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package jalview.io; |
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import java.io.File; |
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import java.io.IOException; |
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import java.util.StringTokenizer; |
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import java.util.Vector; |
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import javax.swing.SwingUtilities; |
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import jalview.api.ComplexAlignFile; |
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import jalview.api.FeatureSettingsModelI; |
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import jalview.api.FeaturesDisplayedI; |
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import jalview.api.FeaturesSourceI; |
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import jalview.bin.Cache; |
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import jalview.bin.Jalview; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.HiddenColumns; |
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import jalview.datamodel.PDBEntry; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.AlignFrame; |
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import jalview.gui.AlignViewport; |
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import jalview.gui.Desktop; |
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import jalview.gui.JvOptionPane; |
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import jalview.gui.QuitHandler; |
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import jalview.json.binding.biojson.v1.ColourSchemeMapper; |
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import jalview.project.Jalview2XML; |
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import jalview.schemes.ColourSchemeI; |
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import jalview.structure.StructureSelectionManager; |
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import jalview.util.MessageManager; |
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import jalview.ws.utils.UrlDownloadClient; |
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| 63.9% |
Uncovered Elements: 108 (299) |
Complexity: 83 |
Complexity Density: 0.45 |
|
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public class FileLoader implements Runnable |
53 |
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{ |
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String file; |
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|
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DataSourceType protocol; |
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FileFormatI format; |
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AlignmentFileReaderI source = null; |
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AlignViewport viewport; |
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AlignFrame alignFrame; |
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|
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long loadtime; |
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|
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long memused; |
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boolean raiseGUI = true; |
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|
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private File selectedFile; |
76 |
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|
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private static boolean useDefaultFileFormat = false; |
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80 |
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|
81 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
82 |
122 |
public FileLoader()... |
83 |
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{ |
84 |
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this(true); |
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} |
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88 |
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89 |
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|
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@param |
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|
92 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public FileLoader(boolean raiseGUI)... |
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{ |
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this.raiseGUI = raiseGUI; |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
98 |
1 |
public void LoadFile(AlignViewport viewport, Object file,... |
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DataSourceType protocol, FileFormatI format) |
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{ |
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1 |
LoadFile(viewport, file, protocol, format, true); |
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} |
103 |
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| 57.1% |
Uncovered Elements: 3 (7) |
Complexity: 2 |
