CutAndPasteTransfer output = new CutAndPasteTransfer();\r
StringBuffer sbuffer = new StringBuffer();\r
boolean uniprotFlag = false;\r
+ boolean running = false;\r
\r
public DBRefFetcher()\r
{}\r
unknownSequences = new ArrayList();\r
this.align = align;\r
this.dataset = align.getDataset();\r
+ }\r
\r
+ public boolean fetchDBRefs(boolean waitTillFinished)\r
+ {\r
Thread thread = new Thread(this);\r
thread.start();\r
+ running = true;\r
+\r
+ if(waitTillFinished)\r
+ {\r
+ while(running)\r
+ {\r
+ try{\r
+ Thread.sleep(500);\r
+ }catch(Exception ex){}\r
+ }\r
+ }\r
+\r
+ return true;\r
}\r
\r
/**\r
{\r
long startTime = System.currentTimeMillis();\r
af.setProgressBar("Fetching db refs", startTime);\r
+ running = true;\r
\r
try\r
{\r
seqIndex++, i++)\r
{\r
Sequence sequence = (Sequence) sequences.get(seqIndex);\r
- Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {\r
+ DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {\r
jalview.datamodel.DBRefSource.UNIPROT});\r
if (uprefs!=null)\r
{\r
// we know the id for this entry, so don't note its ID in the unknownSequences list\r
- for (int j=0,k=uprefs.size(); j<k; j++)\r
- ids.add(((DBRefEntry) uprefs.get(j)).getAccessionId());\r
+ for (int j=0,k=uprefs.length; j<k; j++)\r
+ ids.add(uprefs[j].getAccessionId());\r
unknownSequences.add(sequence);\r
} else {\r
if (!ids.contains(sequence.getName()))\r
af.setProgressBar("DBRef search completed", startTime);\r
// promptBeforeBlast();\r
\r
+ running = false;\r
+\r
}\r
\r
\r
if(!file.exists())\r
return;\r
\r
- SequenceI sequence = null;\r
+ SequenceI [] sequence = null;\r
\r
Vector entries = getUniprotEntries(file);\r
\r
{\r
entry = (UniprotEntry) entries.elementAt(i);\r
String idmatch = entry.getAccession().elementAt(0).toString();\r
- sequence = dataset.findName(idmatch);\r
+ sequence = dataset.findSequenceMatch(idmatch);\r
\r
- if (sequence == null)\r
+ if (sequence.length==0)\r
{\r
//Sequence maybe Name, not Accession\r
idmatch = entry.getName().elementAt(0).toString();\r
- sequence = dataset.findName(idmatch);\r
+ sequence = dataset.findSequenceMatch(idmatch);\r
}\r
\r
- if(sequence!=null)\r
- ids.remove(sequence.getName());\r
+ if(sequence.length>0)\r
+ ids.remove(sequence[0].getName());\r
\r
- else if (sequence == null && uniprotFlag)\r
+ else if (sequence.length==0 && uniprotFlag)\r
{\r
StringBuffer upid = new StringBuffer("UniProt/Swiss-Prot|");\r
for(int u=0; u<entry.getAccession().size(); u++)\r
upid.append(entry.getAccession().elementAt(u)+"|");\r
\r
- sequence = dataset.findName(upid+idmatch);\r
+ sequence = dataset.findSequenceMatch(upid+idmatch);\r
ids.remove(idmatch);\r
}\r
\r
- if(sequence ==null)\r
+ if(sequence.length==0)\r
{\r
System.out.println(idmatch+" not found");\r
continue;\r
}\r
\r
+ for(int m=0; m<sequence.length; m++)\r
+ {\r
\r
- sequence.addDBRef(new DBRefEntry(DBRefSource.UNIPROT,\r
- "1.0",\r
+ sequence[m].addDBRef(new DBRefEntry(DBRefSource.UNIPROT,\r
+ "0",\r
entry.getAccession().elementAt(0).toString()));\r
\r
- System.out.println("Adding dbref to "+sequence.getName()+" : "+\r
+ System.out.println("Adding dbref to "+sequence[m].getName()+" : "+\r
entry.getAccession().elementAt(0).toString());\r
\r
- String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());\r
+ String nonGapped = AlignSeq.extractGaps("-. ", sequence[m].getSequence());\r
\r
int absStart = entry.getUniprotSequence().getContent().indexOf(\r
nonGapped.toString());\r
absStart = nonGapped.toString().indexOf(entry.getUniprotSequence().getContent());\r
if(absStart == -1)\r
{\r
- sbuffer.append(sequence.getName() +\r
+ sbuffer.append(sequence[m].getName() +\r
" SEQUENCE NOT %100 MATCH \n");\r
\r
continue;\r
}\r
- else\r
- {\r
\r
- if(entry.getFeature()!=null)\r
+ if (entry.getFeature() != null)\r
+ {\r
+ Enumeration e = entry.getFeature().elements();\r
+ while (e.hasMoreElements())\r
{\r
- Enumeration e = entry.getFeature().elements();\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- sf.setBegin(sf.getBegin() + absStart + 1);\r
- sf.setEnd(sf.getEnd() + absStart + 1);\r
- }\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ sf.setBegin(sf.getBegin() + absStart + 1);\r
+ sf.setEnd(sf.getEnd() + absStart + 1);\r
}\r
\r
- sbuffer.append(sequence.getName() +\r
- " HAS "+absStart+" PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"\r
- +" HAVE BEEN ADJUSTED ACCORDINGLY \n");\r
+ sbuffer.append(sequence[m].getName() +\r
+ " HAS " + absStart +\r
+ " PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"\r
+ + " HAVE BEEN ADJUSTED ACCORDINGLY \n");\r
absStart = 0;\r
}\r
\r
while(e.hasMoreElements())\r
{\r
PDBEntry pdb = (PDBEntry)e.nextElement();\r
- if(!pdb.getType().equals("PDB"))\r
+ if(!pdb.getType().equals(DBRefSource.PDB))\r
continue;\r
\r
+ sequence[m].addDBRef(new DBRefEntry(DBRefSource.PDB,\r
+ "0",\r
+ pdb.getId()));\r
+\r
onlyPdbEntries.addElement(pdb);\r
}\r
\r
- sequence.setPDBId(onlyPdbEntries);\r
+ sequence[m].setPDBId(onlyPdbEntries);\r
\r
- if (entry.getFeature()!=null) {\r
- //e = entry.getFeature().elements();\r
- // while (e.hasMoreElements())\r
- {\r
- // SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- // sf.setFeatureGroup("Uniprot");\r
- // sequence.addSequenceFeature( sf );\r
- }\r
- }\r
- sequence.setStart(absStart);\r
- sequence.setEnd(absEnd);\r
+ sequence[m].setStart(absStart);\r
+ sequence[m].setEnd(absEnd);\r
\r
\r
- int n = 0;\r
- SequenceI seq2;\r
- while (n < align.getHeight())\r
- {\r
- //This loop enables multiple sequences with the same\r
- //id to have features added and seq limits updated\r
- seq2 = align.getSequenceAt(n);\r
- if (seq2.getName().equals(idmatch))\r
- {\r
- nonGapped = AlignSeq.extractGaps("-. ", seq2.getSequence());\r
-\r
- absStart = sequence.getSequence().indexOf(nonGapped);\r
- absEnd = absStart + nonGapped.toString().length() - 1;\r
-\r
- // This is the Viewd alignment sequences\r
- // No need to tell the user of the dataset updates\r
- if ( (seq2.getStart() != absStart+sequence.getStart())\r
- || (seq2.getEnd() != absEnd+sequence.getStart()))\r
- {\r
- sbuffer.append("Updated: " + seq2.getName() + " " +\r
- seq2.getStart() + "/" + seq2.getEnd() +\r
- " to " + (absStart + sequence.getStart()) + "/" +\r
- (absEnd + sequence.getStart()) + "\n");\r
-\r
- seq2.setStart(absStart + sequence.getStart());\r
- seq2.setEnd(absEnd + sequence.getStart());\r
- }\r
- }\r
-\r
- n++;\r
}\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff