public static String INVALID_CHARACTERS = "Contains invalid characters";
- public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
- + prettyPrint(FileFormat.getReadableFormats());
-
+ /**
+ * Returns an error message with a list of supported readable file formats
+ *
+ * @return
+ */
+ public static String getSupportedFormats()
+ {
+ return "Formats currently supported are\n"
+ + prettyPrint(FileFormats.getInstance().getReadableFormats());
+ }
public AppletFormatAdapter()
{
}
}
else
{
- // todo is MCview parsing obsolete yet?
+ // todo is MCview parsing obsolete yet? JAL-2120
StructureImportSettings.setShowSeqFeatures(true);
alignFile = new MCview.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
}
else
{
- alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+ alignFile = fileFormat.getReader(new FileParse(inFile,
+ sourceType));
}
return buildAlignmentFromFile();
} catch (Exception e)
throw new IOException(e.getMessage());
}
}
- throw new FileFormatException(SUPPORTED_FORMATS);
+ throw new FileFormatException(getSupportedFormats());
}
/**
}
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(alignment);
+ AlignmentFileI 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();
}