Complexity Density: 0.4 |
|
104 |
21 |
public void LoadFile(AlignViewport viewport, Object file,... |
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DataSourceType protocol, FileFormatI format, boolean async) |
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{ |
107 |
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this.viewport = viewport; |
108 |
21 |
if (file instanceof File) |
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{ |
110 |
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this.selectedFile = (File) file; |
111 |
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file = selectedFile.getPath(); |
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} |
113 |
21 |
LoadFile(file.toString(), protocol, format, async); |
114 |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public void LoadFile(String file, DataSourceType protocol,... |
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FileFormatI format) |
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{ |
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LoadFile(file, protocol, format, true); |
120 |
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} |
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|
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| 100% |
Uncovered Elements: 0 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
122 |
21 |
public void LoadFile(String file, DataSourceType protocol,... |
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FileFormatI format, boolean async) |
124 |
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{ |
125 |
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this.file = file; |
126 |
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this.protocol = protocol; |
127 |
21 |
this.format = format; |
128 |
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|
129 |
21 |
if (async) |
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{ |
131 |
1 |
final Thread loader = new Thread(this); |
132 |
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|
133 |
1 |
SwingUtilities.invokeLater(new Runnable() |
134 |
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{ |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
135 |
1 |
@Override... |
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public void run() |
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{ |
138 |
1 |
loader.start(); |
139 |
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} |
140 |
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}); |
141 |
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} |
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else |
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{ |
144 |
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this.run(); |
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} |
146 |
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} |
147 |
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148 |
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149 |
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150 |
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|
151 |
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@param |
152 |
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@param |
153 |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
154 |
0 |
public void LoadFile(String file, DataSourceType protocol)... |
155 |
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{ |
156 |
0 |
LoadFile(file, protocol, null); |
157 |
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} |
158 |
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159 |
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|
160 |
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161 |
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|
162 |
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@param |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
166 |
142 |
public AlignFrame LoadFileWaitTillLoaded(String file,... |
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DataSourceType sourceType) |
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{ |
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return LoadFileWaitTillLoaded(file, sourceType, null); |
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} |
171 |
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172 |
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173 |
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174 |
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|
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@param |
176 |
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@param |
177 |
|
@param |
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@return |
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| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
180 |
317 |
public AlignFrame LoadFileWaitTillLoaded(String file,... |
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DataSourceType sourceType, FileFormatI format) |
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{ |
