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;
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;
private enum ResidueDetailType
{
- NAME_SEC_STRUCTURE("nameSecondaryStructure"), CODE_SEC_STRUCTURE(
- "codeSecondaryStructure"), ANNOTATION("Annotation");
+ NAME_SEC_STRUCTURE("nameSecondaryStructure"),
+ CODE_SEC_STRUCTURE("codeSecondaryStructure"), ANNOTATION("Annotation");
private String code;
private ResidueDetailType(String code)
*/
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);
return new File(siftsFileName);
}
}
+ else
+ {
+ return siftsFile;
+ }
}
try
{
try
{
attr = Files.readAttributes(filePath, BasicFileAttributes.class);
- diffInDays = (int) ((new Date().getTime() - attr.lastModifiedTime()
- .toMillis()) / (1000 * 60 * 60 * 24));
+ diffInDays = (int) ((new Date().getTime()
+ - attr.lastModifiedTime().toMillis())
+ / (1000 * 60 * 60 * 24));
// System.out.println("Diff in days : " + diffInDays);
} catch (IOException e)
{
* @throws SiftsException
* @throws IOException
*/
- public static File downloadSiftsFile(String pdbId) throws SiftsException,
- IOException
+ public static File downloadSiftsFile(String pdbId)
+ throws SiftsException, IOException
{
if (pdbId.contains(".cif"))
{
siftsDownloadDir.mkdirs();
}
// System.out.println(">> Download ftp url : " + siftsFileFTPURL);
+ // long now = System.currentTimeMillis();
URL url = new URL(siftsFileFTPURL);
URLConnection conn = url.openConnection();
InputStream inputStream = conn.getInputStream();
}
outputStream.close();
inputStream.close();
- // System.out.println(">>> File downloaded : " + downloadedSiftsFile);
+ // System.out.println(">>> File downloaded : " + downloadedSiftsFile
+ // + " took " + (System.currentTimeMillis() - now) + "ms");
return new File(downloadedSiftsFile);
}
{
continue;
}
- String canonicalSource = DBRefUtils.getCanonicalName(dbRef
- .getSource());
+ String canonicalSource = DBRefUtils
+ .getCanonicalName(dbRef.getSource());
if (isValidDBRefEntry(dbRef)
- && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT) || canonicalSource
- .equalsIgnoreCase(DBRefSource.PDB)))
+ && (canonicalSource.equalsIgnoreCase(DBRefSource.UNIPROT)
+ || canonicalSource.equalsIgnoreCase(DBRefSource.PDB)))
{
return dbRef;
}
int orignalSeqStart = seq.getStart();
if (orignalSeqStart >= 1)
{
- int subSeqStart = (seqStart >= orignalSeqStart) ? seqStart
- - orignalSeqStart : 0;
+ int subSeqStart = (seqStart >= orignalSeqStart)
+ ? seqStart - orignalSeqStart
+ : 0;
int subSeqEnd = seqEnd - (orignalSeqStart - 1);
subSeqEnd = originalSeq.length() < subSeqEnd ? originalSeq.length()
: subSeqEnd;
{
pdbRefDb = cRefDb;
}
- if (cRefDb.getDbCoordSys()
- .equalsIgnoreCase(seqCoordSys.getName())
+ if (cRefDb.getDbCoordSys().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)
- {
- resNum = (pdbRefDb == null) ? Integer.valueOf(residue
- .getDbResNum()) : 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)
omitNonObserved.add(currSeqIndex);
++nonObservedShiftIndex;
}
- mapping.put(currSeqIndex - nonObservedShiftIndex, new int[] {
- Integer.valueOf(resNum), UNASSIGNED });
+ mapping.put(currSeqIndex - nonObservedShiftIndex,
+ new int[]
+ { Integer.valueOf(resNum), UNASSIGNED });
}
}
}
}
/**
+ * 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.
*/
public Entity getEntityByMostOptimalMatchedId(String chainId)
{
- // System.out.println("---> advanced greedy entityId matching block entered..");
+ // System.out.println("---> advanced greedy entityId matching block
+ // entered..");
List<Entity> entities = siftsEntry.getEntity();
SiftsEntitySortPojo[] sPojo = new SiftsEntitySortPojo[entities.size()];
int count = 0;
return null;
}
- private class SiftsEntitySortPojo implements
- Comparable<SiftsEntitySortPojo>
+ private class SiftsEntitySortPojo
+ implements Comparable<SiftsEntitySortPojo>
{
public String entityId;
private int nonObservedShiftIndex;
- public SegmentHelperPojo(SequenceI seq,
- HashMap<Integer, int[]> mapping,
+ public SegmentHelperPojo(SequenceI seq, HashMap<Integer, int[]> mapping,
TreeMap<Integer, String> resNumMap,
List<Integer> omitNonObserved, int nonObservedShiftIndex)
{
}
@Override
- public StringBuffer getMappingOutput(MappingOutputPojo mp)
+ public StringBuilder getMappingOutput(MappingOutputPojo mp)
throws SiftsException
{
String seqRes = mp.getSeqResidue();
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("Sequence \u27f7 Structure mapping details")
+ .append(NEWLINE);
output.append("Method: SIFTS");
output.append(NEWLINE).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++)
{
// Print the first aligned sequence
- output.append(new Format("%" + (maxid) + "s").form(seqName)).append(
- " ");
+ output.append(new Format("%" + (maxid) + "s").form(seqName))
+ .append(" ");
for (int i = 0; i < len; i++)
{
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(".");
}
{
throw new SiftsException(">>> Low PID detected for SIFTs mapping...");
}
- output.append("Length of alignment = " + seqRes.length()).append(
- NEWLINE);
+ output.append("Length of alignment = " + seqRes.length())
+ .append(NEWLINE);
output.append(new Format("Percentage ID = %2.2f").form(pid));
return output;
}
return siftsEntry.getDbVersion();
}
+ public static void setMockSiftsFile(File file)
+ {
+ mockSiftsFile = file;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff