/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
* This file is part of Jalview.\r
* \r
String[] defdb = null, otherdb = sfetcher\r
.getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);\r
Vector selsources = new Vector(), dasselsrc = (af.featureSettings != null) ? af.featureSettings\r
- .getSelectedSources()\r
- : new jalview.gui.DasSourceBrowser().getSelectedSources();\r
+ .getSelectedSources() : new jalview.gui.DasSourceBrowser()\r
+ .getSelectedSources();\r
Enumeration en = dasselsrc.elements();\r
while (en.hasMoreElements())\r
{\r
{\r
String[] newsrc = new String[dbSources.length + otherdb.length];\r
System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);\r
- System\r
- .arraycopy(otherdb, 0, newsrc, dbSources.length,\r
- otherdb.length);\r
+ System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);\r
dbSources = newsrc;\r
}\r
}\r
for (int j = 0; j < uprefs.length; j++)\r
{\r
addSeqId(sequence, uprefs[j].getAccessionId());\r
- queries\r
- .addElement(uprefs[j].getAccessionId()\r
- .toUpperCase());\r
+ queries.addElement(uprefs[j].getAccessionId().toUpperCase());\r
}\r
}\r
else\r
try\r
{\r
presp = picrClient\r
- .getUPIForAccession(token, null, picrClient\r
- .getMappedDatabaseNames(), null, true);\r
+ .getUPIForAccession(token, null,\r
+ picrClient.getMappedDatabaseNames(),\r
+ null, true);\r
} catch (Exception e)\r
{\r
System.err.println("Exception with Picr for '" + token\r
} // all databases have been queries.\r
if (sbuffer.length() > 0)\r
{\r
- output\r
- .setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"\r
- + "altered, most likely the start/end residue will have been updated.\n"\r
- + "Save your alignment to maintain the updated id.\n\n"\r
- + sbuffer.toString());\r
+ output.setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"\r
+ + "altered, most likely the start/end residue will have been updated.\n"\r
+ + "Save your alignment to maintain the updated id.\n\n"\r
+ + sbuffer.toString());\r
Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
// The above is the dataset, we must now find out the index\r
// of the viewed sequence\r
// taking into account all accessionIds and names in the file\r
Vector sequenceMatches = new Vector();\r
// look for corresponding accession ids\r
- DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry\r
- .getDBRef(), new String[]\r
- { dbSource });\r
+ DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(\r
+ entry.getDBRef(), new String[]\r
+ { dbSource });\r
if (entryRefs == null)\r
{\r
System.err\r