\r
\r
import jalview.bin.Cache;\r
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;\r
\r
+import javax.swing.*;\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public class DasSequenceFeatureFetcher implements Runnable\r
{\r
- final AlignmentI dataset;\r
- final AlignFrame af;\r
+ SequenceI [] sequences;\r
+ AlignFrame af;\r
StringBuffer sbuffer = new StringBuffer();\r
Vector selectedSources;\r
\r
* @param align DOCUMENT ME!\r
* @param ap DOCUMENT ME!\r
*/\r
- public DasSequenceFeatureFetcher(AlignmentI align,\r
- AlignFrame af,\r
+ public DasSequenceFeatureFetcher(SequenceI [] sequences,\r
+ final AlignFrame af,\r
Vector selectedSources)\r
{\r
this.selectedSources = selectedSources;\r
- this.dataset = align.getDataset();\r
+ this.sequences = sequences;\r
this.af = af;\r
\r
+ int uniprotCount = 0;\r
+ for (int i = 0; i < selectedSources.size(); i++)\r
+ {\r
+ DasSource source = (DasSource) selectedSources.elementAt(i);\r
+ DasCoordinateSystem[] coords = source.getCoordinateSystem();\r
+ for (int c = 0; c < coords.length; c++)\r
+ {\r
+ System.out.println(coords[c].getName());\r
+ if (coords[c].getName().indexOf("UniProt")>-1)\r
+ {\r
+ uniprotCount++;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+\r
+ int refCount = 0;\r
+ for(int i=0; i<sequences.length; i++)\r
+ {\r
+ Vector dbref = sequences[i].getDBRef();\r
+ if(dbref!=null)\r
+ {\r
+ for(int j=0; j<dbref.size(); j++)\r
+ {\r
+ DBRefEntry entry = (DBRefEntry)dbref.elementAt(j);\r
+ System.out.println(entry.getSource()\r
+ +" "+jalview.datamodel.DBRefSource.UNIPROT);\r
+ if(entry.getSource()\r
+ .equals(jalview.datamodel.DBRefSource.UNIPROT))\r
+ {\r
+ System.out.println("got a match");\r
+ refCount++;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ System.out.println(refCount+" "+uniprotCount+" "+sequences.length);\r
+ if(refCount<sequences.length && uniprotCount>0)\r
+ {\r
+\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ "Do you want Jalview to find\n"\r
+ +"Uniprot Accession ids for given sequence names?",\r
+ "Find Uniprot Accession Ids",\r
+ JOptionPane.YES_NO_OPTION,\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if(reply == JOptionPane.YES_OPTION)\r
+ {\r
+ new DBRefFetcher(\r
+ af.getViewport().getAlignment(), af).fetchDBRefs(true);\r
+\r
+ }\r
+ }\r
+\r
+ System.out.println("User selection is "\r
+ +\r
+ ( ( (float) uniprotCount / (float) selectedSources.size()) * 100)\r
+ + " % Uniprot, and "+refCount+" / " +sequences.length+" have uniprot accession");\r
+\r
+\r
Thread thread = new Thread(this);\r
thread.start();\r
}\r
* @param SourceUrl\r
* @param id\r
*/\r
- protected void createFeatureFetcher(final Sequence seq,\r
+ protected void createFeatureFetcher(final SequenceI seq,\r
final String sourceUrl,\r
String id,\r
- String nickname) {\r
+ String nickname)\r
+ {\r
//////////////\r
/// fetch DAS features\r
final Das1Source source = new Das1Source();\r
\r
Cache.log.debug("new Das Feature Fetcher for " + id + " querying " +\r
sourceUrl);\r
+\r
if (id != null && id.length() > 0)\r
{\r
setThreadsRunning(+1);\r
\r
+ int start=seq.getStart(), end = seq.getEnd();\r
+\r
+ if(af.getViewport().getSelectionGroup()!=null)\r
+ {\r
+ SequenceI tmp = af.getViewport().getAlignment().findName(seq.getName());\r
+ start = tmp.findPosition(\r
+ af.getViewport().getSelectionGroup().getStartRes()\r
+ );\r
+\r
+ end = tmp.findPosition(\r
+ af.getViewport().getSelectionGroup().getEndRes()\r
+ );\r
+ }\r
+\r
FeatureThread fetcher = new FeatureThread(id\r
- + ":" + seq.getStart() + "," +seq.getEnd()\r
- , source);\r
+ + ":" + start + "," + end, source);\r
\r
fetcher.addFeatureListener(new FeatureListener()\r
{\r
try\r
{\r
int seqIndex = 0;\r
- Vector sequences = dataset.getSequences();\r
- while (seqIndex < sequences.size())\r
+ while (seqIndex < sequences.length)\r
{\r
- Sequence sequence = (Sequence) sequences.get(seqIndex);\r
- Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(),\r
+ Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequences[seqIndex].getDBRef(),\r
new String[] {\r
jalview.datamodel.DBRefSource.PDB,\r
jalview.datamodel.DBRefSource.UNIPROT});\r
cs[l].getName());\r
\r
\r
- createFeatureFetcher(sequence,\r
+ createFeatureFetcher(sequences[seqIndex],\r
dasSource.getUrl(),\r
( (DBRefEntry) uprefs.get(j)).\r
getAccessionId(),\r
{\r
String id = null;\r
// try and use the name as the sequence id\r
- if (sequence.getName().indexOf("|") > -1)\r
+ if (sequences[seqIndex].getName().indexOf("|") > -1)\r
{\r
- id = sequence.getName().substring(\r
- sequence.getName().lastIndexOf("|") + 1);\r
+ id = sequences[seqIndex].getName().substring(\r
+ sequences[seqIndex].getName().lastIndexOf("|") + 1);\r
}\r
else\r
{\r
- id = sequence.getName();\r
+ id = sequences[seqIndex].getName();\r
}\r
if (id != null)\r
{\r
// Should try to call a general feature fetcher that queries many sources with name to discover applicable ID references\r
- createFeatureFetcher(sequence,\r
+ createFeatureFetcher(sequences[seqIndex],\r
dasSource.getUrl(),\r
id,\r
dasSource.getNickname());\r
DasSourceReaderImpl reader = new DasSourceReaderImpl();\r
\r
String registryURL =jalview.bin.Cache.getDefault("DAS_REGISTRY_URL",\r
- "http://www.spice-3d.org/dasregistry/das1/sources"\r
+ "http://das.sanger.ac.uk/registry/das1/sources/"\r
);\r
\r
try\r
git://source.jalview.org / jalview.git / blobdiff