Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FTSDataColumnPreferences	44	64	15	0.816901481.7%	Show methods
FTSDataColumnPreferences.PreferenceSource	57	0	0	-1.0 -	Show methods
FTSDataColumnPreferences.FTSDataColumnPrefsTableModel	186	46	25	0.1857142918.6%	Show methods

Class FTSDataColumnPreferences

Class FTSDataColumnPreferences	Line # 44	Total Statements 64	Complexity 15	TOTAL Coverage 0.816901481.7%
compare(FTSDataColumnGroupI,FTSDataColumnGroupI) : int   compare(FTSDataColumnGroupI,FTSDataColumnGroupI) : int	161161	1.01	1.01	1.0 1.0100%
FTSDataColumnPreferences(PreferenceSource,FTSRestClientI)   FTSDataColumnPreferences(PreferenceSource,FTSRestClientI)	6666	62.062	13.013	0.8030303 0.803030380.3%
getStructureSummaryFields() : Collection<FTSDataColumnI>   getStructureSummaryFields() : Collection<FTSDataColumnI>	181181	1.01	1.01	1.0 1.0100%

 

Class FTSDataColumnPreferences.PreferenceSource

Class FTSDataColumnPreferences.PreferenceSource	Line # 57	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

Class FTSDataColumnPreferences.FTSDataColumnPrefsTableModel

Class FTSDataColumnPreferences.FTSDataColumnPrefsTableModel	Line # 186	Total Statements 46	Complexity 25	TOTAL Coverage 0.1857142918.6%
FTSDataColumnPrefsTableModel(String[],Object[][])   FTSDataColumnPrefsTableModel(String[],Object[][])	189189	2.02	1.01	1.0 1.0100%
getColumnCount() : int   getColumnCount() : int	200200	1.01	1.01	1.0 1.0100%
getRowCount() : int   getRowCount() : int	206206	1.01	1.01	1.0 1.0100%
getColumnName(int) : String   getColumnName(int) : String	212212	1.01	1.01	1.0 1.0100%
getValueAt(int,int) : Object   getValueAt(int,int) : Object	218218	1.01	1.01	1.0 1.0100%
getColumnClass(int) : Class   getColumnClass(int) : Class	229229	1.01	1.01	1.0 1.0100%
isCellEditable(int,int) : boolean   isCellEditable(int,int) : boolean	238238	8.08	4.04	0.0 0.00%
isPrimaryKeyCell(int,int) : boolean   isPrimaryKeyCell(int,int) : boolean	267267	3.03	1.01	0.0 0.00%
setValueAt(Object,int,int) : void   setValueAt(Object,int,int) : void	277277	24.024	9.09	0.0 0.00%
updatePrefs(Collection<FTSDataColumnI>,FTSDataColumnI,boolean) : void   updatePrefs(Collection<FTSDataColumnI>,FTSDataColumnI,boolean) : void	323323	4.04	5.05	0.0 0.00%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.44680852	jalview.gui.StructureChooserTest.populateFilterComboBoxTestjalview.gui.StructureChooserTest.populateFilterComboBoxTest	1PASS
	0.42553192	jalview.fts.service.pdb.PDBFTSPanelTest.populateCmbSearchTargetOptionsTestjalview.fts.service.pdb.PDBFTSPanelTest.populateCmbSearchTargetOptionsTest	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		package jalview.fts.core;
22
23		import jalview.fts.api.FTSDataColumnI;
24		import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
25		import jalview.fts.api.FTSRestClientI;
26		import jalview.fts.service.pdb.PDBFTSRestClient;
27
28		import java.util.ArrayList;
29		import java.util.Collection;
30		import java.util.Comparator;
31		import java.util.HashMap;
32		import java.util.LinkedHashSet;
33		import java.util.List;
34
35		import javax.swing.JScrollPane;
36		import javax.swing.JTable;
37		import javax.swing.RowSorter;
38		import javax.swing.SortOrder;
39		import javax.swing.table.AbstractTableModel;
40		import javax.swing.table.TableModel;
41		import javax.swing.table.TableRowSorter;
42
43		@SuppressWarnings("serial")
		81.7% Uncovered Elements: 13 (71) Complexity: 15 Complexity Density: 0.23
44		public class FTSDataColumnPreferences extends JScrollPane
45		{
46		protected JTable tbl_FTSDataColumnPrefs = new JTable();
47
48		protected JScrollPane scrl_pdbDocFieldConfig = new JScrollPane(
49		tbl_FTSDataColumnPrefs);
50
51		private HashMap<String, FTSDataColumnI> map = new HashMap<String, FTSDataColumnI>();
52
53		private Collection<FTSDataColumnI> structSummaryColumns = new LinkedHashSet<FTSDataColumnI>();
54
55		private Collection<FTSDataColumnI> allFTSDataColumns = new LinkedHashSet<FTSDataColumnI>();
56
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
57		public enum PreferenceSource
58		{
59		SEARCH_SUMMARY, STRUCTURE_CHOOSER, PREFERENCES;
60		}
61
62		private PreferenceSource currentSource;
63
64		private FTSRestClientI ftsRestClient;
65
