Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
PDBFTSPanel	41	105	33	0.00%	Show methods

Class PDBFTSPanel

Class PDBFTSPanel	Line # 41	Total Statements 105	Complexity 33	TOTAL Coverage 0.00%
PDBFTSPanel(SequenceFetcher)   PDBFTSPanel(SequenceFetcher)	5252	4.04	2.02	0.0 0.00%
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	154154	15.015	5.05	0.0 0.00%
okAction() : void   okAction() : void	190190	21.021	2.02	0.0 0.00%
getPDBIdwithSpecifiedChain(String,String) : String   getPDBIdwithSpecifiedChain(String,String) : String	232232	10.010	4.04	0.0 0.00%
getFTSRestClient() : FTSRestClientI   getFTSRestClient() : FTSRestClientI	258258	1.01	1.01	0.0 0.00%
getFTSFrameTitle() : String   getFTSFrameTitle() : String	264264	1.01	1.01	0.0 0.00%
isPaginationEnabled() : boolean   isPaginationEnabled() : boolean	270270	1.01	1.01	0.0 0.00%
getTempUserPrefs() : Map<String, Integer>   getTempUserPrefs() : Map<String, Integer>	276276	1.01	1.01	0.0 0.00%
getCacheKey() : String   getCacheKey() : String	282282	1.01	1.01	0.0 0.00%
getAutosearchPreference() : String   getAutosearchPreference() : String	288288	1.01	1.01	0.0 0.00%
showHelp() : void   showHelp() : void	294294	3.03	2.02	0.0 0.00%
getDbName() : String   getDbName() : String	306306	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.pdb;
23
24		import java.util.HashMap;
25		import java.util.HashSet;
26		import java.util.Map;
27
28		import javax.help.HelpSetException;
29
30		import jalview.fts.api.FTSDataColumnI;
31		import jalview.fts.api.FTSRestClientI;
32		import jalview.fts.core.FTSRestRequest;
33		import jalview.fts.core.FTSRestResponse;
34		import jalview.fts.core.GFTSPanel;
35		import jalview.gui.Help;
36		import jalview.gui.Help.HelpId;
37		import jalview.gui.SequenceFetcher;
38		import jalview.util.MessageManager;
39
40		@SuppressWarnings("serial")
		0% Uncovered Elements: 147 (147) Complexity: 33 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
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
52	0	public PDBFTSPanel(SequenceFetcher fetcher)...
53		{
54	0	super(fetcher);
55	0	pageLimit = PDBFTSRestClient.getInstance().getDefaultResponsePageSize();
56	0	this.seqFetcher = fetcher;
57	0	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
129		.format(Integer.valueOf(offSet + 1));
130	0	String f2 = totalNumberformatter
131		.format(Integer.valueOf(offSet + resultSetCount));
132	0	String f3 = totalNumberformatter
133		.format(Integer.valueOf(totalResultSetCount));
134	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - " + result
135		+ " " + f1 + " to " + f2 + " of " + f3 + " " + " ("
136		+ (endTime - startTime) + " milli secs)");
137		}
138		else
139		{
140	0	updateSearchFrameTitle(defaultFTSFrameTitle + " - "
141		+ resultSetCount + " " + result + " ("
142		+ (endTime - startTime) + " milli secs)");
143		}
144
145	0	setSearchInProgress(false);
146	0	refreshPaginatorState();
147	0	updateSummaryTableSelections();
148		}
149	0	txt_search.updateCache();
150		}
151		}.start();
152		}
153
		0% Uncovered Elements: 23 (23) Complexity: 5 Complexity Density: 0.33
154	0	public static String decodeSearchTerm(String enteredText,...
155		String targetField)
156		{
157	0	String foundSearchTerms = enteredText;
158	0	StringBuilder foundSearchTermsBuilder = new StringBuilder();
159	0	if (enteredText.contains(";"))
160		{
161	0	String[] searchTerms = enteredText.split(";");
162	0	for (String searchTerm : searchTerms)
163		{
164	0	if (searchTerm.contains(":"))
165		{
166	0	foundSearchTermsBuilder.append(targetField).append(":")
167		.append(searchTerm.split(":")[0]).append(" OR ");
168		}
169		else
170		{
171	0	foundSearchTermsBuilder.append(targetField).append(":")
172		.append(searchTerm).append(" OR ");
173		}
174		}
175	0	int endIndex = foundSearchTermsBuilder.lastIndexOf(" OR ");
176	0	foundSearchTerms = foundSearchTermsBuilder.toString();
177	0	if (foundSearchTerms.contains(" OR "))
178		{
179	0	foundSearchTerms = foundSearchTerms
180		.substring(targetField.length() + 1, endIndex);
181		}
182		}
183	0	else if (enteredText.contains(":"))
184		{
185	0	foundSearchTerms = foundSearchTerms.split(":")[0];
186		}
187	0	return foundSearchTerms;
188		}
189
		0% Uncovered Elements: 21 (21) Complexity: 2 Complexity Density: 0.1
190	0	@Override...
191		public void okAction()
192		{
193		// mainFrame.dispose();
194	0	disableActionButtons();
195	0	StringBuilder selectedIds = new StringBuilder();
196	0	HashSet<String> selectedIdsSet = new HashSet<>();
197	0	int primaryKeyColIndex = 0;
198	0	try
199		{
200	0	primaryKeyColIndex = getFTSRestClient()
201		.getPrimaryKeyColumIndex(wantedFields, false);
202		} catch (Exception e)
203		{
204	0	e.printStackTrace();
205		}
206	0	int[] selectedRows = getResultTable().getSelectedRows();
207	0	String searchTerm = getTypedText();
208	0	for (int summaryRow : selectedRows)
209		{
210	0	String idStr = getResultTable()
211		.getValueAt(summaryRow, primaryKeyColIndex).toString();
212	0	selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
213		}
214
215	0	for (String idStr : paginatorCart)
216		{
217	0	selectedIdsSet.add(getPDBIdwithSpecifiedChain(idStr, searchTerm));
218		}
219
220	0	for (String selectedId : selectedIdsSet)
221		{
222	0	selectedIds.append(selectedId).append(";");
223		}
224
225	0	String ids = selectedIds.toString();
226	0	seqFetcher.setQuery(ids);
227	0	Thread worker = new Thread(seqFetcher);
228	0	worker.start();
229	0	delayAndEnableActionButtons();
230		}
231
		0% Uncovered Elements: 16 (16) Complexity: 4 Complexity Density: 0.4
232	0	public static String getPDBIdwithSpecifiedChain(String pdbId,...
233		String searchTerm)
234		{
235	0	String pdbIdWithChainCode = "";
236	0	if (searchTerm.contains(";"))
237		{
238	0	String[] foundTerms = searchTerm.split(";");
239	0	for (String foundTerm : foundTerms)
240		{
241	0	if (foundTerm.contains(pdbId))
242		{
243	0	pdbIdWithChainCode = foundTerm;
244		}
245		}
246		}
247	0	else if (searchTerm.contains(pdbId))
248		{
249	0	pdbIdWithChainCode = searchTerm;
250		}
251		else
252		{
253	0	pdbIdWithChainCode = pdbId;
254		}
255	0	return pdbIdWithChainCode;
256		}
257
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
258	0	@Override...
259		public FTSRestClientI getFTSRestClient()
260		{
261	0	return PDBFTSRestClient.getInstance();
262		}
263
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
264	0	@Override...
265		public String getFTSFrameTitle()
266		{
267	0	return defaultFTSFrameTitle;
268		}
269
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
270	0	@Override...
271		public boolean isPaginationEnabled()
272		{
273	0	return true;
274		}
275
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
276	0	@Override...
277		public Map<String, Integer> getTempUserPrefs()
278		{
279	0	return tempUserPrefs;
280		}
281
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
282	0	@Override...
283		public String getCacheKey()
284		{
285	0	return PDB_FTS_CACHE_KEY;
286		}
287
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
288	0	@Override...
289		public String getAutosearchPreference()
290		{
291	0	return PDB_AUTOSEARCH;
292		}
293
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 0.67
294	0	@Override...
295		protected void showHelp()
296		{
297	0	try
298		{
299	0	Help.showHelpWindow(HelpId.PdbFts);
300		} catch (HelpSetException e1)
301		{
302	0	e1.printStackTrace();
303		}
304		}
305
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
306	0	public String getDbName()...
307		{
308	0	return "PDB";
309		}
310		}