-/*\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
- * \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.seqfetcher;\r
-\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.DBRefSource;\r
-import jalview.io.FormatAdapter;\r
-import jalview.io.IdentifyFile;\r
-\r
-import java.util.Hashtable;\r
-\r
-/**\r
- * common methods for implementations of the DbSourceProxy interface.\r
- * \r
- * @author JimP\r
- * \r
- */\r
-public abstract class DbSourceProxyImpl implements DbSourceProxy\r
-{\r
- public DbSourceProxyImpl()\r
- {\r
- // default constructor - do nothing probably.\r
- }\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
- if (props == null)\r
- {\r
- props = new Hashtable();\r
- }\r
- return props;\r
- }\r
-\r
- protected void addDbSourceProperty(Object propname)\r
- {\r
- addDbSourceProperty(propname, propname);\r
- }\r
-\r
- protected void addDbSourceProperty(Object propname, Object propvalue)\r
- {\r
- if (props == null)\r
- {\r
- props = new Hashtable();\r
- }\r
- props.put(propname, propvalue);\r
- }\r
-\r
- boolean queryInProgress = false;\r
-\r
- protected StringBuffer results = null;\r
-\r
- /*\r
- * (non-Javadoc)\r
- * \r
- * @see jalview.ws.DbSourceProxy#getRawRecords()\r
- */\r
- public StringBuffer getRawRecords()\r
- {\r
- return results;\r
- }\r
-\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
- protected void startQuery()\r
- {\r
- queryInProgress = true;\r
- }\r
-\r
- /**\r
- * call to clear the queryInProgress flag\r
- * \r
- */\r
- protected void stopQuery()\r
- {\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
- {\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
- }\r
- return sequences;\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.seqfetcher;
+
+import jalview.api.FeatureSettingsModelI;
+import jalview.datamodel.AlignmentI;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+
+/**
+ * common methods for implementations of the DbSourceProxy interface.
+ *
+ * @author JimP
+ *
+ */
+public abstract class DbSourceProxyImpl implements DbSourceProxy
+{
+
+ boolean queryInProgress = false;
+
+ protected StringBuffer results = null;
+
+ public DbSourceProxyImpl()
+ {
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#getRawRecords()
+ */
+ @Override
+ public StringBuffer getRawRecords()
+ {
+ return results;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.ws.DbSourceProxy#queryInProgress()
+ */
+ @Override
+ public boolean queryInProgress()
+ {
+ return queryInProgress;
+ }
+
+ /**
+ * call to set the queryInProgress flag
+ *
+ */
+ protected void startQuery()
+ {
+ queryInProgress = true;
+ }
+
+ /**
+ * call to clear the queryInProgress flag
+ *
+ */
+ protected void stopQuery()
+ {
+ queryInProgress = false;
+ }
+
+ /**
+ * create an alignment from raw text file...
+ *
+ * @param result
+ * @return null or a valid alignment
+ * @throws Exception
+ */
+ protected AlignmentI parseResult(String result) throws Exception
+ {
+ AlignmentI sequences = null;
+ String format = new IdentifyFile().identify(result, "Paste");
+ if (FormatAdapter.isValidFormat(format))
+ {
+ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
+ format);
+ }
+ return sequences;
+ }
+
+ /**
+ * Returns the first accession id in the query (up to the first accession id
+ * separator), or the whole query if there is no separator or it is not found
+ */
+ @Override
+ public String getAccessionIdFromQuery(String query)
+ {
+ String sep = getAccessionSeparator();
+ if (sep == null)
+ {
+ return query;
+ }
+ int sepPos = query.indexOf(sep);
+ return sepPos == -1 ? query : query.substring(0, sepPos);
+ }
+
+ /**
+ * Default is only one accession id per query - override if more are allowed.
+ */
+ @Override
+ public int getMaximumQueryCount()
+ {
+ return 1;
+ }
+
+ /**
+ * Returns false - override to return true for DNA coding data sources
+ */
+ @Override
+ public boolean isDnaCoding()
+ {
+ return false;
+ }
+
+ /**
+ * Answers false - override as required in subclasses
+ */
+ @Override
+ public boolean isAlignmentSource()
+ {
+ return false;
+ }
+
+ @Override
+ public String getDescription()
+ {
+ return "";
+ }
+
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return null;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff