*/
boolean serviceSecondaryStruct = false;
- private AlignmentFileI alignFile = null;
+ private AlignmentFileReaderI alignFile = null;
String inFile;
private AlignExportSettingI exportSettings;
- /**
- * List of valid format strings used in the isValidFormat method
- */
- public static final String[] READABLE_FORMATS = new String[] { "BLC",
- "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "STH", "PDB",
- "JnetFile", "RNAML", "PHYLIP", "JSON",
- IdentifyFile.FeaturesFile, "HTML", "mmCIF" };
-
- /**
- * List of readable format file extensions by application in order
- * corresponding to READABLE_FNAMES
- */
- public static final String[] READABLE_EXTENSIONS = new String[] {
- "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
- "sto,stk", "xml,rnaml", "phy", "json",
- ".gff2,gff3", "jar,jvp", "html", "cif" };
-
- /**
- * List of readable formats by application in order corresponding to
- * READABLE_EXTENSIONS
- */
- public static final String[] READABLE_FNAMES = new String[] { "Fasta",
- "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "Stockholm", "RNAML",
- "PHYLIP", "JSON", IdentifyFile.FeaturesFile,
- "Jalview", HtmlFile.FILE_DESC, "mmCIF" };
-
- /**
- * List of valid format strings for use by callers of the formatSequences
- * method
- */
- public static final String[] WRITEABLE_FORMATS = new String[] { "BLC",
- "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM", "AMSA", "STH",
- "PHYLIP", "JSON" };
-
- /**
- * List of extensions corresponding to file format types in WRITABLE_FNAMES
- * that are writable by the application.
- */
- public static final String[] WRITABLE_EXTENSIONS = new String[] {
- "fa, fasta, mfa, fastq", "aln", "pfam", "msf", "pir", "blc", "amsa",
- "sto,stk", "phy", "json", "jvp" };
+ public static String INVALID_CHARACTERS = "Contains invalid characters";
/**
- * List of writable formats by the application. Order must correspond with the
- * WRITABLE_EXTENSIONS list of formats.
+ * Returns an error message with a list of supported readable file formats
+ *
+ * @return
*/
- public static final String[] WRITABLE_FNAMES = new String[] { "Fasta",
- "Clustal", "PFAM", "MSF", "PIR", "BLC", "AMSA", "STH",
- "PHYLIP", "JSON", "Jalview" };
-
- public static String INVALID_CHARACTERS = "Contains invalid characters";
-
- // TODO: make these messages dynamic
- public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
- + prettyPrint(READABLE_FORMATS);
-
+ public static String getSupportedFormats()
+ {
+ return "Formats currently supported are\n"
+ + prettyPrint(FileFormats.getInstance().getReadableFormats());
+ }
public AppletFormatAdapter()
{
}
}
/**
- *
- * @param els
- * @return grammatically correct(ish) list consisting of els elements.
+ * Formats a grammatically correct(ish) list consisting of the given objects
+ *
+ * @param things
+ * @return
*/
- public static String prettyPrint(String[] els)
+ public static String prettyPrint(List<? extends Object> things)
{
StringBuffer list = new StringBuffer();
- for (int i = 0, iSize = els.length - 1; i < iSize; i++)
+ for (int i = 0, iSize = things.size() - 1; i < iSize; i++)
{
- list.append(els[i]);
+ list.append(things.get(i).toString());
list.append(", ");
}
- list.append(" and " + els[els.length - 1] + ".");
+ // could i18n 'and' here
+ list.append(" and " + things.get(things.size() - 1).toString() + ".");
return list.toString();
}
this.inFile = file;
try
{
- if (fileFormat == FileFormat.PDB || fileFormat == FileFormat.MMCif)
+ if (fileFormat.isStructureFile())
{
- // TODO obtain config value from preference settings.
