X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FDbSourceProxyImpl.java;h=ab4644ebff4bd86d859020784d4447e4e15017c9;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=be8424c36eae59ae2824847d59b9465b9b9ff56e;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git
diff --git a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
index be8424c..ab4644e 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -1,29 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ws.seqfetcher;
-import jalview.datamodel.Alignment;
+import jalview.api.FeatureSettingsModelI;
+import jalview.datamodel.AlignmentI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
-import java.util.Hashtable;
-
/**
* common methods for implementations of the DbSourceProxy interface.
*
@@ -32,50 +35,21 @@ import java.util.Hashtable;
*/
public abstract class DbSourceProxyImpl implements DbSourceProxy
{
- public DbSourceProxyImpl()
- {
- // default constructor - do nothing probably.
- }
- private Hashtable props = null;
-
- /*
- * (non-Javadoc)
- *
- * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
- */
- public Hashtable getDbSourceProperties()
- {
- if (props == null)
- {
- props = new Hashtable();
- }
- return props;
- }
+ boolean queryInProgress = false;
- protected void addDbSourceProperty(Object propname)
- {
- addDbSourceProperty(propname, propname);
- }
+ protected StringBuffer results = null;
- protected void addDbSourceProperty(Object propname, Object propvalue)
+ public DbSourceProxyImpl()
{
- if (props == null)
- {
- props = new Hashtable();
- }
- props.put(propname, propvalue);
}
- boolean queryInProgress = false;
-
- protected StringBuffer results = null;
-
/*
* (non-Javadoc)
*
* @see jalview.ws.DbSourceProxy#getRawRecords()
*/
+ @Override
public StringBuffer getRawRecords()
{
return results;
@@ -86,6 +60,7 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
*
* @see jalview.ws.DbSourceProxy#queryInProgress()
*/
+ @Override
public boolean queryInProgress()
{
return queryInProgress;
@@ -116,23 +91,71 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
* @return null or a valid alignment
* @throws Exception
*/
- protected Alignment parseResult(String result) throws Exception
+ protected AlignmentI parseResult(String result) throws Exception
{
- Alignment sequences = null;
- String format = new IdentifyFile().Identify(result, "Paste");
- if (FormatAdapter.isValidFormat(format))
+ AlignmentI sequences = null;
+ FileFormatI format = new IdentifyFile().identify(result,
+ DataSourceType.PASTE);
+ if (format != null)
{
- sequences = new FormatAdapter().readFile(result.toString(), "Paste",
- format);
+ sequences = new FormatAdapter().readFile(result.toString(),
+ DataSourceType.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 boolean isA(Object dbsourceproperty)
+ public String getAccessionIdFromQuery(String query)
{
- assert (dbsourceproperty != null);
- return (props == null) ? false : props.containsKey(dbsourceproperty);
+ 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;
+ }
}