSearchTerms;
187		}
188
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
189	0	@Override...
190		public boolean isPaginationEnabled()
191		{
192	0	return true;
193		}
194
		0% Uncovered Elements: 19 (19) Complexity: 2 Complexity Density: 0.11
195	0	@Override...
196		public void okAction()
197		{
198	0	disableActionButtons();
199	0	StringBuilder selectedIds = new StringBuilder();
200	0	HashSet<String> selectedIdsSet = new HashSet<>();
201	0	int primaryKeyColIndex = 0;
202	0	try
203		{
204	0	primaryKeyColIndex = getFTSRestClient()
205		.getPrimaryKeyColumIndex(wantedFields, false);
206		} catch (Exception e)
207		{
208	0	e.printStackTrace();
209		}
210	0	int[] selectedRows = getResultTable().getSelectedRows();
211	0	for (int summaryRow : selectedRows)
212		{
213	0	String idStr = getResultTable()
214		.getValueAt(summaryRow, primaryKeyColIndex).toString();
215	0	selectedIdsSet.add(idStr);
216		}
217	0	selectedIdsSet.addAll(paginatorCart);
218	0	for (String selectedId : selectedIdsSet)
219		{
220	0	selectedIds.append(selectedId).append(";");
221		}
222
223	0	String ids = selectedIds.toString();
224	0	seqFetcher.setQuery(ids);
225	0	Thread worker = new Thread(seqFetcher);
226	0	worker.start();
227	0	delayAndEnableActionButtons();
228		}
229
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
230	0	@Override...
231		public FTSRestClientI getFTSRestClient()
232		{
233	0	return UniProtFTSRestClient.getInstance();
234		}
235
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
236	0	@Override...
237		public String getFTSFrameTitle()
238		{
239	0	return defaultFTSFrameTitle;
240		}
241
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
242	0	@Override...
243		public Map<String, Integer> getTempUserPrefs()
244		{
245	0	return tempUserPrefs;
246		}
247
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
248	0	@Override...
249		public String getCacheKey()
250		{
251	0	return UNIPROT_FTS_CACHE_KEY;
252		}
253
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
254	0	@Override...
255		public String getAutosearchPreference()
256		{
257	0	return UNIPROT_AUTOSEARCH;
258		}
259
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
260	0	@Override...
261		protected void showHelp()
262		{
263	0	try
264		{
265	0	Help.showHelpWindow(HelpId.UniprotFts);
266		} catch (HelpSetException e1)
267		{
268	0	e1.printStackTrace();
269		}
270		}
271		}