private AlignExportSettingI exportSettings;
+ private File selectedFile;
+
public static String INVALID_CHARACTERS = "Contains invalid characters";
/**
public AlignmentI readFile(String file, DataSourceType sourceType,
FileFormatI fileFormat) throws IOException
{
+ return readFile(null, file, sourceType, fileFormat);
+ }
+
+ public AlignmentI readFile(File selectedFile, String file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
+
+ this.selectedFile = selectedFile;
+ if (selectedFile != null)
+ this.inFile = selectedFile.getPath();
this.inFile = file;
try
{
localSecondaryStruct, serviceSecondaryStruct);
if (isParseWithJMOL)
{
+ // needs a File option
alignFile = new JmolParser(inFile, sourceType);
}
else
((StructureFile) alignFile).setDbRefType(
FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
}
- else
+ else if (selectedFile != null) {
+ alignFile = fileFormat.getReader(new FileParse(selectedFile, sourceType));
+ } else
{
// alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));