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this.file = file; |
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this.protocol = sourceType; |
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this.format = format; |
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return _LoadFileWaitTillLoaded(); |
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} |
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189 |
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@param |
193 |
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@param |
194 |
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@param |
195 |
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@return |
196 |
|
|
|
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
197 |
6 |
public AlignFrame LoadFileWaitTillLoaded(File file,... |
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DataSourceType sourceType, FileFormatI format) |
199 |
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{ |
200 |
6 |
this.selectedFile = file; |
201 |
6 |
this.file = file.getPath(); |
202 |
6 |
this.protocol = sourceType; |
203 |
6 |
this.format = format; |
204 |
6 |
return _LoadFileWaitTillLoaded(); |
205 |
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} |
206 |
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|
207 |
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|
208 |
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|
209 |
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|
210 |
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@param |
211 |
|
@param |
212 |
|
@return |
213 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
214 |
0 |
public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,... |
215 |
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FileFormatI format) |
216 |
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{ |
217 |
0 |
this.source = source; |
218 |
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|
219 |
0 |
file = source.getInFile(); |
220 |
0 |
protocol = source.getDataSourceType(); |
221 |
0 |
this.format = format; |
222 |
0 |
return _LoadFileWaitTillLoaded(); |
223 |
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} |
224 |
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|
225 |
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|
226 |
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|
227 |
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|
228 |
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|
229 |
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@return |
230 |
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|
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|
| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
231 |
323 |
protected AlignFrame _LoadFileWaitTillLoaded()... |
232 |
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{ |
233 |
323 |
this.run(); |
234 |
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|
235 |
319 |
return alignFrame; |
236 |
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} |
237 |
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|
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| 94.6% |
Uncovered Elements: 2 (37) |
Complexity: 11 |
Complexity Density: 0.52 |
|
238 |
340 |
public void updateRecentlyOpened()... |
239 |
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{ |
240 |
340 |
Vector<String> recent = new Vector<>(); |
241 |
340 |
if (protocol == DataSourceType.PASTE) |
242 |
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{ |
243 |
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|
244 |
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|
245 |
48 |
return; |
246 |
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} |
247 |
292 |
if (file != null |
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&& file.indexOf(System.getProperty("java.io.tmpdir")) > -1) |
249 |
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{ |
250 |
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|
251 |
19 |
return; |
252 |
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} |
253 |
273 |
String type = protocol == DataSourceType.FILE ? "RECENT_FILE" |
254 |
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: "RECENT_URL"; |
255 |
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|
256 |
273 |
String historyItems = Cache.getProperty(type); |
257 |
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|
258 |
273 |
StringTokenizer st; |
259 |
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|
260 |
273 |
if (historyItems != null) |
261 |
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{ |
262 |
261 |
st = new StringTokenizer(historyItems, "\t"); |
263 |
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|
264 |
2127 |
while (st.hasMoreTokens()) |
265 |
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{ |
266 |
1866 |
recent.addElement(st.nextToken().trim()); |
267 |
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} |
268 |
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} |
269 |
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|
270 |
273 |
if (recent.contains(file)) |
271 |
