git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
30df9d5
)
JAL-3881 split on any nonalphanumeric symbol (plus _) to generate putative sequence...
author
Jim Procter
<j.procter@dundee.ac.uk>
Wed, 29 Sep 2021 14:32:09 +0000
(15:32 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Wed, 29 Sep 2021 14:32:09 +0000
(15:32 +0100)
src/jalview/ws/DBRefFetcher.java
patch
|
blob
|
history
diff --git
a/src/jalview/ws/DBRefFetcher.java
b/src/jalview/ws/DBRefFetcher.java
index
9420465
..
67b44d7
100644
(file)
--- a/
src/jalview/ws/DBRefFetcher.java
+++ b/
src/jalview/ws/DBRefFetcher.java
@@
-31,6
+31,8
@@
import java.util.List;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import jalview.analysis.AlignSeq;
import jalview.api.FeatureSettingsModelI;
import jalview.analysis.AlignSeq;
import jalview.api.FeatureSettingsModelI;
@@
-404,12
+406,14
@@
public class DBRefFetcher implements Runnable
}
else
{
}
else
{
+ Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
// generate queries from sequence ID string
// generate queries from sequence ID string
- StringTokenizer st = new StringTokenizer(sequence.getName(),
- "|");
- while (st.hasMoreTokens())
+ Matcher tokens = possibleIds.matcher(sequence.getName());
+ int p=0;
+ while (tokens.find(p))
{
{
- String token = st.nextToken();
+ String token = tokens.group();
+ p = tokens.end();
UPEntry[] presp = null;
if (picrClient != null)
{
UPEntry[] presp = null;
if (picrClient != null)
{