Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
UniprotFTSPanel	37	83	26	116	0.00%	Show methods

Class UniprotFTSPanel

Class UniprotFTSPanel	Line # 37	Total Statements 83	Complexity 26	Uncovered Elements 116	TOTAL Coverage 0.00%
UniprotFTSPanel(SequenceFetcher)   UniprotFTSPanel(SequenceFetcher)	4949	4.04	2.02	6.06	0.0 0.00%
run() : void   run() : void	6969	37.037	9.09	47.047	0.0 0.00%
searchAction(boolean) : void   searchAction(boolean) : void	5959	4.04	2.02	6.06	0.0 0.00%
decodeSearchTerm(String,String) : String   decodeSearchTerm(String,String) : String	150150	13.013	5.05	21.021	0.0 0.00%
isPaginationEnabled() : boolean   isPaginationEnabled() : boolean	177177	1.01	1.01	1.01	0.0 0.00%
okAction() : void   okAction() : void	183183	19.019	2.02	19.019	0.0 0.00%
getFTSRestClient() : FTSRestClientI   getFTSRestClient() : FTSRestClientI	219219	1.01	1.01	1.01	0.0 0.00%
getFTSFrameTitle() : String   getFTSFrameTitle() : String	225225	1.01	1.01	1.01	0.0 0.00%
getTempUserPrefs() : Map<String, Integer>   getTempUserPrefs() : Map<String, Integer>	231231	1.01	1.01	1.01	0.0 0.00%
getCacheKey() : String   getCacheKey() : String	237237	1.01	1.01	1.01	0.0 0.00%
getAutosearchPreference() : String   getAutosearchPreference() : String	243243	1.01	1.01	1.01	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.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")
		0% Uncovered Elements: 116 (116) Complexity: 26 Complexity Density: 0.31
37		public class UniprotFTSPanel extends GFTSPanel
38		{
39
40		private static String defaultFTSFrameTitle = MessageManager
41		.getString("label.uniprot_sequence_fetcher");
42
43		private static Map<String, Integer> tempUserPrefs = new HashMap<>();
44
45		private static final String UNIPROT_FTS_CACHE_KEY = "CACHE.UNIPROT_FTS";
46
47		private static final String UNIPROT_AUTOSEARCH = "FTS.UNIPROT.AUTOSEARCH";
48
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
49	0	public UniprotFTSPanel(SequenceFetcher fetcher)...
50		{
51	0	super(fetcher);
52	0	pageLimit = UniProtFTSRestClient.getInstance()
53		.getDefaultResponsePageSize();
54	0	this.seqFetcher = fetcher;
55	0	this.progressIndicator = (fetcher == null) ? null
56		: fetcher.getProgressIndicator();
57		}
58
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
59	0	@Override...
60		public void searchAction(boolean isFreshSearch)
61		{
62	0	mainFrame.requestFocusInWindow();
63	0	if (isFreshSearch)
64		{
65	0	offSet = 0;
66		}
67	0	new Thread()
68		{
		0% Uncovered Elements: 47 (47) Complexity: 9 Complexity Density: 0.24
69	0	@Override...
70		public void run()
71		{
72	0	reset();
73	0	String searchInput = getTypedText();
74	0	if (searchInput.length() > 0)
75		{
76	0	setSearchInProgress(true);
77	0	long startTime = System.currentTimeMillis();
78	0	searchInput = getTypedText();
79	0	String searchTarget = ((FTSDataColumnI) cmb_searchTarget
80		.getSelectedItem()).getAltCode();
81	0	wantedFields = UniProtFTSRestClient.getInstance()
82		.getAllDefaultDisplayedFTSDataColumns();
83	0	String searchTerm = decodeSearchTerm(searchInput, searchTarget);
84
85	0	FTSRestRequest request = new FTSRestRequest();
86	0	request.setFieldToSearchBy(searchTarget);
87	0	request.setSearchTerm(searchTerm);
88	0	request.setOffSet(offSet);
89	0	request.setWantedFields(wantedFields);
90	0	FTSRestClientI uniProtRestClient = UniProtFTSRestClient
91		.getInstance();
92	0	FTSRestResponse resultList;
93	0	try
94		{
95	0	resultList = uniProtRestClient.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	0	if (isPaginationEnabled() && resultSetCount > 0)
122		{
123	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
124		+ " "
125		+ totalNumberformatter.format((Number) (offSet + 1))
126		+ " to "
127		+ totalNumberformatter
128		.format((Number) (offSet + resultSetCount))
129		+ " of "
130		+ totalNumberformatter
131		.format((Number) totalResultSetCount)
132		+ " " + " (" + (endTime - startTime) + " milli secs)");
133		}
134		else
135		{
136	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - "
137		+ resultSetCount + " " + result + " ("
138		+ (endTime - startTime) + " milli secs)");
139		}
140	0	setSearchInProgress(false);
141	0	refreshPaginatorState();
142	0	updateSummaryTableSelections();
143		}
144	0	txt_search.updateCache();
145		}
146		}.start();
147
148		}
149
		0% Uncovered Elements: 21 (21) Complexity: 5 Complexity Density: 0.38
150	0	public String decodeSearchTerm(String enteredText, String targetField)...
151		{
152	0	int searchTargetLength = targetField.equalsIgnoreCase("Search All") ? 0
153		: targetField.length() + 1;
154	0	String searchTarget = targetField.equalsIgnoreCase("Search All") ? ""
155		: targetField + ":";
156	0	String foundSearchTerms = enteredText;
157	0	StringBuilder foundSearchTermsBuilder = new StringBuilder();
158	0	if (enteredText.contains(";"))
159		{
160	0	String[] searchTerms = enteredText.split(";");
161	0	for (String searchTerm : searchTerms)
162		{
163	0	foundSearchTermsBuilder.append(searchTarget).append(searchTerm)
164		.append(" OR ");
165		}
166	0	int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
167	0	foundSearchTerms = foundSearchTermsBuilder.toString();
168	0	if (foundSearchTerms.contains(" OR "))
169		{
170	0	foundSearchTerms = foundSearchTerms.substring(searchTargetLength,
171		endIndex);
172		}
173		}
174	0	return foundSearchTerms;
175		}
176
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
177	0	@Override...
178		public boolean isPaginationEnabled()
179		{
180	0	return true;
181		}
182
		0% Uncovered Elements: 19 (19) Complexity: 2 Complexity Density: 0.11
183	0	@Override...
184		public void okAction()
185		{
186	0	disableActionButtons();
187	0	StringBuilder selectedIds = new StringBuilder();
188	0	HashSet<String> selectedIdsSet = new HashSet<>();
189	0	int primaryKeyColIndex = 0;
190	0	try
191		{
192	0	primaryKeyColIndex = getFTSRestClient()
193		.getPrimaryKeyColumIndex(wantedFields, false);
194		} catch (Exception e)
195		{
196	0	e.printStackTrace();
197		}
198	0	int[] selectedRows = getResultTable().getSelectedRows();
199	0	for (int summaryRow : selectedRows)
200		{
201	0	String idStr = getResultTable()
202		.getValueAt(summaryRow, primaryKeyColIndex).toString();
203	0	selectedIdsSet.add(idStr);
204		}
205	0	selectedIdsSet.addAll(paginatorCart);
206	0	for (String selectedId : selectedIdsSet)
207		{
208	0	selectedIds.append(selectedId).append(";");
209		}
210
211	0	String ids = selectedIds.toString();
212		// System.out.println(">>>>>>>>>>>>>>>> selected Ids: " + ids);
213	0	seqFetcher.getTextArea().setText(ids);
214	0	Thread worker = new Thread(seqFetcher);
215	0	worker.start();
216	0	delayAndEnableActionButtons();
217		}
218
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
219	0	@Override...
220		public FTSRestClientI getFTSRestClient()
221		{
222	0	return UniProtFTSRestClient.getInstance();
223		}
224
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
225	0	@Override...
226		public String getFTSFrameTitle()
227		{
228	0	return defaultFTSFrameTitle;
229		}
230
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
231	0	@Override...
232		public Map<String, Integer> getTempUserPrefs()
233		{
234	0	return tempUserPrefs;
235		}
236
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
237	0	@Override...
238		public String getCacheKey()
239		{
240	0	return UNIPROT_FTS_CACHE_KEY;
241		}
242
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
243	0	@Override...
244		public String getAutosearchPreference()
245		{
246	0	return UNIPROT_AUTOSEARCH;
247		}
248		}