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JAL-2136 merged develop into branch to fix build failure
[jalview.git]
/
src
/
jalview
/
ws
/
dbsources
/
Pfam.java
diff --git
a/src/jalview/ws/dbsources/Pfam.java
b/src/jalview/ws/dbsources/Pfam.java
index
9acaa96
..
941bf1a
100644
(file)
--- a/
src/jalview/ws/dbsources/Pfam.java
+++ b/
src/jalview/ws/dbsources/Pfam.java
@@
-23,6
+23,8
@@
package jalview.ws.dbsources;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
import com.stevesoft.pat.Regex;
import jalview.io.FormatAdapter;
import com.stevesoft.pat.Regex;
@@
-119,8
+121,8
@@
abstract public class Pfam extends Xfam
// retrieved.
startQuery();
AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
// retrieved.
startQuery();
AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
- + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
- "STH");
+ + queries.trim().toUpperCase(), DataSourceType.URL,
+ FileFormat.Stockholm);
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(DBRefSource.PFAM,
for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
{
rcds.getSequenceAt(s).addDBRef(new DBRefEntry(DBRefSource.PFAM,