+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ */\r
package jalview.ws.dbsources.das;\r
\r
import jalview.datamodel.AlignmentI;\r
import org.biojava.dasobert.eventmodel.SequenceListener;\r
\r
/**\r
- * Listen for sequence fetch events from a dasobert SequenceThread started with a \r
- * query string and collect sequences returned from the DAS sequence source. \r
+ * Listen for sequence fetch events from a dasobert SequenceThread started with\r
+ * a query string and collect sequences returned from the DAS sequence source.\r
+ * \r
* @author JimP\r
- *\r
+ * \r
*/\r
public class DasSequenceSourceListener implements SequenceListener\r
{\r
- \r
+\r
String ourAccession = null;\r
- DasSequenceSource oursource=null;\r
+\r
+ DasSequenceSource oursource = null;\r
+\r
/**\r
* \r
- * @param source the DAS Sequence DbProxy object containing database details for this source\r
- * @param query the query string sent to the das source that we should be listening for.\r
+ * @param source\r
+ * the DAS Sequence DbProxy object containing database details for\r
+ * this source\r
+ * @param query\r
+ * the query string sent to the das source that we should be\r
+ * listening for.\r
*/\r
public DasSequenceSourceListener(DasSequenceSource source, String query)\r
{\r
- oursource=source;\r
- ourAccession=query;\r
+ oursource = source;\r
+ ourAccession = query;\r
}\r
\r
public void clearSelection()\r
// TODO Auto-generated method stub\r
\r
}\r
+\r
java.util.Vector seqs = null;\r
+\r
public void newSequence(SequenceEvent e)\r
{\r
if (!e.getAccessionCode().equals(ourAccession))\r
{\r
- System.err.println("Warning - received sequence event for strange accession code ("\r
- +e.getAccessionCode()+") - we expected "+ourAccession);\r
- \r
+ System.err\r
+ .println("Warning - received sequence event for strange accession code ("\r
+ + e.getAccessionCode()\r
+ + ") - we expected "\r
+ + ourAccession);\r
+\r
return;\r
}\r
- if (seqs==null)\r
+ if (seqs == null)\r
{\r
- if (e.getSequence().length()==0)\r
+ if (e.getSequence().length() == 0)\r
{\r
System.err.println("Empty sequence returned for accession code ("\r
- +e.getAccessionCode()+") from "+oursource.getDbName());\r
- called=true;\r
- noSequences=true;\r
+ + e.getAccessionCode() + ") from " + oursource.getDbName());\r
+ called = true;\r
+ noSequences = true;\r
return;\r
}\r
seqs = new java.util.Vector();\r
}\r
Sequence sq = new Sequence(e.getAccessionCode(), e.getSequence());\r
- sq.addDBRef(new DBRefEntry(oursource.getDbSource(), oursource.getDbVersion()+":"+e.getVersion(), e.getAccessionCode()));\r
+ sq.addDBRef(new DBRefEntry(oursource.getDbSource(), oursource\r
+ .getDbVersion() + ":" + e.getVersion(), e.getAccessionCode()));\r
seqs.addElement(sq);\r
- called=true;\r
+ called = true;\r
}\r
\r
public void selectedSeqPosition(int position)\r
// TODO Auto-generated method stub\r
\r
}\r
- boolean noSequences=false;\r
+\r
+ boolean noSequences = false;\r
+\r
public void noObjectFound(String accessionCode)\r
{\r
if (accessionCode.equals(ourAccession))\r
{\r
- noSequences=true;\r
+ noSequences = true;\r
called = true;\r
}\r
}\r
- public boolean hasNoSequences() {\r
+\r
+ public boolean hasNoSequences()\r
+ {\r
return noSequences;\r
}\r
- boolean called=false;\r
+\r
+ boolean called = false;\r
+\r
public boolean isNotCalled()\r
{\r
return !called;\r
\r
public AlignmentI getSequences()\r
{\r
- if (noSequences || seqs!=null && seqs.size()==0)\r
+ if (noSequences || seqs != null && seqs.size() == 0)\r
return null;\r
SequenceI[] sqs = new SequenceI[seqs.size()];\r
- for (int i=0,iSize=seqs.size(); i<iSize;i++)\r
+ for (int i = 0, iSize = seqs.size(); i < iSize; i++)\r
{\r
sqs[i] = (SequenceI) seqs.elementAt(i);\r
}\r
{\r
java.util.Vector src = new java.util.Vector();\r
src.addElement(oursource.getSource());\r
- new jalview.ws.DasSequenceFeatureFetcher(sqs, \r
- null,\r
- src, false, false);\r
+ new jalview.ws.DasSequenceFeatureFetcher(sqs, null, src, false, false);\r
}\r
- \r
+\r
return al;\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff