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JAL-1479 small tidy of error message when Sifts mapping fails
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 11 Oct 2016 08:33:13 +0000
(09:33 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Tue, 11 Oct 2016 08:33:13 +0000
(09:33 +0100)
src/jalview/ws/sifts/SiftsClient.java
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diff --git
a/src/jalview/ws/sifts/SiftsClient.java
b/src/jalview/ws/sifts/SiftsClient.java
index
fb59071
..
e85edd2
100644
(file)
--- a/
src/jalview/ws/sifts/SiftsClient.java
+++ b/
src/jalview/ws/sifts/SiftsClient.java
@@
-390,8
+390,8
@@
public class SiftsClient implements SiftsClientI
String pdbFile, String chain) throws SiftsException
{
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
String pdbFile, String chain) throws SiftsException
{
structId = (chain == null) ? pdbId : pdbId + "|" + chain;
- System.out.println("Getting mapping for: " + pdbId + "|" + chain
- + " : seq- " + seq.getName());
+ System.out.println("Getting SIFTS mapping for " + structId + ": seq "
+ + seq.getName());
final StringBuilder mappingDetails = new StringBuilder(128);
PrintStream ps = new PrintStream(System.out)
final StringBuilder mappingDetails = new StringBuilder(128);
PrintStream ps = new PrintStream(System.out)
@@
-470,12
+470,14
@@
public class SiftsClient implements SiftsClientI
int pdbStart = UNASSIGNED;
int pdbEnd = UNASSIGNED;
int pdbStart = UNASSIGNED;
int pdbEnd = UNASSIGNED;
- Integer[] keys = mapping.keySet().toArray(new Integer[0]);
- Arrays.sort(keys);
- if (keys.length < 1)
+ if (mapping.isEmpty())
{
{
- throw new SiftsException(">>> Empty SIFTS mapping generated!!");
+ throw new SiftsException(
+ "SIFTS mapping failed - falling back on Needleman-Wunsch");
}
}
+
+ Integer[] keys = mapping.keySet().toArray(new Integer[0]);
+ Arrays.sort(keys);
seqStart = keys[0];
seqEnd = keys[keys.length - 1];
seqStart = keys[0];
seqEnd = keys[keys.length - 1];