* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-package jalview.io;
+package jalview.ws.sifts;
import jalview.analysis.AlignSeq;
import jalview.api.DBRefEntryI;
import jalview.xml.binding.sifts.Entry.Entity.Segment.ListMapRegion.MapRegion;
import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue;
import jalview.xml.binding.sifts.Entry.Entity.Segment.ListResidue.Residue.CrossRefDb;
-import jalview.xml.binding.sifts.Entry.EntryDetail;
import jalview.xml.binding.sifts.Entry.ListDB.Db;
import java.io.File;
import java.io.PrintStream;
import java.net.URL;
import java.net.URLConnection;
-import java.util.HashMap;
+import java.util.ArrayList;
import java.util.HashSet;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.zip.GZIPInputStream;
private String pdbId;
+ private String structId;
+
+ private String segStartEnd;
+
private static final int BUFFER_SIZE = 4096;
private static final String SIFTS_FTP_BASE_URL = "ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/xml/";
* @throws Exception
* if no valid source DBRefEntry was found for the given sequences
*/
- public DBRefEntryI getValidSourceDBRef(SequenceI seq) throws Exception
+ public DBRefEntryI getValidSourceDBRef(SequenceI seq)
+ throws SiftsException
{
DBRefEntryI sourceDBRef = null;
sourceDBRef = seq.getSourceDBRef();
if (dbRefs == null || dbRefs.length < 1)
{
- throw new Exception("Could not get source DB Ref");
+ throw new SiftsException("Could not get source DB Ref");
}
for (DBRefEntryI dbRef : dbRefs)
{
return sourceDBRef;
}
- throw new Exception("Could not get source DB Ref");
+ throw new SiftsException("Could not get source DB Ref");
}
return accessions;
}
+ @Override
+ public StructureMapping getSiftsStructureMapping(SequenceI seq,
+ String pdbFile, String chain) throws SiftsException
+ {
+ structId = (chain == null) ? pdbId : pdbId + "|" + chain;
+ System.out.println("Getting mapping for: " + pdbId + "|" + chain
+ + " : seq- " + seq.getName());
+
+ final StringBuilder mappingDetails = new StringBuilder(128);
+ PrintStream ps = new PrintStream(System.out)
+ {
+ @Override
+ public void print(String x)
+ {
+ mappingDetails.append(x);
+ }
+
+ @Override
+ public void println()
+ {
+ mappingDetails.append(NEWLINE);
+ }
+ };
+ int[][] mapping = getGreedyMapping(chain, seq, ps);
+
+ String mappingOutput = mappingDetails.toString();
+ return new StructureMapping(seq, pdbFile, pdbId, chain, mapping,
+ mappingOutput);
+ }
@Override
public int[][] getGreedyMapping(String entityId, SequenceI seq,
java.io.PrintStream os)
- throws Exception
+ throws SiftsException
{
+ int matchedResStart = -1;
+ int matchedResEnd = -1;
+ int counter = 0;
+ int pdbStart = -1;
+ int pdbEnd = -1;
+ int sStart = -1;
+ int sEnd = -1;
+ boolean startDetected = false;
+
System.out.println("Generating mappings for : " + entityId);
Entity entity = null;
entity = getEntityById(entityId);
String seqStr = AlignSeq.extractGaps(jalview.util.Comparison.GapChars,
seq.getSequenceAsString());
- // StringBuilder mappedStrucSeq = new StringBuilder(seqStr.length());
- String[] mappedStrucSeq = new String[seqStr.length()];
- int mapping[][] = new int[seqStr.length()][2];
+ int mapping[][] = new int[seqStr.length() + seq.getStart()][2];
DBRefEntryI sourceDBRef = seq.getSourceDBRef();
if (sourceDBRef == null)
{
sourceDBRef = getValidSourceDBRef(seq);
- // TODO if sourceDBRef is null at this point then throw an Exception
-
// TODO update sequence start/end with sourceDBRef start/end
// seq.setStart(sourceDBRef.getStartRes());
// seq.setEnd(sourceDBRef.getEndRes());
}
String crossRefAccessionId = sourceDBRef.getAccessionId();
- int start = seq.getStart() - 1;
+ int count = 0;
for (int residue[] : mapping)
{
- residue[1] = start++;
+ residue[1] = count++;
+ residue[0] = -1;
}
- HashMap<Integer, String> resNumMap = new HashMap<Integer, String>();
+ LinkedHashMap<Integer, String> resNumMap = new LinkedHashMap<Integer, String>();
List<Segment> segments = entity.getSegment();
for (Segment segment : segments)
{
+ segStartEnd = segment.getStart() + " - " + segment.getEnd();
System.out.println("Mappging segments : " + segment.getSegId() + "\\"
- + segment.getStart() + "-" + segment.getEnd());
+ + segStartEnd);
List<Residue> residues = segment.getListResidue().getResidue();
for (Residue residue : residues)
{
{
continue;
}
+ int loopCount = 0;
for (int[] x : mapping)
{
- if (x[1] == refDbResNum)
+ if (loopCount > seq.getStart() && x[1] == refDbResNum)
{
int resNum = Integer.valueOf(residue.getDbResNum());
x[0] = resNum;
- String value = "x";
- resNumMap.put(resNum, value);
+ char resCharCode = ResidueProperties
+ .getSingleCharacterCode(residue.getDbResName());
+ resNumMap.put(resNum, String.valueOf(resCharCode));
}
+ ++loopCount;
}
}
}
-
- //Generate visual mapping output
- // StringBuilder strucSeq = new StringBuilder();
- // for(int[] x : mapping){
- // if(mapping[0] == 0){
- // strucSeq.append(b)
- // }
- // }
- mappedStrucSeq[1] = "x";
+
+ for (int[] x : mapping)
+ {
+ if (!startDetected && x[0] > -1)
+ {
+ matchedResStart = counter;
+ // System.out.println(matchedResStart);
+ startDetected = true;
+ }
+
+ if (startDetected && x[0] == -1)
+ {
+ matchedResEnd = counter;
+ }
+ ++counter;
+ }
+
+ String matchedSeqStr = seqStr;
+ if (matchedResStart != -1)
+ {
+ matchedResEnd = (matchedResEnd == -1) ? counter : matchedResEnd;
+ pdbStart = mapping[matchedResStart][0];
+ pdbEnd = mapping[matchedResEnd - 1][0];
+ sStart = mapping[matchedResStart][1];
+ sEnd = mapping[matchedResEnd - 1][1];
+ int seqStart = seq.getStart();
+ if (seqStart > 1)
+ {
+ matchedResStart = matchedResStart - seqStart;
+ matchedResEnd = matchedResEnd - seqStart;
+ }
+ else
+ {
+ --matchedResStart;
+ --matchedResEnd;
+ }
+ matchedSeqStr = seqStr.substring(matchedResStart, matchedResEnd);
+ }
+
+ StringBuilder targetStrucSeqs = new StringBuilder();
+ for (String res : resNumMap.values())
+ {
+ targetStrucSeqs.append(res);
+ }
+
try
{
- System.out.println(">>>> seq: " + seqStr + "\nlength "
- + seqStr.length());
- System.out.println(">>>> pdb: " + mappedStrucSeq.toString()
- + "\nlength " + mappedStrucSeq.toString().length());
-
- String printedMapping = getMappingOutput(mappedStrucSeq.toString(),
- seqStr, "seqAccession", "strucAccession", "pep", 3)
- .toString();
if (os != null)
{
- os.print(printedMapping);
+ MappingOutputPojo mop = new MappingOutputPojo();
+ mop.setSeqStart(sStart);
+ mop.setSeqEnd(sEnd);
+ mop.setSeqName(seq.getName());
+ mop.setSeqResidue(matchedSeqStr);
+
+ mop.setStrStart(pdbStart);
+ mop.setStrEnd(pdbEnd);
+ mop.setStrName(structId);
+ mop.setStrResidue(targetStrucSeqs.toString());
+
+ mop.setType("pep");
+ os.print(getMappingOutput(mop).toString());
}
- System.out.println();
} catch (Exception ex)
{
ex.printStackTrace();
&& getAllMappingAccession().contains(accessionId);
}
- @Override
- public StructureMapping getSiftsStructureMapping(SequenceI seq,
- String pdbFile, String chain)
- {
- System.out.println("Getting mapping for: " + pdbId + "|" + chain
- + " : seq- " + seq.getName());
-
- final StringBuilder mappingDetails = new StringBuilder(128);
- PrintStream ps = new PrintStream(System.out)
- {
- @Override
- public void print(String x)
- {
- mappingDetails.append(x);
- }
-
- @Override
- public void println()
- {
- mappingDetails.append(NEWLINE);
- }
- };
- int[][] mapping = null;
- try
- {
- mapping = getGreedyMapping(chain, seq, ps);
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- // String mappingOutput = mappingDetails.toString();
- String mappingOutput = null;
- return new StructureMapping(seq, pdbFile, pdbId, chain, mapping,
- mappingOutput);
- }
@Override
- public Entity getEntityById(String id) throws Exception
+ public Entity getEntityById(String id) throws SiftsException
{
List<Entity> entities = siftsEntry.getEntity();
for (Entity entity : entities)
}
return entity;
}
- throw new Exception("Entity " + id + " not found");
+ throw new SiftsException("Entity " + id + " not found");
}
@Override
public String[] getEntryDBs()
{
System.out.println("\nListing DB entries...");
+ List<String> availDbs = new ArrayList<String>();
List<Db> dbs = siftsEntry.getListDB().getDb();
for (Db db : dbs)
{
+ availDbs.add(db.getDbSource());
System.out.println(db.getDbSource() + " | " + db.getDbCoordSys());
}
- return null;
- }
-
- @Override
- public void getEntryDetails()
- {
- List<EntryDetail> eds = siftsEntry.getEntryDetail();
- for (EntryDetail ed : eds)
- {
- System.out.println("Entry Details: " + ed.getContent() + " "
- + ed.getDbSource() + " " + ed.getProperty() + " "
- + ed.toString());
- }
+ return availDbs.toArray(new String[0]);
}
@Override
- public StringBuffer getMappingOutput(String astr1, String astr2, String s1id,
- String s2id, String type, int nochunks)
+ public StringBuffer getMappingOutput(MappingOutputPojo mp)
{
- int maxid = s1id.length();
+ String seqRes = mp.getSeqResidue();
+ String seqName = mp.getSeqName();
+ int sStart = mp.getSeqStart();
+ int sEnd = mp.getSeqEnd();
+
+ String strRes = mp.getStrResidue();
+ String strName = mp.getStrName();
+ int pdbStart = mp.getStrStart();
+ int pdbEnd = mp.getStrEnd();
+
+ String type = mp.getType();
+
+ int maxid = (seqName.length() >= strName.length()) ? seqName.length()
+ : strName.length();
int len = 72 - maxid - 1;
- StringBuffer output = new StringBuffer();
+
+ // int nochunks = 2;// mp.getWrapHeight();
+ int nochunks = ((seqRes.length()) / len)
+ + ((seqRes.length()) % len > 0 ? 1 : 0);
// output mappings
+ StringBuffer output = new StringBuffer();
+ output.append(NEWLINE);
+ output.append("Sequence ⟷ Structure mapping details:");
+ output.append(NEWLINE).append(NEWLINE);
+
+ output.append(new Format("%" + maxid + "s").form(seqName));
+ output.append(" : ");
+ output.append(String.valueOf(sStart));
+ output.append(" - ");
+ output.append(String.valueOf(sEnd));
+ output.append(" Maps to ");
+ output.append(NEWLINE);
+ output.append(new Format("%" + maxid + "s").form(structId));
+ output.append(" : ");
+ output.append(String.valueOf(pdbStart));
+ output.append(" - ");
+ output.append(String.valueOf(pdbEnd));
+ output.append(NEWLINE).append(NEWLINE);
+
float pid = 0;
for (int j = 0; j < nochunks; j++)
{
// Print the first aligned sequence
- output.append(new Format("%" + (maxid) + "s").form(s1id)).append(" ");
+ output.append(new Format("%" + (maxid) + "s").form(seqName)).append(
+ " ");
for (int i = 0; i < len; i++)
{
- if ((i + (j * len)) < astr1.length())
+ if ((i + (j * len)) < seqRes.length())
{
- output.append(astr1.charAt(i + (j * len)));
+ output.append(seqRes.charAt(i + (j * len)));
}
}
// Print out the matching chars
for (int i = 0; i < len; i++)
{
- if ((i + (j * len)) < astr1.length())
+ if ((i + (j * len)) < seqRes.length())
{
- if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len))
- && !jalview.util.Comparison.isGap(astr1.charAt(i
+ if (seqRes.charAt(i + (j * len)) == strRes.charAt(i + (j * len))
+ && !jalview.util.Comparison.isGap(seqRes.charAt(i
+ (j * len))))
{
pid++;
}
else if (type.equals("pep"))
{
- if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)),
- astr2.charAt(i + (j * len))) > 0)
+ if (ResidueProperties.getPAM250(seqRes.charAt(i + (j * len)),
+ strRes.charAt(i + (j * len))) > 0)
{
output.append(".");
}
}
// Now print the second aligned sequence
output = output.append(NEWLINE);
- output = output.append(new Format("%" + (maxid) + "s").form(s2id))
+ output = output.append(new Format("%" + (maxid) + "s").form(strName))
.append(" ");
for (int i = 0; i < len; i++)
{
- if ((i + (j * len)) < astr2.length())
+ if ((i + (j * len)) < strRes.length())
{
- output.append(astr2.charAt(i + (j * len)));
+ output.append(strRes.charAt(i + (j * len)));
}
}
output.append(NEWLINE).append(NEWLINE);
}
- pid = pid / (astr1.length()) * 100;
- System.out.println(output);
- System.out.println(pid);
- // TODO return output & pid
+ pid = pid / (seqRes.length()) * 100;
+ output.append("Length of alignment = " + seqRes.length())
+ .append(NEWLINE);
+ output.append(new Format("Percentage ID = %2.2f").form(pid));
+ output.append(NEWLINE);
+ output.append("Mapping method: SIFTS").append(NEWLINE);
return output;
}
git://source.jalview.org / jalview.git / blobdiff