+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)\r
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * \r
+ * This program 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 2\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.ws.seqfetcher;\r
\r
import jalview.datamodel.Alignment;\r
* common methods for implementations of the DbSourceProxy interface.\r
* \r
* @author JimP\r
- *\r
+ * \r
*/\r
public abstract class DbSourceProxyImpl implements DbSourceProxy\r
{\r
{\r
// default constructor - do nothing probably.\r
}\r
- private Hashtable props=null;\r
- /* (non-Javadoc)\r
+\r
+ private Hashtable props = null;\r
+\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#getDbSourceProperties()\r
*/\r
public Hashtable getDbSourceProperties()\r
{\r
return props;\r
}\r
+\r
protected void addDbSourceProperty(Object propname)\r
{\r
addDbSourceProperty(propname, propname);\r
\r
protected void addDbSourceProperty(Object propname, Object propvalue)\r
{\r
- if (props==null)\r
+ if (props == null)\r
{\r
props = new Hashtable();\r
}\r
props.put(propname, propvalue);\r
}\r
- boolean queryInProgress=false;\r
+\r
+ boolean queryInProgress = false;\r
+\r
protected StringBuffer results = null;\r
+\r
/*\r
* (non-Javadoc)\r
* \r
return results;\r
}\r
\r
- /* (non-Javadoc)\r
+ /*\r
+ * (non-Javadoc)\r
+ * \r
* @see jalview.ws.DbSourceProxy#queryInProgress()\r
*/\r
public boolean queryInProgress()\r
{\r
return queryInProgress;\r
}\r
+\r
/**\r
* call to set the queryInProgress flag\r
- *\r
+ * \r
*/\r
protected void startQuery()\r
{\r
- queryInProgress=true;\r
+ queryInProgress = true;\r
}\r
+\r
/**\r
* call to clear the queryInProgress flag\r
- *\r
+ * \r
*/\r
protected void stopQuery()\r
{\r
- queryInProgress=false;\r
+ queryInProgress = false;\r
}\r
\r
/**\r
* create an alignment from raw text file...\r
+ * \r
* @param result\r
* @return null or a valid alignment\r
* @throws Exception\r
*/\r
- protected Alignment parseResult(String result) throws Exception {\r
+ protected Alignment parseResult(String result) throws Exception\r
+ {\r
Alignment sequences = null;\r
String format = new IdentifyFile().Identify(result, "Paste");\r
if (FormatAdapter.isValidFormat(format))\r
{\r
sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
- format);\r
+ format);\r
}\r
return sequences;\r
}\r
- \r
+\r
}\r