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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.io.InputStream; |
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import java.util.List; |
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import java.util.Locale; |
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import jalview.api.AlignExportSettingsI; |
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import jalview.api.AlignmentViewPanel; |
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import jalview.datamodel.Alignment; |
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import jalview.datamodel.AlignmentAnnotation; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.AlignmentView; |
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import jalview.datamodel.PDBEntry.Type; |
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import jalview.datamodel.SequenceI; |
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import jalview.ext.jmol.JmolParser; |
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import jalview.structure.StructureImportSettings; |
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import jalview.util.Platform; |
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@author |
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@version |
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| 30.4% |
Uncovered Elements: 224 (322) |
Complexity: 86 |
Complexity Density: 0.42 |
|
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public class AppletFormatAdapter |
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{ |
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private AlignmentViewPanel viewpanel; |
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boolean annotFromStructure = false; |
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boolean localSecondaryStruct = false; |
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boolean serviceSecondaryStruct = false; |
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private AlignmentFileReaderI alignFile = null; |
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String inFile; |
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protected String newline = System.getProperty("line.separator"); |
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private AlignExportSettingsI exportSettings; |
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private File selectedFile; |
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public static String INVALID_CHARACTERS = "Contains invalid characters"; |
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@return |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public static String getSupportedFormats()... |
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{ |
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return "Formats currently supported are\n" |
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+ prettyPrint(FileFormats.getInstance().getReadableFormats()); |
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} |
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| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
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543 |
public AppletFormatAdapter()... |
96 |
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{ |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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2 |
public AppletFormatAdapter(AlignmentViewPanel viewpanel)... |
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{ |
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2 |
this.viewpanel = viewpanel; |
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} |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
|
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126 |
public AppletFormatAdapter(AlignmentViewPanel alignPanel,... |
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AlignExportSettingsI settings) |
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{ |
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viewpanel = alignPanel; |
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exportSettings = settings; |
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} |
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@param |
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@return |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 2 |
Complexity Density: 0.33 |
|
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313 |
public static String prettyPrint(List<? extends Object> things)... |
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{ |
119 |
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StringBuffer list = new StringBuffer(); |
120 |
5947 |
for (int i = 0, iSize = things.size() - 1; i < iSize; i++) |
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{ |
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5634 |
list.append(things.get(i).toString()); |
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5634 |
list.append(", "); |
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} |
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list.append(" and " + things.get(things.size() - 1).toString() + "."); |
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return list.toString(); |
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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 setNewlineString(String nl)... |
131 |
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{ |
132 |
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newline = nl; |
133 |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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0 |
public String getNewlineString()... |
136 |
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{ |
137 |
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return newline; |
138 |
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} |
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@param |
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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 |
|
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186 |
public AlignmentI readFile(String file, DataSourceType sourceType,... |
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FileFormatI fileFormat) throws IOException |
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{ |
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return readFile(null, file, sourceType, fileFormat); |
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} |
156 |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
157 |
500 |
public AlignmentI readFile(File selectedFile, String file,... |
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DataSourceType sourceType, FileFormatI fileFormat) |
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throws IOException |
160 |
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{ |
161 |
500 |
return readFile(selectedFile, file, sourceType, fileFormat, null); |
162 |
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} |
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| 51.9% |
Uncovered Elements: 26 (54) |
Complexity: 15 |
Complexity Density: 0.47 |
|
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public AlignmentI readFile(File selectedFile, String file,... |
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DataSourceType sourceType, FileFormatI fileFormat, |
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StructureImportSettings.TFType tempfacType) throws IOException |
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{ |
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this.selectedFile = selectedFile; |
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this.inFile = selectedFile != null ? selectedFile.getPath() : file; |
171 |
500 |
try |
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{ |
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500 |
if (fileFormat.isStructureFile()) |
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{ |
175 |
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String structureParser = StructureImportSettings |
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.getDefaultPDBFileParser(); |
177 |
18 |
boolean isParseWithJMOL = structureParser.equalsIgnoreCase( |
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StructureImportSettings.StructureParser.JMOL_PARSER |
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.toString()); |
180 |
18 |
StructureImportSettings.addSettings(annotFromStructure, |
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localSecondaryStruct, serviceSecondaryStruct); |
182 |
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if (tempfacType != null) |
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{ |
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StructureImportSettings.setTemperatureFactorType(tempfacType); |
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} |
186 |
18 |
if (isParseWithJMOL) |
187 |
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{ |
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|
189 |
15 |
alignFile = new JmolParser( |
190 |
15 |
selectedFile == null ? inFile : selectedFile, sourceType, |
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StructureImportSettings.getTemperatureFactorType()); |
192 |
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} |
193 |
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else |
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{ |
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|
196 |
3 |
StructureImportSettings.setShowSeqFeatures(true); |
197 |
3 |
alignFile = new mc_view.PDBfile(annotFromStructure, |
198 |
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localSecondaryStruct, serviceSecondaryStruct, inFile, |
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sourceType); |
200 |
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} |
201 |
18 |
((StructureFile) alignFile).setDbRefType( |
202 |
18 |
FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF); |
203 |
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} |
204 |
482 |
else if (selectedFile != null) |
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{ |
206 |
7 |
alignFile = fileFormat |
207 |
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.getReader(new FileParse(selectedFile, sourceType)); |
208 |
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} |
209 |
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else |
210 |
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{ |
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212 |
475 |
alignFile = fileFormat.getReader(new FileParse(inFile, sourceType)); |
213 |
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} |
214 |
500 |
return buildAlignmentFromFile(); |
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} catch (Exception e) |
216 |
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{ |
217 |
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e.printStackTrace(); |
218 |
0 |
jalview.bin.Console.errPrintln("Failed to read alignment using the '" |
219 |
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+ fileFormat + "' reader.\n" + e); |
220 |
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|
221 |
0 |
if (e.getMessage() != null |
222 |
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&& e.getMessage().startsWith(INVALID_CHARACTERS)) |
223 |
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{ |
224 |
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throw new IOException(e.getMessage()); |
225 |
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} |
226 |
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227 |
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228 |
0 |
if (sourceType == DataSourceType.PASTE) |
229 |
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{ |
230 |
0 |
try |
231 |
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{ |
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233 |
0 |
alignFile = new FastaFile(">UNKNOWN\n" + inFile, |
234 |
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DataSourceType.PASTE); |
235 |
0 |
return buildAlignmentFromFile(); |
236 |
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|
237 |
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} catch (Exception ex) |
238 |
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{ |
239 |
0 |
if (ex.toString().startsWith(INVALID_CHARACTERS)) |
240 |
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{ |
241 |
0 |
throw new IOException(e.getMessage()); |
242 |
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} |
243 |
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244 |
0 |
ex.printStackTrace(); |
245 |
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} |
246 |
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} |
247 |
0 |
if (FileFormat.Html.equals(fileFormat)) |
248 |
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{ |
249 |
0 |
throw new IOException(e.getMessage()); |
250 |
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} |
251 |
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} |
252 |
0 |
throw new FileFormatException(getSupportedFormats()); |
253 |
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} |
254 |
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255 |
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256 |
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257 |
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258 |
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@param |
259 |
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260 |
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@param |
261 |
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262 |
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263 |
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@return |
264 |
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| 0% |
Uncovered Elements: 35 (35) |
Complexity: 10 |
Complexity Density: 0.4 |
|
265 |
0 |
public AlignmentI readFromFile(FileParse source, FileFormatI format)... |
266 |
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throws IOException |
267 |
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{ |
268 |
0 |
this.inFile = source.getInFile(); |
269 |
0 |
DataSourceType type = source.dataSourceType; |
270 |
0 |
try |
271 |
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{ |
272 |
0 |
if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format)) |
273 |
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{ |
274 |
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|
275 |
0 |
boolean isParseWithJMOL = false; |
276 |
0 |
if (isParseWithJMOL) |
277 |
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{ |
278 |
0 |
StructureImportSettings.addSettings(annotFromStructure, |
279 |
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localSecondaryStruct, serviceSecondaryStruct); |
280 |
0 |
alignFile = new JmolParser(source); |
281 |
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} |
282 |
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else |
283 |
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{ |
284 |
0 |
StructureImportSettings.setShowSeqFeatures(true); |
285 |
0 |
alignFile = new mc_view.PDBfile(annotFromStructure, |
286 |
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localSecondaryStruct, serviceSecondaryStruct, source); |
287 |
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} |
288 |
0 |
((StructureFile) alignFile).setDbRefType(Type.PDB); |
289 |
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} |
290 |
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else |
291 |
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{ |
292 |
0 |
alignFile = format.getReader(source); |
293 |
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} |
294 |
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|
295 |
0 |
return buildAlignmentFromFile(); |
296 |
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297 |
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} catch (Exception e) |
298 |
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{ |
299 |
0 |
e.printStackTrace(); |
300 |
0 |
jalview.bin.Console.errPrintln("Failed to read alignment using the '" |
301 |
|
+ format + "' reader.\n" + e); |
302 |
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|
303 |
0 |
if (e.getMessage() != null |
304 |
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&& e.getMessage().startsWith(INVALID_CHARACTERS)) |
305 |
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{ |
306 |
0 |
throw new FileFormatException(e.getMessage()); |
307 |
|
} |
308 |
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|
309 |
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|
310 |
0 |
if (type == DataSourceType.PASTE) |
311 |
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{ |
312 |
0 |
try |
313 |
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{ |
314 |
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|
315 |
0 |
alignFile = new FastaFile(">UNKNOWN\n" + inFile, |
316 |
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DataSourceType.PASTE); |
317 |
0 |
return buildAlignmentFromFile(); |
318 |
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|
319 |
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} catch (Exception ex) |
320 |
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{ |
321 |
0 |
if (ex.toString().startsWith(INVALID_CHARACTERS)) |
322 |
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{ |
323 |
0 |
throw new IOException(e.getMessage()); |
324 |
|
} |
325 |
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|
326 |
0 |
ex.printStackTrace(); |
327 |
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} |
328 |
|
} |
329 |
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|
330 |
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|
331 |
0 |
throw new FileFormatException(getSupportedFormats()); |
332 |
|
} |
333 |
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} |
334 |
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|
335 |
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|
336 |
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|
337 |
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|
338 |
|
|
339 |
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@return |
340 |
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|
|
|
| 100% |
Uncovered Elements: 0 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
341 |
500 |
private AlignmentI buildAlignmentFromFile()... |
342 |
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{ |
343 |
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|
344 |
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|
345 |
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|
346 |
500 |
AlignmentI al = new Alignment(alignFile.getSeqsAsArray()); |
347 |
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|
348 |
500 |
alignFile.addAnnotations(al); |
349 |
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|
350 |
500 |
alignFile.addGroups(al); |
351 |
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|
352 |
500 |
return al; |
353 |
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} |
354 |
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355 |
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356 |
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357 |
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|
358 |
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@param |
359 |
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@param |
360 |
|
@param |
361 |
|
@param |
362 |
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@return |
363 |
|
|
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|
| 90% |
Uncovered Elements: 1 (10) |
Complexity: 2 |
Complexity Density: 0.25 |
|
364 |
1 |
public String formatSequences(FileFormatI format, boolean jvsuffix,... |
365 |
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AlignmentViewPanel ap, boolean selectedOnly) |
366 |
|
{ |
367 |
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|
368 |
1 |
AlignmentView selvew = ap.getAlignViewport() |
369 |
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.getAlignmentView(selectedOnly, false); |
370 |
1 |
AlignmentI aselview = selvew |
371 |
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.getVisibleAlignment(ap.getAlignViewport().getGapCharacter()); |
372 |
1 |
List<AlignmentAnnotation> ala = (ap.getAlignViewport() |
373 |
|
.getVisibleAlignmentAnnotation(selectedOnly)); |
374 |
1 |
if (ala != null) |
375 |
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{ |
376 |
1 |
for (AlignmentAnnotation aa : ala) |
377 |
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{ |
378 |
4 |
aselview.addAnnotation(aa); |
379 |
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} |
380 |
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} |
381 |
1 |
viewpanel = ap; |
382 |
1 |
return formatSequences(format, aselview, jvsuffix); |
383 |
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} |
384 |
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|
385 |
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|
386 |
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|
387 |
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|
388 |
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|
389 |
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|
390 |
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@param |
391 |
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|
392 |
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@param |
393 |
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394 |
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@param |
395 |
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|
396 |
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|
397 |
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|
398 |
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@return |
399 |
|
|
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| 75% |
Uncovered Elements: 5 (20) |
Complexity: 6 |
Complexity Density: 0.38 |
|
400 |
177 |
public String formatSequences(FileFormatI format, AlignmentI alignment,... |
401 |
|
boolean jvsuffix) |
402 |
|
{ |
403 |
177 |
try |
404 |
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{ |
405 |
177 |
AlignmentFileWriterI afile = format.getWriter(alignment); |
406 |
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|
407 |
177 |
afile.setNewlineString(newline); |
408 |
177 |
afile.setExportSettings(exportSettings); |
409 |
177 |
afile.configureForView(viewpanel); |
410 |
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|
411 |
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|
412 |
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|
413 |
177 |
SequenceI[] seqs = null; |
414 |
177 |
if (viewpanel == null || viewpanel.getAlignment() == null |
415 |
|
|| viewpanel.getAlignment() != alignment) |
416 |
|
{ |
417 |
50 |
seqs = alignment.getSequencesArray(); |
418 |
|
} |
419 |
|
else |
420 |
|
{ |
421 |
127 |
seqs = viewpanel.getAlignment().getSequencesArray(); |
422 |
|
} |
423 |
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|
424 |
177 |
String afileresp = afile.print(seqs, jvsuffix); |
425 |
177 |
if (afile.hasWarningMessage()) |
426 |
|
{ |
427 |
0 |
jalview.bin.Console.errPrintln("Warning raised when writing as " |
428 |
|
+ format + " : " + afile.getWarningMessage()); |
429 |
|
} |
430 |
177 |
return afileresp; |
431 |
|
} catch (Exception e) |
432 |
|
{ |
433 |
0 |
jalview.bin.Console.errPrintln("Failed to write alignment as a '" |
434 |
|
+ format.getName() + "' file\n"); |
435 |
0 |
e.printStackTrace(); |
436 |
|
} |
437 |
|
|
438 |
0 |
return null; |
439 |
|
} |
440 |
|
|
441 |
|
|
442 |
|
|
443 |
|
|
444 |
|
|
445 |
|
|
446 |
|
|
447 |
|
@param |
448 |
|
|
449 |
|
@return |
450 |
|
|
|
|
| 70% |
Uncovered Elements: 6 (20) |
Complexity: 7 |
Complexity Density: 0.58 |
|
451 |
350 |
public static DataSourceType checkProtocol(Object dataObject)... |
452 |
|
{ |
453 |
350 |
if (dataObject instanceof File) |
454 |
|
{ |
455 |
0 |
return DataSourceType.FILE; |
456 |
|
} |
457 |
|
|
458 |
350 |
String data = dataObject.toString(); |
459 |
350 |
DataSourceType protocol = DataSourceType.PASTE; |
460 |
350 |
String ft = data.toLowerCase(Locale.ROOT).trim(); |
461 |
350 |
if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0 |
462 |
|
|| ft.indexOf("file:") == 0) |
463 |
|
{ |
464 |
0 |
protocol = DataSourceType.URL; |
465 |
|
} |
466 |
350 |
else if (Platform.isJS()) |
467 |
|
{ |
468 |
0 |
protocol = DataSourceType.RELATIVE_URL; |
469 |
|
} |
470 |
350 |
else if (new File(data).exists()) |
471 |
|
{ |
472 |
338 |
protocol = DataSourceType.FILE; |
473 |
|
} |
474 |
350 |
return protocol; |
475 |
|
} |
476 |
|
|
477 |
|
|
478 |
|
@param |
479 |
|
|
480 |
|
|
|
|
| 0% |
Uncovered Elements: 33 (33) |
Complexity: 6 |
Complexity Density: 0.22 |
|
481 |
0 |
public static void main(String[] args)... |
482 |
|
{ |
483 |
0 |
int i = 0; |
484 |
0 |
while (i < args.length) |
485 |
|
{ |
486 |
0 |
File f = new File(args[i]); |
487 |
0 |
if (f.exists()) |
488 |
|
{ |
489 |
0 |
try |
490 |
|
{ |
491 |
0 |
jalview.bin.Console.outPrintln("Reading file: " + f); |
492 |
0 |
AppletFormatAdapter afa = new AppletFormatAdapter(); |
493 |
0 |
Runtime r = Runtime.getRuntime(); |
494 |
0 |
System.gc(); |
495 |
0 |
long memf = -r.totalMemory() + r.freeMemory(); |
496 |
0 |
long t1 = -System.currentTimeMillis(); |
497 |
0 |
AlignmentI al = afa.readFile(args[i], DataSourceType.FILE, |
498 |
|
new IdentifyFile().identify(args[i], |
499 |
|
DataSourceType.FILE)); |
500 |
0 |
t1 += System.currentTimeMillis(); |
501 |
0 |
System.gc(); |
502 |
0 |
memf += r.totalMemory() - r.freeMemory(); |
503 |
0 |
if (al != null) |
504 |
|
{ |
505 |
0 |
jalview.bin.Console.outPrintln("Alignment contains " |
506 |
|
+ al.getHeight() + " sequences and " + al.getWidth() |
507 |
|
+ " columns."); |
508 |
0 |
try |
509 |
|
{ |
510 |
0 |
jalview.bin.Console.outPrintln(new AppletFormatAdapter() |
511 |
|
.formatSequences(FileFormat.Fasta, al, true)); |
512 |
|
} catch (Exception e) |
513 |
|
{ |
514 |
0 |
jalview.bin.Console.errPrintln( |
515 |
|
"Couln't format the alignment for output as a FASTA file."); |
516 |
0 |
e.printStackTrace(System.err); |
517 |
|
} |
518 |
|
} |
519 |
|
else |
520 |
|
{ |
521 |
0 |
jalview.bin.Console.outPrintln("Couldn't read alignment"); |
522 |
|
} |
523 |
0 |
jalview.bin.Console |
524 |
|
.outPrintln("Read took " + (t1 / 1000.0) + " seconds."); |
525 |
0 |
jalview.bin.Console.outPrintln( |
526 |
|
"Difference between free memory now and before is " |
527 |
|
+ (memf / (1024.0 * 1024.0) * 1.0) + " MB"); |
528 |
|
} catch (Exception e) |
529 |
|
{ |
530 |
0 |
jalview.bin.Console.errPrintln("Exception when dealing with " + i |
531 |
|
+ "'th argument: " + args[i] + "\n" + e); |
532 |
|
} |
533 |
|
} |
534 |
|
else |
535 |
|
{ |
536 |
0 |
jalview.bin.Console.errPrintln("Ignoring argument '" + args[i] |
537 |
|
+ "' (" + i + "'th)- not a readable file."); |
538 |
|
} |
539 |
0 |
i++; |
540 |
|
} |
541 |
|
} |
542 |
|
|
543 |
|
|
544 |
|
|
545 |
|
|
546 |
|
|
547 |
|
@param |
548 |
|
@param |
549 |
|
@return |
550 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
551 |
0 |
public static DataSourceType resolveProtocol(String file,... |
552 |
|
FileFormatI format) |
553 |
|
{ |
554 |
0 |
return resolveProtocol(file, format, false); |
555 |
|
} |
556 |
|
|
|
|
| 0% |
Uncovered Elements: 109 (109) |
Complexity: 27 |
Complexity Density: 0.42 |
|
557 |
0 |
public static DataSourceType resolveProtocol(String file,... |
558 |
|
FileFormatI format, boolean debug) |
559 |
|
{ |
560 |
|
|
561 |
0 |
DataSourceType protocol = null; |
562 |
0 |
if (debug) |
563 |
|
{ |
564 |
0 |
jalview.bin.Console |
565 |
|
.outPrintln("resolving datasource started with:\n>>file\n" |
566 |
|
+ file + ">>endfile"); |
567 |
|
} |
568 |
|
|
569 |
|
|
570 |
|
|
571 |
0 |
try |
572 |
|
{ |
573 |
0 |
boolean rtn = false; |
574 |
0 |
InputStream is = System.getSecurityManager().getClass() |
575 |
|
.getResourceAsStream("/" + file); |
576 |
0 |
if (is != null) |
577 |
|
{ |
578 |
0 |
rtn = true; |
579 |
0 |
is.close(); |
580 |
|
} |
581 |
0 |
if (debug) |
582 |
|
{ |
583 |
0 |
jalview.bin.Console.errPrintln("Resource '" + file + "' was " |
584 |
0 |
+ (rtn ? "" : "not") + " located by classloader."); |
585 |
|
} |
586 |
0 |
if (rtn) |
587 |
|
{ |
588 |
0 |
protocol = DataSourceType.CLASSLOADER; |
589 |
|
} |
590 |
|
|
591 |
|
} catch (Exception ex) |
592 |
|
{ |
593 |
0 |
System.err |
594 |
|
.println("Exception checking resources: " + file + " " + ex); |
595 |
|
} |
596 |
|
|
597 |
0 |
if (file.indexOf("://") > -1) |
598 |
|
{ |
599 |
0 |
protocol = DataSourceType.URL; |
600 |
|
} |
601 |
|
else |
602 |
|
{ |
603 |
|
|
604 |
0 |
protocol = DataSourceType.FILE; |
605 |
|
} |
606 |
0 |
FileParse fp = null; |
607 |
0 |
try |
608 |
|
{ |
609 |
0 |
if (debug) |
610 |
|
{ |
611 |
0 |
jalview.bin.Console.outPrintln( |
612 |
|
"Trying to get contents of resource as " + protocol + ":"); |
613 |
|
} |
614 |
0 |
fp = new FileParse(file, protocol); |
615 |
0 |
if (!fp.isValid()) |
616 |
|
{ |
617 |
0 |
fp = null; |
618 |
|
} |
619 |
|
else |
620 |
|
{ |
621 |
0 |
if (debug) |
622 |
|
{ |
623 |
0 |
jalview.bin.Console.outPrintln("Successful."); |
624 |
|
} |
625 |
|
} |
626 |
|
} catch (Exception e) |
627 |
|
{ |
628 |
0 |
if (debug) |
629 |
|
{ |
630 |
0 |
jalview.bin.Console |
631 |
|
.errPrintln("Exception when accessing content: " + e); |
632 |
|
} |
633 |
0 |
fp = null; |
634 |
|
} |
635 |
0 |
if (fp == null) |
636 |
|
{ |
637 |
0 |
if (debug) |
638 |
|
{ |
639 |
0 |
jalview.bin.Console.outPrintln("Accessing as paste."); |
640 |
|
} |
641 |
0 |
protocol = DataSourceType.PASTE; |
642 |
0 |
fp = null; |
643 |
0 |
try |
644 |
|
{ |
645 |
0 |
fp = new FileParse(file, protocol); |
646 |
0 |
if (!fp.isValid()) |
647 |
|
{ |
648 |
0 |
fp = null; |
649 |
|
} |
650 |
|
} catch (Exception e) |
651 |
|
{ |
652 |
0 |
jalview.bin.Console |
653 |
|
.errPrintln("Failed to access content as paste!"); |
654 |
0 |
e.printStackTrace(); |
655 |
0 |
fp = null; |
656 |
|
} |
657 |
|
} |
658 |
0 |
if (fp == null) |
659 |
|
{ |
660 |
0 |
return null; |
661 |
|
} |
662 |
0 |
if (format == null) |
663 |
|
{ |
664 |
0 |
return protocol; |
665 |
|
} |
666 |
|
else |
667 |
|
{ |
668 |
0 |
try |
669 |
|
{ |
670 |
0 |
FileFormatI idformat = new IdentifyFile().identify(file, protocol); |
671 |
0 |
if (idformat == null) |
672 |
|
{ |
673 |
0 |
if (debug) |
674 |
|
{ |
675 |
0 |
jalview.bin.Console.outPrintln( |
676 |
|
"Format not identified. Inaccessible file."); |
677 |
|
} |
678 |
0 |
return null; |
679 |
|
} |
680 |
0 |
if (debug) |
681 |
|
{ |
682 |
0 |
jalview.bin.Console.outPrintln("Format identified as " + idformat |
683 |
|
+ "and expected as " + format); |
684 |
|
} |
685 |
0 |
if (idformat.equals(format)) |
686 |
|
{ |
687 |
0 |
if (debug) |
688 |
|
{ |
689 |
0 |
jalview.bin.Console |
690 |
|
.outPrintln("Protocol identified as " + protocol); |
691 |
|
} |
692 |
0 |
return protocol; |
693 |
|
} |
694 |
|
else |
695 |
|
{ |
696 |
0 |
if (debug) |
697 |
|
{ |
698 |
0 |
System.out |
699 |
|
.println("File deemed not accessible via " + protocol); |
700 |
|
} |
701 |
0 |
fp.close(); |
702 |
0 |
return null; |
703 |
|
} |
704 |
|
} catch (Exception e) |
705 |
|
{ |
706 |
0 |
if (debug) |
707 |
|
{ |
708 |
0 |
jalview.bin.Console |
709 |
|
.errPrintln("File deemed not accessible via " + protocol); |
710 |
0 |
e.printStackTrace(); |
711 |
|
} |
712 |
|
} |
713 |
|
} |
714 |
0 |
return null; |
715 |
|
} |
716 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
717 |
323 |
public AlignmentFileReaderI getAlignFile()... |
718 |
|
{ |
719 |
323 |
return alignFile; |
720 |
|
} |
721 |
|
} |