		80.3% Uncovered Elements: 13 (66) Complexity: 13 Complexity Density: 0.21
66	2	public FTSDataColumnPreferences(PreferenceSource source,...
67		FTSRestClientI ftsRestClient)
68		{
69	2	this.ftsRestClient = ftsRestClient;
70	2	if (source.equals(PreferenceSource.STRUCTURE_CHOOSER)
71		|| source.equals(PreferenceSource.PREFERENCES))
72		{
73	1	structSummaryColumns = ((PDBFTSRestClient) ftsRestClient)
74		.getAllDefaultDisplayedStructureDataColumns();
75		}
76	2	allFTSDataColumns.addAll(ftsRestClient.getAllFTSDataColumns());
77
78	2	tbl_FTSDataColumnPrefs.setAutoCreateRowSorter(true);
79	2	this.getViewport().add(tbl_FTSDataColumnPrefs);
80	2	this.currentSource = source;
81
82	2	String[] columnNames = null;
83	2	switch (source)
84		{
85	1	case SEARCH_SUMMARY:
86	1	columnNames = new String[] { "", "Display", "Group" };
87	1	break;
88	1	case STRUCTURE_CHOOSER:
89	1	columnNames = new String[] { "", "Display", "Group" };
90	1	break;
91	0	case PREFERENCES:
92	0	columnNames = new String[] { "PDB Field", "Show in search summary",
93		"Show in structure summary" };
94	0	break;
95	0	default:
96	0	break;
97		}
98
99	2	Object[][] data = new Object[allFTSDataColumns.size() - 1][3];
100
101	2	int x = 0;
102	2	for (FTSDataColumnI field : allFTSDataColumns)
103		{
104	168	if (field.getName().equalsIgnoreCase("all"))
105		{
106	2	continue;
107		}
108
109	166	switch (source)
110		{
111	83	case SEARCH_SUMMARY:
112	83	data[x++] = new Object[] { ftsRestClient
113		.getAllDefaultDisplayedFTSDataColumns().contains(field),
114		field.getName(), field.getGroup() };
115	83	break;
116	83	case STRUCTURE_CHOOSER:
117	83	data[x++] = new Object[] { structSummaryColumns.contains(field),
118		field.getName(), field.getGroup() };
119	83	break;
120	0	case PREFERENCES:
121	0	data[x++] = new Object[] {
122		field.getName(), ftsRestClient
123		.getAllDefaultDisplayedFTSDataColumns().contains(field),
124		structSummaryColumns.contains(field) };
125	0	break;
126	0	default:
127	0	break;
128		}
129	166	map.put(field.getName(), field);
130		}
131
132	2	FTSDataColumnPrefsTableModel model = new FTSDataColumnPrefsTableModel(
133		columnNames, data);
134	2	tbl_FTSDataColumnPrefs.setModel(model);
135
136	2	switch (source)
137		{
138	1	case SEARCH_SUMMARY:
139	1	case STRUCTURE_CHOOSER:
140	2	tbl_FTSDataColumnPrefs.getColumnModel().getColumn(0)
141		.setPreferredWidth(30);
142	2	tbl_FTSDataColumnPrefs.getColumnModel().getColumn(0).setMinWidth(20);
143	2	tbl_FTSDataColumnPrefs.getColumnModel().getColumn(0).setMaxWidth(40);
144	2	tbl_FTSDataColumnPrefs.getColumnModel().getColumn(1)
145		.setPreferredWidth(150);
146	2	tbl_FTSDataColumnPrefs.getColumnModel().getColumn(1).setMinWidth(150);
147	2	tbl_FTSDataColumnPrefs.getColumnModel().getColumn(2)
148		.setPreferredWidth(150);
149	2	tbl_FTSDataColumnPrefs.getColumnModel().getColumn(2).setMinWidth(150);
150
151	2	TableRowSorter<TableModel> sorter = new TableRowSorter<>(
152		tbl_FTSDataColumnPrefs.getModel());
153	2	tbl_FTSDataColumnPrefs.setRowSorter(sorter);
154	2	List<RowSorter.SortKey> sortKeys = new ArrayList<>();
155	2	int columnIndexToSort = 2;
156	2	sortKeys.add(new RowSorter.SortKey(columnIndexToSort,
157		SortOrder.ASCENDING));
158	2	sorter.setComparator(columnIndexToSort,
159		new Comparator<FTSDataColumnGroupI>()
160		{
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
161	748	@Override...
162		public int compare(FTSDataColumnGroupI o1,
163		FTSDataColumnGroupI o2)
164		{
165	748	return o1.getSortOrder() - o2.getSortOrder();
166		}
167		});
168	2	sorter.setSortKeys(sortKeys);
169		// BH 2018 setSortKeys does a sort sorter.sort();
170
171	2	tbl_FTSDataColumnPrefs
172		.setAutoResizeMode(JTable.AUTO_RESIZE_NEXT_COLUMN);
173	2	break;
174	0	case PREFERENCES:
175	0	default:
176	0	break;
177		}
178
179		}
180
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
181	1	public Collection<FTSDataColumnI> getStructureSummaryFields()...
182		{
183	1	return structSummaryColumns;
184		}
185
		18.6% Uncovered Elements: 57 (70) Complexity: 25 Complexity Density: 0.54
186		class FTSDataColumnPrefsTableModel extends AbstractTableModel
187		{
188
		100% Uncovered Elements: 0 (2) Complexity: 1 Complexity Density: 0.5
189	2	public FTSDataColumnPrefsTableModel(String[] columnNames,...
190		Object[][] data)
191		{
192	2	this.data = data;
193	2	this.columnNames = columnNames;
194		}
195
196		private Object[][] data;
197
198		private String[] columnNames;
199
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
200	24	@Override...
201		public int getColumnCount()
202		{
203	24	return columnNames.length;
204		}
205
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
206	10	@Override...
207		public int getRowCount()
208		{
209	10	return data.length;
210		}
211
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
212	6	@Override...
213		public String getColumnName(int col)
214		{
215	6	return columnNames[col];
216		}
217
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
218	1500	@Override...
219		public Object getValueAt(int row, int col)
220		{
221	1500	return data[row][col];
222		}
223
224		/*
225		* JTable uses this method to determine the default renderer/ editor for
226		* each cell. If we didn't implement this method, then the last column would
227		* contain text ("true"/"false"), rather than a check box.
228		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
229	4	@Override...
230		public Class getColumnClass(int c)
231		{
232	4	return getValueAt(0, c).getClass();
233		}
234
235		/*
236		* Don't need to implement this method unless your table's editable.
237		*/
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 0.5
238	0	@Override...
239		public boolean isCellEditable(int row, int col)
240		{
241		// Note that the data/cell address is constant,
242		// no matter where the cell appears onscreen.
243		// !isPDBID(row, col) ensures the PDB_Id cell is never editable as it
244		// serves as a unique id for each row.
245		// return (col == 1 || col == 2) && !isPDBID(row, col);
246	0	switch (currentSource)
247		{
248	0	case SEARCH_SUMMARY:
249	0	case STRUCTURE_CHOOSER:
250	0	return (col == 0) && !isPrimaryKeyCell(row, 1);
251	0	case PREFERENCES:
252	0	return (col == 1 || col == 2) && !isPrimaryKeyCell(row, 0);
253	0	default:
254	0	return false;
255		}
256
257		}
258
259		/**
260		* Determines whether the data in a given cell is a PDB ID.
261		*
262		* @param row
263		* @param col
264		* @return
265		*/
266
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
267	0	public boolean isPrimaryKeyCell(int row, int col)...
268		{
269	0	String name = getValueAt(row, col).toString();
270	0	FTSDataColumnI pdbField = map.get(name);
271	0	return pdbField.isPrimaryKeyColumn();
272		}
273
274		/*
275		* Don't need to implement this method unless your table's data can change.
276		*/
		0% Uncovered Elements: 34 (34) Complexity: 9 Complexity Density: 0.38
277	0	@Override...
278		public void setValueAt(Object value, int row, int col)
279		{
280	0	data[row][col] = value;
281	0	fireTableCellUpdated(row, col);
282
283	0	String name = null;
284	0	switch (currentSource)
285		{
286	0	case SEARCH_SUMMARY:
287	0	case STRUCTURE_CHOOSER:
288	0	name = getValueAt(row, 1).toString();
289	0	break;
290	0	case PREFERENCES:
291	0	name = getValueAt(row, 0).toString();
292	0	break;
293	0	default:
294	0	break;
295		}
296	0	boolean selected = ((Boolean) value).booleanValue();
297
298	0	FTSDataColumnI ftsDataColumn = map.get(name);
299
300	0	if (currentSource == PreferenceSource.SEARCH_SUMMARY)
301		{
302	0	updatePrefs(ftsRestClient.getAllDefaultDisplayedFTSDataColumns(),
303		ftsDataColumn, selected);
304		}
305	0	else if (currentSource == PreferenceSource.STRUCTURE_CHOOSER)
306		{
307	0	updatePrefs(structSummaryColumns, ftsDataColumn, selected);
308		}
309	0	else if (currentSource == PreferenceSource.PREFERENCES)
310		{
311	0	if (col == 1)
312		{
313	0	updatePrefs(ftsRestClient.getAllDefaultDisplayedFTSDataColumns(),
314		ftsDataColumn, selected);
315		}
316	0	else if (col == 2)
317		{
318	0	updatePrefs(structSummaryColumns, ftsDataColumn, selected);
319		}
320		}
321		}
322
		0% Uncovered Elements: 8 (8) Complexity: 5 Complexity Density: 1.25
323	0	private void updatePrefs(Collection<FTSDataColumnI> prefConfig,...
324		FTSDataColumnI dataColumn, boolean selected)
325		{
326	0	if (prefConfig.contains(dataColumn) && !selected)
327		{
328	0	prefConfig.remove(dataColumn);
329		}
330
331	0	if (!prefConfig.contains(dataColumn) && selected)
332		{
333	0	prefConfig.add(dataColumn);
334		}
335		}
336
337		}
338		}