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JAL-4059 Tidy getting the namespace, and save the namespace in the Jalview instance...
[jalview.git]
/
src
/
jalview
/
ws
/
seqfetcher
/
DbSourceProxyImpl.java
diff --git
a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
index
1e1468f
..
ab4644e
100644
(file)
--- a/
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/
src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@
-20,12
+20,13
@@
*/
package jalview.ws.seqfetcher;
*/
package jalview.ws.seqfetcher;
+import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentI;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
-import com.stevesoft.pat.Regex;
-
/**
* common methods for implementations of the DbSourceProxy interface.
*
/**
* common methods for implementations of the DbSourceProxy interface.
*
@@
-93,32
+94,30
@@
public abstract class DbSourceProxyImpl implements DbSourceProxy
protected AlignmentI parseResult(String result) throws Exception
{
AlignmentI sequences = null;
protected AlignmentI parseResult(String result) throws Exception
{
AlignmentI sequences = null;
- String format = new IdentifyFile().identify(result, "Paste");
- if (FormatAdapter.isValidFormat(format))
+ 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;
}
}
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)
{
@Override
public String getAccessionIdFromQuery(String query)
{
- Regex vgr = getAccessionValidator();
- if (vgr == null)
+ String sep = getAccessionSeparator();
+ if (sep == null)
{
return query;
}
{
return query;
}
- vgr.search(query);
- if (vgr.numSubs() > 0)
- {
- return (vgr.stringMatched(1));
- }
- else
- {
- return (vgr.stringMatched());
- }
+ int sepPos = query.indexOf(sep);
+ return sepPos == -1 ? query : query.substring(0, sepPos);
}
/**
}
/**
@@
-147,4
+146,16
@@
public abstract class DbSourceProxyImpl implements DbSourceProxy
{
return false;
}
{
return false;
}
+
+ @Override
+ public String getDescription()
+ {
+ return "";
+ }
+
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return null;
+ }
}
}