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{ |
272 |
185 |
recent.remove(file); |
273 |
|
} |
274 |
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|
275 |
273 |
StringBuffer newHistory = new StringBuffer(file); |
276 |
1923 |
for (int i = 0; i < recent.size() && i < 10; i++) |
277 |
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{ |
278 |
1650 |
newHistory.append("\t"); |
279 |
1650 |
newHistory.append(recent.elementAt(i)); |
280 |
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} |
281 |
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|
282 |
273 |
Cache.setProperty(type, newHistory.toString()); |
283 |
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|
284 |
273 |
if (protocol == DataSourceType.FILE) |
285 |
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{ |
286 |
273 |
Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName()); |
287 |
|
} |
288 |
|
} |
289 |
|
|
|
|
| 56.1% |
Uncovered Elements: 75 (171) |
Complexity: 45 |
Complexity Density: 0.41 |
|
290 |
344 |
@Override... |
291 |
|
public void run() |
292 |
|
{ |
293 |
344 |
String title = protocol == DataSourceType.PASTE |
294 |
|
? "Copied From Clipboard" |
295 |
|
: file; |
296 |
344 |
Runtime rt = Runtime.getRuntime(); |
297 |
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|
298 |
344 |
try |
299 |
|
{ |
300 |
344 |
if (Desktop.instance != null) |
301 |
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{ |
302 |
293 |
Desktop.instance.startLoading(file); |
303 |
|
} |
304 |
344 |
if (format == null) |
305 |
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{ |
306 |
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|
307 |
162 |
if (source != null) |
308 |
|
{ |
309 |
0 |
format = new IdentifyFile().identify(source, false); |
310 |
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|
311 |
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} |
312 |
162 |
else if (selectedFile != null) |
313 |
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{ |
314 |
0 |
format = new IdentifyFile().identify(selectedFile, protocol); |
315 |
|
} |
316 |
|
else |
317 |
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{ |
318 |
162 |
format = new IdentifyFile().identify(file, protocol); |
319 |
|
} |
320 |
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|
321 |
|
} |
322 |
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|
323 |
344 |
if (format == null) |
324 |
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{ |
325 |
0 |
Desktop.instance.stopLoading(); |
326 |
0 |
jalview.bin.Console.errPrintln("The input file \"" + file |
327 |
|
+ "\" has null or unidentifiable data content!"); |
328 |
0 |
if (!Jalview.isHeadlessMode() && !Jalview.isBatchMode()) |
329 |
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{ |
330 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
331 |
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MessageManager.getString("label.couldnt_read_data") |
332 |
|
+ " in " + file + "\n" |
333 |
|
+ AppletFormatAdapter.getSupportedFormats(), |
334 |
|
MessageManager.getString("label.couldnt_read_data"), |
335 |
|
JvOptionPane.WARNING_MESSAGE); |
336 |
|
} |
337 |
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|
338 |
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|
339 |
0 |
return; |
340 |
|
} |
341 |
|
|
342 |
|
|
343 |
344 |
if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) |
344 |
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{ |
345 |
0 |
System.gc(); |
346 |
0 |
memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); |
347 |
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|
348 |
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|
349 |
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|
350 |
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} |
351 |
344 |
loadtime = -System.currentTimeMillis(); |
352 |
344 |
AlignmentI al = null; |
353 |
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|
354 |
344 |
if (FileFormat.Jalview.equals(format)) |
355 |
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{ |
356 |
30 |
if (source != null) |
357 |
|
{ |
358 |
|
|
359 |
0 |
jalview.bin.Console.errPrintln( |
360 |
|
"IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream."); |
361 |
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|
362 |
|
} |
363 |
|
|
364 |
30 |
alignFrame = new Jalview2XML(raiseGUI && !Jalview.isBatchMode()) |
365 |
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.loadJalviewAlign( |
366 |
30 |
selectedFile == null ? file : selectedFile); |
367 |
|
} |
368 |
|
else |
369 |
|
{ |
370 |
314 |
String error = AppletFormatAdapter.getSupportedFormats(); |
371 |
314 |
try |
372 |
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{ |
373 |
314 |
if (source != null) |
374 |
|
{ |
375 |
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|
376 |
0 |
al = new FormatAdapter().readFromFile(source, format); |
377 |
|
} |
378 |
|
else |
379 |
|
{ |
380 |
|
|
381 |
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|
382 |
314 |
FormatAdapter fa = new FormatAdapter(); |
383 |
314 |
boolean downloadStructureFile = format.isStructureFile() |
384 |
|
&& protocol.equals(DataSourceType.URL); |
385 |
314 |
if (downloadStructureFile) |
386 |
|
{ |
387 |
0 |
String structExt = format.getExtensions().split(",")[0]; |
388 |
0 |
String urlLeafName = file.substring( |
389 |
|
file.lastIndexOf( |
390 |
|
System.getProperty("file.separator")), |
391 |
|
file.lastIndexOf(".")); |
392 |
0 |
String tempStructureFileStr = createNamedJvTempFile( |
393 |
|
urlLeafName, structExt); |
394 |
|
|
395 |
|
|
396 |
|
|
397 |
0 |
File tempFile = new File(tempStructureFileStr); |
398 |
0 |
UrlDownloadClient.download(file, tempFile); |
399 |
|
|
400 |
0 |
al = fa.readFile(tempFile, DataSourceType.FILE, format); |
401 |
0 |
source = fa.getAlignFile(); |
402 |
|
} |
403 |
|
else |
404 |
|
{ |
405 |
314 |
if (selectedFile == null) |
406 |
|
{ |
407 |
308 |
al = fa.readFile(null, file, protocol, format); |
408 |
|
|
409 |
|
} |
410 |
|
else |
411 |
|
{ |
412 |
6 |
al = fa.readFile(selectedFile, null, protocol, format); |
413 |
|
} |
414 |
314 |
source = fa.getAlignFile(); |
415 |
|
|
416 |
|
|
417 |
|
} |
418 |
|
} |
419 |
|
} catch (java.io.IOException ex) |
420 |
|
{ |
421 |
0 |
error = ex.getMessage(); |
422 |
|
} |
423 |
|
|
424 |
314 |
if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence()) |
425 |
|
{ |
426 |
|
|
427 |
314 |
for (SequenceI sq : al.getSequences()) |
428 |
|
{ |
429 |
2524 |
while (sq.getDatasetSequence() != null) |
430 |
|
{ |
431 |
2 |
sq = sq.getDatasetSequence(); |
432 |
|
} |
433 |
2522 |
if (sq.getAllPDBEntries() != null) |
434 |
|
{ |
435 |
2522 |
for (PDBEntry pdbe : sq.getAllPDBEntries()) |
436 |
|
{ |
437 |
|
|
438 |
|
|
439 |
50 |
StructureSelectionManager |
440 |
|
.getStructureSelectionManager(Desktop.instance) |
441 |
|
.registerPDBEntry(pdbe); |
442 |
|
} |
443 |
|
} |
444 |
|
} |
445 |
|
|
446 |
314 |
FeatureSettingsModelI proxyColourScheme = source |
447 |
|
.getFeatureColourScheme(); |
448 |
314 |
if (viewport != null) |
449 |
|
{ |
450 |
|
|
451 |
21 |
viewport.addAlignment(al, title); |
452 |
21 |
viewport.applyFeaturesStyle(proxyColourScheme); |
453 |
|
} |
454 |
|
else |
455 |
|
{ |
456 |
|
|
457 |
|
|
458 |
293 |
if (source instanceof ComplexAlignFile) |
459 |
|
{ |
460 |
0 |
HiddenColumns colSel = ((ComplexAlignFile) source) |
461 |
|
.getHiddenColumns(); |
462 |
0 |
SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) |
463 |
|
.getHiddenSequences(); |
464 |
0 |
String colourSchemeName = ((ComplexAlignFile) source) |
465 |
|
.getGlobalColourScheme(); |
466 |
0 |
FeaturesDisplayedI fd = ((ComplexAlignFile) source) |
467 |
|
.getDisplayedFeatures(); |
468 |
0 |
alignFrame = new AlignFrame(al, hiddenSeqs, colSel, |
469 |
|
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); |
470 |
0 |
alignFrame.getViewport().setFeaturesDisplayed(fd); |
471 |
0 |
alignFrame.getViewport().setShowSequenceFeatures( |
472 |
|
((ComplexAlignFile) source).isShowSeqFeatures()); |
473 |
0 |
ColourSchemeI cs = ColourSchemeMapper |
474 |
|
.getJalviewColourScheme(colourSchemeName, al); |
475 |
0 |
if (cs != null) |
476 |
|
{ |
477 |
0 |
alignFrame.changeColour(cs); |
478 |
|
} |
479 |
|
} |
480 |
|
else |
481 |
|
{ |
482 |
293 |
alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, |
483 |
|
AlignFrame.DEFAULT_HEIGHT); |
484 |
289 |
if (source instanceof FeaturesSourceI) |
485 |
|
{ |
486 |
1 |
alignFrame.getViewport().setShowSequenceFeatures(true); |
487 |
|
} |
488 |
|
} |
489 |
|
|
490 |
289 |
if (!(protocol == DataSourceType.PASTE)) |
491 |
|
{ |
492 |
241 |
alignFrame.setFileName(file, format); |
493 |
241 |
alignFrame.setFileObject(selectedFile); |
494 |
|
} |
495 |
289 |
if (proxyColourScheme != null) |
496 |
|
{ |
497 |
14 |
alignFrame.getViewport() |
498 |
|
.applyFeaturesStyle(proxyColourScheme); |
499 |
|
} |
500 |
289 |
alignFrame.setStatus(MessageManager.formatMessage( |
501 |
|
"label.successfully_loaded_file", new String[] |
502 |
|
{ title })); |
503 |
|
|
504 |
289 |
if (raiseGUI) |
505 |
|
{ |
506 |
|
|
507 |
|
|
508 |
|
|
509 |
|
|
510 |
|
|
511 |
216 |
Desktop.addInternalFrame(alignFrame, title, |
512 |
|
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); |
513 |
|
|
514 |
|
|
515 |
|
|
516 |
|
|
517 |
|
|
518 |
216 |
alignFrame.alignPanel.setOverviewTitle(alignFrame); |
519 |
|
} |
520 |
|
|
521 |
289 |
try |
522 |
|
{ |
523 |
289 |
alignFrame.setMaximum( |
524 |
|
Cache.getDefault("SHOW_FULLSCREEN", false)); |
525 |
|
} catch (java.beans.PropertyVetoException ex) |
526 |
|
{ |
527 |
|
} |
528 |
|
} |
529 |
|
} |
530 |
|
else |
531 |
|
{ |
532 |
0 |
if (Desktop.instance != null) |
533 |
|
{ |
534 |
0 |
Desktop.instance.stopLoading(); |
535 |
|
} |
536 |
|
|
537 |
0 |
final String errorMessage = MessageManager.getString( |
538 |
|
"label.couldnt_load_file") + " " + title + "\n" + error; |
539 |
|
|
540 |
|
|
541 |
0 |
if (raiseGUI && !Jalview.isBatchMode() && Desktop.desktop != null) |
542 |
|
{ |
543 |
0 |
javax.swing.SwingUtilities.invokeLater(new Runnable() |
544 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
545 |
0 |
@Override... |
546 |
|
public void run() |
547 |
|
{ |
548 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
549 |
|
errorMessage, |
550 |
|
MessageManager |
551 |
|
.getString("label.error_loading_file"), |
552 |
|
JvOptionPane.WARNING_MESSAGE); |
553 |
|
} |
554 |
|
}); |
555 |
|
} |
556 |
|
else |
557 |
|
{ |
558 |
0 |
jalview.bin.Console.errPrintln(errorMessage); |
559 |
|
} |
560 |
|
} |
561 |
|
} |
562 |
|
|
563 |
340 |
updateRecentlyOpened(); |
564 |
|
|
565 |
|
} catch (Exception er) |
566 |
|
{ |
567 |
0 |
jalview.bin.Console |
568 |
|
.errPrintln("Exception whilst opening file '" + file); |
569 |
0 |
er.printStackTrace(); |
570 |
0 |
if (raiseGUI && !Jalview.isBatchMode()) |
571 |
|
{ |
572 |
0 |
javax.swing.SwingUtilities.invokeLater(new Runnable() |
573 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
574 |
0 |
@Override... |
575 |
|
public void run() |
576 |
|
{ |
577 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
578 |
|
MessageManager.formatMessage( |
579 |
|
"label.problems_opening_file", new String[] |
580 |
|
{ file }), |
581 |
|
MessageManager.getString("label.file_open_error"), |
582 |
|
JvOptionPane.WARNING_MESSAGE); |
583 |
|
} |
584 |
|
}); |
585 |
|
} |
586 |
0 |
alignFrame = null; |
587 |
|
} catch (OutOfMemoryError er) |
588 |
|
{ |
589 |
|
|
590 |
0 |
er.printStackTrace(); |
591 |
0 |
alignFrame = null; |
592 |
0 |
if (raiseGUI && !Jalview.isBatchMode()) |
593 |
|
{ |
594 |
0 |
javax.swing.SwingUtilities.invokeLater(new Runnable() |
595 |
|
{ |
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
596 |
0 |
@Override... |
597 |
|
public void run() |
598 |
|
{ |
599 |
0 |
JvOptionPane.showInternalMessageDialog(Desktop.desktop, |
600 |
|
MessageManager.formatMessage( |
601 |
|
"warn.out_of_memory_loading_file", new String[] |
602 |
|
{ file }), |
603 |
|
MessageManager.getString("label.out_of_memory"), |
604 |
|
JvOptionPane.WARNING_MESSAGE); |
605 |
|
} |
606 |
|
}); |
607 |
|
} |
608 |
0 |
jalview.bin.Console |
609 |
|
.errPrintln("Out of memory loading file " + file + "!!"); |
610 |
|
|
611 |
|
} |
612 |
340 |
loadtime += System.currentTimeMillis(); |
613 |
|
|
614 |
|
|
615 |
|
|
616 |
340 |
memused = memused |
617 |
|
- (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); |
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
|
622 |
340 |
if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) |
623 |
|
{ |
624 |
0 |
if (alignFrame != null) |
625 |
|
{ |
626 |
0 |
AlignmentI al = alignFrame.getViewport().getAlignment(); |
627 |
|
|
628 |
0 |
jalview.bin.Console.outPrintln("Loaded '" + title + "' in " |
629 |
|
+ (loadtime / 1000.0) + "s, took an additional " |
630 |
|
+ (1.0 * memused / (1024.0 * 1024.0)) + " MB (" |
631 |
|
+ al.getHeight() + " seqs by " + al.getWidth() + " cols)"); |
632 |
|
} |
633 |
|
else |
634 |
|
{ |
635 |
|
|
636 |
|
|
637 |
0 |
jalview.bin.Console.outPrintln("Failed to load '" + title + "' in " |
638 |
|
+ (loadtime / 1000.0) + "s, took an additional " |
639 |
|
+ (1.0 * memused / (1024.0 * 1024.0)) |
640 |
|
+ " MB (alignment is null)"); |
641 |
|
} |
642 |
|
} |
643 |
|
|
644 |
340 |
if (Desktop.instance != null) |
645 |
|
{ |
646 |
289 |
Desktop.instance.stopLoading(); |
647 |
|
} |
648 |
|
|
649 |
340 |
this.setShouldBeSaved(); |
650 |
|
|
651 |
340 |
useDefaultFileFormat = true; |
652 |
|
} |
653 |
|
|
654 |
|
|
655 |
|
|
656 |
|
|
657 |
|
|
658 |
|
|
659 |
|
@param |
660 |
|
|
661 |
|
@param |
662 |
|
|
663 |
|
@return |
664 |
|
|
|
|
| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
665 |
0 |
private static String createNamedJvTempFile(String fileName,... |
666 |
|
String extension) throws IOException |
667 |
|
{ |
668 |
0 |
String seprator = System.getProperty("file.separator"); |
669 |
0 |
String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview" |
670 |
|
+ seprator + System.currentTimeMillis(); |
671 |
0 |
File tempStructFile = new File( |
672 |
|
jvTempDir + seprator + fileName + "." + extension); |
673 |
0 |
tempStructFile.mkdirs(); |
674 |
0 |
return tempStructFile.toString(); |
675 |
|
} |
676 |
|
|
677 |
|
|
678 |
|
|
679 |
|
|
|
|
| 72.7% |
Uncovered Elements: 6 (22) |
Complexity: 7 |
Complexity Density: 0.58 |
|
680 |
340 |
private void setShouldBeSaved()... |
681 |
|
{ |
682 |
340 |
if (protocol == null) |
683 |
0 |
return; |
684 |
340 |
AlignFrame af = this.alignFrame; |
685 |
340 |
if (af == null) |
686 |
21 |
return; |
687 |
319 |
AlignViewport avp = af.getViewport(); |
688 |
319 |
if (avp == null) |
689 |
0 |
return; |
690 |
319 |
boolean upToDate = !protocol.isDynamic(); |
691 |
319 |
if (protocol.isUrl() && !Cache |
692 |
|
.getDefault(PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS, true)) |
693 |
|
{ |
694 |
0 |
upToDate = true; |
695 |
|
} |
696 |
319 |
avp.setSavedUpToDate(upToDate, |
697 |
319 |
upToDate ? null : QuitHandler.Message.UNSAVED_ALIGNMENTS); |
698 |
|
} |
699 |
|
|
700 |
|
public static final String PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS = "PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS"; |
701 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
702 |
75 |
public static boolean getUseDefaultFileFormat()... |
703 |
|
{ |
704 |
75 |
return useDefaultFileFormat; |
705 |
|
} |
706 |
|
|
707 |
|
} |