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Merge branch 'features/JAL-2110_crossRefDuplications' into merge_JAL-2110
[jalview.git]
/
src
/
jalview
/
datamodel
/
xdb
/
embl
/
EmblEntry.java
diff --git
a/src/jalview/datamodel/xdb/embl/EmblEntry.java
b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index
43581da
..
5409d5b
100644
(file)
--- a/
src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/
src/jalview/datamodel/xdb/embl/EmblEntry.java
@@
-198,6
+198,7
@@
public class EmblEntry
retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
new int[] { 1, dna.getLength() }, 1, 1));
retrievedref.setMap(new Mapping(null, new int[] { 1, dna.getLength() },
new int[] { 1, dna.getLength() }, 1, 1));
+
/*
* transform EMBL Database refs to canonical form
*/
/*
* transform EMBL Database refs to canonical form
*/
@@
-282,13
+283,13
@@
public class EmblEntry
}
else if (qname.equals("protein_id"))
{
}
else if (qname.equals("protein_id"))
{
- prid = q.getValues()[0];
+ prid = q.getValues()[0].trim();
}
else if (qname.equals("codon_start"))
{
try
{
}
else if (qname.equals("codon_start"))
{
try
{
- codonStart = Integer.parseInt(q.getValues()[0]);
+ codonStart = Integer.parseInt(q.getValues()[0].trim());
} catch (NumberFormatException e)
{
System.err.println("Invalid codon_start in XML for "
} catch (NumberFormatException e)
{
System.err.println("Invalid codon_start in XML for "
@@
-298,7
+299,7
@@
public class EmblEntry
else if (qname.equals("product"))
{
// sometimes name is returned e.g. for V00488
else if (qname.equals("product"))
{
// sometimes name is returned e.g. for V00488
- prname = q.getValues()[0];
+ prname = q.getValues()[0].trim();
}
else
{
}
else
{