import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
+import jalview.structures.models.MappingOutputModel;
import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import jalview.util.Format;
*/
private static File mockSiftsFile;
+ private static final int UNASSIGNED = StructureMapping.UNASSIGNED; // -1
+
+ private static final int PDB_RES_POS = StructureMapping.PDB_RES_NUM_INDEX; // 0
+
private Entry siftsEntry;
- private StructureFile pdb;
+ private StructureFile structureFile;
private String pdbId;
private static final int BUFFER_SIZE = 4096;
- public static final int UNASSIGNED = -1;
-
- private static final int PDB_RES_POS = 0;
-
private static final int PDB_ATOM_POS = 1;
private static final String NOT_OBSERVED = "Not_Observed";
* @param pdbId
* @throws SiftsException
*/
- public SiftsClient(StructureFile pdb) throws SiftsException
+ public SiftsClient(StructureFile structureFile) throws SiftsException
{
- this.pdb = pdb;
- this.pdbId = pdb.getId();
+ this.structureFile = structureFile;
+ this.pdbId = structureFile.getId();
File siftsFile = getSiftsFile(pdbId);
siftsEntry = parseSIFTs(siftsFile);
}
if (os != null)
{
- MappingOutputPojo mop = new MappingOutputPojo();
+ MappingOutputModel mop = new MappingOutputModel();
mop.setSeqStart(seqStart);
mop.setSeqEnd(seqEnd);
mop.setSeqName(seq.getName());
{
try
{
- PDBChain chain = pdb.findChain(chainId);
+ PDBChain chain = structureFile.findChain(chainId);
if (chain == null || mapping == null)
{
}
@Override
- public StringBuilder getMappingOutput(MappingOutputPojo mp)
+ public StringBuilder getMappingOutput(MappingOutputModel mp)
throws SiftsException
{
String seqRes = mp.getSeqResidue();
mockSiftsFile = file;
}
+
}