- UrlDownloadClient.download(file, tempStructureFileStr);
- file = tempStructureFileStr;
- protocol = DataSourceType.FILE;
+
+ // BH - switching to File object here so as to hold
+ // ._bytes array directly
+ File tempFile = new File(tempStructureFileStr);
+ UrlDownloadClient.download(file, tempFile);
+
+ al = fa.readFile(tempFile, DataSourceType.FILE,
+ format);
+ source = fa.getAlignFile();
+ }
+ else
+ {
+ if (selectedFile == null) {
+ al = fa.readFile(file, protocol, format);
+
+ } else {
+ al = fa.readFile(selectedFile, protocol, format);
+ }
+ source = fa.getAlignFile(); // keep reference for later if
+
+ // necessary.