package jalview.ws.sifts;
import jalview.analysis.AlignSeq;
-import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
+import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.DBRefEntryI;
import jalview.api.SiftsClientI;
public class SiftsClient implements SiftsClientI
{
+ /*
+ * for use in mocking out file fetch for tests only
+ * - reset to null after testing!
+ */
+ private static File mockSiftsFile;
+
private Entry siftsEntry;
private StructureFile pdb;
*/
public static File getSiftsFile(String pdbId) throws SiftsException
{
+ /*
+ * return mocked file if it has been set
+ */
+ if (mockSiftsFile != null)
+ {
+ return mockSiftsFile;
+ }
+
String siftsFileName = SiftsSettings.getSiftDownloadDirectory()
+ pdbId.toLowerCase() + ".xml.gz";
File siftsFile = new File(siftsFileName);
.getDbResNum());
} catch (NumberFormatException nfe)
{
- resNum = (pdbRefDb == null) ? Integer.valueOf(residue
- .getDbResNum()) : Integer.valueOf(pdbRefDb
+ if (pdbRefDb == null || pdbRefDb.getDbResNum().equals("null"))
+ {
+ resNum = UNASSIGNED;
+ continue;
+ }
+ resNum = Integer.valueOf(pdbRefDb
.getDbResNum().split("[a-zA-Z]")[0]);
continue;
}
output.append(String.valueOf(pdbEnd));
output.append(NEWLINE).append(NEWLINE);
- PairwiseSeqScoreModel pam250 = (PairwiseSeqScoreModel) ScoreModels
- .getInstance().forName(ScoreModels.PAM250);
+ ScoreMatrix pam250 = ScoreModels.getInstance().getPam250();
int matchedSeqCount = 0;
for (int j = 0; j < nochunks; j++)
{
return siftsEntry.getDbVersion();
}
+ public static void setMockSiftsFile(File file)
+ {
+ mockSiftsFile = file;
+ }
+
}