- // Set value to 'true' to test PDB processing with Jmol: JAL-1213
- boolean isParseWithJMOL = StructureImportSettings
- .getDefaultPDBFileParser().equalsIgnoreCase(
+ String structureParser = StructureImportSettings
+ .getDefaultPDBFileParser();
+ boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
StructureImportSettings.StructureParser.JMOL_PARSER
.toString());
+ StructureImportSettings.addSettings(annotFromStructure,
+ localSecondaryStruct, serviceSecondaryStruct);
if (isParseWithJMOL)
{
- StructureImportSettings.addSettings(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, inFile,
- sourceType);
+ alignFile = new JmolParser(inFile, sourceType);
}
else
{
- StructureImportSettings.addSettings(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct);
+ // todo is MCview parsing obsolete yet? JAL-2120
StructureImportSettings.setShowSeqFeatures(true);
alignFile = new MCview.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
sourceType);
}
- ((StructureFile) alignFile)
- .setDbRefType(fileFormat == FileFormat.PDB ? Type.PDB
- : Type.MMCIF);
+ ((StructureFile) alignFile).setDbRefType(FileFormat.PDB
+ .equals(fileFormat) ? Type.PDB : Type.MMCIF);
}
else
{
- alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ alignFile = fileFormat.getReader(new FileParse(inFile,
+ sourceType));
}
- // new FastaFile(inFile, sourceType);
- // new MSFfile(inFile, sourceType);
- // new PileUpfile(inFile, sourceType);
- // new ClustalFile(inFile, sourceType);
- // new BLCFile(inFile, sourceType);
- // new PIRFile(inFile, sourceType);
- // new PfamFile(inFile, sourceType);
- // alignFile = new JPredFile(inFile, sourceType);
- // ((JPredFile) alignFile).removeNonSequences();
- // new StockholmFile(inFile, sourceType);
- // new SimpleBlastFile(inFile, sourceType);
- // new PhylipFile(inFile, sourceType);
- // new JSONFile(inFile, sourceType);
- // new HtmlFile(inFile, sourceType);
- // new RnamlFile(inFile, sourceType);
-// alignFile = new FeaturesFile(true, inFile, sourceType);
return buildAlignmentFromFile();
} catch (Exception e)
{
e.printStackTrace();
System.err.println("Failed to read alignment using the '"
- + fileFormat
- + "' reader.\n" + e);
+ + fileFormat + "' reader.\n" + e);
if (e.getMessage() != null
&& e.getMessage().startsWith(INVALID_CHARACTERS))
ex.printStackTrace();
}
}
- if (fileFormat == FileFormat.Html)
+ if (FileFormat.Html.equals(fileFormat))
{
throw new IOException(e.getMessage());
}
}
- throw new FileFormatException(SUPPORTED_FORMATS);
+ throw new FileFormatException(getSupportedFormats());
}
/**
DataSourceType type = source.dataSourceType;
try
{
- if (format == FileFormat.PDB || format == FileFormat.MMCif)
+ if (FileFormat.PDB.equals(format) || FileFormat.MMCif.equals(format))
{
// TODO obtain config value from preference settings
boolean isParseWithJMOL = false;
{
StructureImportSettings.addSettings(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct);
- alignFile = new JmolParser(annotFromStructure,
- localSecondaryStruct, serviceSecondaryStruct, source);
+ alignFile = new JmolParser(source);
}
else
{
}
else
{
- alignFile = format.getAlignmentFile(source);
+ alignFile = format.getReader(source);
}
return buildAlignmentFromFile();
}
// If we get to this stage, the format was not supported
- throw new FileFormatException(SUPPORTED_FORMATS);
+ throw new FileFormatException(getSupportedFormats());
}
}
{
try
{
- AlignmentFileI afile = format.getAlignmentFile();
+ AlignmentFileWriterI afile = format.getWriter(alignment);
afile.setNewlineString(newline);
afile.setExportSettings(exportSettings);
return afileresp;
} catch (Exception e)
{
- System.err.println("Failed to write alignment as a '" + format
+ System.err.println("Failed to write alignment as a '"
+ + format.getName()
+ "' file\n");
e.printStackTrace();
}
return null;
}
- public static DataSourceType checkProtocol(String file)
+ /**
+ * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
+ * data
+ *
+ * @param data
+ * @return the protocol for the input data
+ */
+ public static DataSourceType checkProtocol(String data)
{
- DataSourceType protocol = DataSourceType.FILE;
- String ft = file.toLowerCase().trim();
+ DataSourceType protocol = DataSourceType.PASTE;
+ String ft = data.toLowerCase().trim();
if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
|| ft.indexOf("file:") == 0)
{
protocol = DataSourceType.URL;
}
+ else if (new File(data).exists())
+ {
+ protocol = DataSourceType.FILE;
+ }
return protocol;
}
{
try
{
- FileFormatI idformat = new IdentifyFile().identify(file,
- protocol);
+ FileFormatI idformat = new IdentifyFile().identify(file, protocol);
if (idformat == null)
{
if (debug)
return null;
}
- public AlignmentFileI getAlignFile()
+ public AlignmentFileReaderI getAlignFile()
{
return alignFile;
}
git://source.jalview.org / jalview.git / blobdiff