package jalview.ws.sifts;
import jalview.analysis.AlignSeq;
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.DBRefEntryI;
import jalview.api.SiftsClientI;
import jalview.datamodel.DBRefEntry;
import jalview.io.StructureFile;
import jalview.schemes.ResidueProperties;
import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingClient;
import jalview.structures.models.MappingOutputModel;
import jalview.util.Comparison;
import jalview.util.DBRefUtils;
import java.nio.file.attribute.BasicFileAttributes;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import javax.xml.stream.XMLInputFactory;
import javax.xml.stream.XMLStreamReader;
-public class SiftsClient extends StructureMappingClient implements
- SiftsClientI
+import MCview.Atom;
+import MCview.PDBChain;
+
+public class SiftsClient implements SiftsClientI
{
/*
* for use in mocking out file fetch for tests only
*/
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 structureFile;
+
private String pdbId;
private String structId;
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";
}
@Override
- public StructureMapping getStructureMapping(SequenceI seq,
- String pdbFile, String chain) throws Exception,
- StructureMappingException
+ public StructureMapping getSiftsStructureMapping(SequenceI seq,
+ String pdbFile, String chain) throws SiftsException
{
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
System.out.println("Getting SIFTS mapping for " + structId + ": seq "
@Override
public HashMap<Integer, int[]> getGreedyMapping(String entityId,
- SequenceI seq, java.io.PrintStream os) throws SiftsException,
- StructureMappingException
+ SequenceI seq, java.io.PrintStream os) throws SiftsException
{
List<Integer> omitNonObserved = new ArrayList<Integer>();
int nonObservedShiftIndex = 0;
.equalsIgnoreCase(seqCoordSys.getName())
&& isAccessionMatched(cRefDb.getDbAccessionId()))
{
- String resNumIndexString = cRefDb.getDbResNum()
- .equalsIgnoreCase("None") ? String.valueOf(UNASSIGNED)
- : cRefDb.getDbResNum();
- try
- {
- currSeqIndex = Integer.valueOf(resNumIndexString);
- } catch (NumberFormatException nfe)
- {
- currSeqIndex = Integer.valueOf(resNumIndexString
- .split("[a-zA-Z]")[0]);
- continue;
- }
+ currSeqIndex = getLeadingIntegerValue(
+ cRefDb.getDbResNum(), UNASSIGNED);
if (pdbRefDb != null)
{
break;// exit loop if pdb and uniprot are already found
}
if (currSeqIndex >= seq.getStart() && currSeqIndex <= seq.getEnd())
{
- int resNum;
- try
- {
- resNum = (pdbRefDb == null) ? Integer.valueOf(residue
- .getDbResNum()) : Integer.valueOf(pdbRefDb
- .getDbResNum());
- } catch (NumberFormatException nfe)
- {
- if (pdbRefDb == null || pdbRefDb.getDbResNum().equals("null"))
- {
- resNum = UNASSIGNED;
- continue;
- }
- resNum = Integer.valueOf(pdbRefDb
- .getDbResNum().split("[a-zA-Z]")[0]);
- continue;
- }
+
+ int resNum = (pdbRefDb == null) ? getLeadingIntegerValue(
+ residue.getDbResNum(), UNASSIGNED)
+ : getLeadingIntegerValue(pdbRefDb.getDbResNum(),
+ UNASSIGNED);
if (isResidueObserved(residue)
|| seqCoordSys == CoordinateSys.UNIPROT)
}
}
+ /**
+ * Get the leading integer part of a string that begins with an integer.
+ *
+ * @param input
+ * - the string input to process
+ * @param failValue
+ * - value returned if unsuccessful
+ * @return
+ */
+ static int getLeadingIntegerValue(String input, int failValue)
+ {
+ if (input == null)
+ {
+ return failValue;
+ }
+ String[] parts = input.split("(?=\\D)(?<=\\d)");
+ if (parts != null && parts.length > 0 && parts[0].matches("[0-9]+"))
+ {
+ return Integer.valueOf(parts[0]);
+ }
+ return failValue;
+ }
+
+
+ /**
+ *
+ * @param chainId
+ * Target chain to populate mapping of its atom positions.
+ * @param mapping
+ * Two dimension array of residue index versus atom position
+ * @throws IllegalArgumentException
+ * Thrown if chainId or mapping is null
+ * @throws SiftsException
+ */
+ void populateAtomPositions(String chainId, Map<Integer, int[]> mapping)
+ throws IllegalArgumentException, SiftsException
+ {
+ try
+ {
+ PDBChain chain = structureFile.findChain(chainId);
+
+ if (chain == null || mapping == null)
+ {
+ throw new IllegalArgumentException(
+ "Chain id or mapping must not be null.");
+ }
+ for (int[] map : mapping.values())
+ {
+ if (map[PDB_RES_POS] != UNASSIGNED)
+ {
+ map[PDB_ATOM_POS] = getAtomIndex(map[PDB_RES_POS], chain.atoms);
+ }
+ }
+ } catch (NullPointerException e)
+ {
+ throw new SiftsException(e.getMessage());
+ } catch (Exception e)
+ {
+ throw new SiftsException(e.getMessage());
+ }
+ }
+
+ /**
+ *
+ * @param residueIndex
+ * The residue index used for the search
+ * @param atoms
+ * A collection of Atom to search
+ * @return atom position for the given residue index
+ */
+ int getAtomIndex(int residueIndex, Collection<Atom> atoms)
+ {
+ if (atoms == null)
+ {
+ throw new IllegalArgumentException(
+ "atoms collection must not be null!");
+ }
+ for (Atom atom : atoms)
+ {
+ if (atom.resNumber == residueIndex)
+ {
+ return atom.atomIndex;
+ }
+ }
+ return UNASSIGNED;
+ }
/**
* Checks if the residue instance is marked 'Not_observed' or not
}
@Override
- public StringBuffer getMappingOutput(MappingOutputModel mp)
- throws StructureMappingException
+ public StringBuilder getMappingOutput(MappingOutputModel mp)
+ throws SiftsException
{
String seqRes = mp.getSeqResidue();
String seqName = mp.getSeqName();
int nochunks = ((seqRes.length()) / len)
+ ((seqRes.length()) % len > 0 ? 1 : 0);
// output mappings
- StringBuffer output = new StringBuffer();
+ StringBuilder output = new StringBuilder(512);
output.append(NEWLINE);
output.append("Sequence \u27f7 Structure mapping details").append(
NEWLINE);
output.append(String.valueOf(pdbEnd));
output.append(NEWLINE).append(NEWLINE);
+ ScoreMatrix pam250 = ScoreModels.getInstance().getPam250();
int matchedSeqCount = 0;
for (int j = 0; j < nochunks; j++)
{
output.append(NEWLINE);
output.append(new Format("%" + (maxid) + "s").form(" ")).append(" ");
- // Print out the matching chars
+ /*
+ * Print out the match symbols:
+ * | for exact match (ignoring case)
+ * . if PAM250 score is positive
+ * else a space
+ */
for (int i = 0; i < len; i++)
{
try
{
if ((i + (j * len)) < seqRes.length())
{
- boolean sameChar = Comparison.isSameResidue(
- seqRes.charAt(i + (j * len)),
- strRes.charAt(i + (j * len)), false);
- if (sameChar
- && !jalview.util.Comparison.isGap(seqRes.charAt(i
- + (j * len))))
+ char c1 = seqRes.charAt(i + (j * len));
+ char c2 = strRes.charAt(i + (j * len));
+ boolean sameChar = Comparison.isSameResidue(c1, c2, false);
+ if (sameChar && !Comparison.isGap(c1))
{
matchedSeqCount++;
output.append("|");
}
else if (type.equals("pep"))
{
- if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)),
- strRes.charAt(i + (j * len))) > 0)
+ if (pam250.getPairwiseScore(c1, c2) > 0)
{
output.append(".");
}
float pid = (float) matchedSeqCount / seqRes.length() * 100;
if (pid < SiftsSettings.getFailSafePIDThreshold())
{
- throw new StructureMappingException(
- ">>> Low PID detected for SIFTs mapping...");
+ throw new SiftsException(">>> Low PID detected for SIFTs mapping...");
}
output.append("Length of alignment = " + seqRes.length()).append(
NEWLINE);
mockSiftsFile = file;
}
+
}
git://source.jalview.org / jalview.git / blobdiff