- String structExt = format.getExtensions().split(",")[0];
- String tempStructurefile = Files.createTempFile(".jalview_",
- "." + structExt).toString();
- UrlDownloadClient.download(file, tempStructurefile);
- file = tempStructurefile;
- protocol = DataSourceType.FILE;
+ // read from the provided source
+ al = new FormatAdapter().readFromFile(source, format);
+ }
+ else
+ {
+
+ // open a new source and read from it
+ FormatAdapter fa = new FormatAdapter();
+ boolean downloadStructureFile = format.isStructureFile()
+ && protocol.equals(DataSourceType.URL);
+ if (downloadStructureFile)
+ {
+ String structExt = format.getExtensions().split(",")[0];
+ String urlLeafName = file.substring(
+ file.lastIndexOf(
+ System.getProperty("file.separator")),
+ file.lastIndexOf("."));
+ String tempStructureFileStr = createNamedJvTempFile(
+ urlLeafName, structExt);
+ UrlDownloadClient.download(file, tempStructureFileStr);
+ al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+ format);
+ source = fa.getAlignFile();
+ }
+ else
+ {
+ al = fa.readFile(file, protocol, format);
+ source = fa.getAlignFile(); // keep reference for later if
+ // necessary.
+ }