git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-3247 Adjusted Uninstall Old Jalview.app to just run the old uninstaller if it...
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblSymbol.java
diff --git
a/src/jalview/ext/ensembl/EnsemblSymbol.java
b/src/jalview/ext/ensembl/EnsemblSymbol.java
index
7862fce
..
40d6cad
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblSymbol.java
+++ b/
src/jalview/ext/ensembl/EnsemblSymbol.java
@@
-44,8
+44,6
@@
public class EnsemblSymbol extends EnsemblXref
{
private static final String GENE = "gene";
private static final String TYPE = "type";
{
private static final String GENE = "gene";
private static final String TYPE = "type";
- private static final String ID = "id";
-
/**
* Constructor given the target domain to fetch data from
*
/**
* Constructor given the target domain to fetch data from
*
@@
-77,7
+75,7
@@
public class EnsemblSymbol extends EnsemblXref
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
- String id = val.get(ID).toString();
+ String id = val.get(JSON_ID).toString();
String type = val.get(TYPE).toString();
if (id != null && GENE.equals(type))
{
String type = val.get(TYPE).toString();
if (id != null && GENE.equals(type))
{
@@
-143,22
+141,18
@@
public class EnsemblSymbol extends EnsemblXref
{
for (String query : queries)
{
{
for (String query : queries)
{
- for (Species taxon : Species.values())
+ for (Species taxon : Species.getModelOrganisms())
{
{
- if (taxon.isModelOrganism())
+ URL url = getUrl(query, taxon, GENE);
+ if (url != null)
{
{
- URL url = getUrl(query, taxon, GENE);
- if (url != null)
+ br = getHttpResponse(url, ids);
+ if (br != null)
{
{
- br = getHttpResponse(url, ids);
- if (br != null)
+ String geneId = parseSymbolResponse(br);
+ if (geneId != null && !result.contains(geneId))
{
{
- String geneId = parseSymbolResponse(br);
- System.out.println(url + " returned " + geneId);
- if (geneId != null && !result.contains(geneId))
- {
- result.add(geneId);
- }
+ result.add(geneId);
}
}
}
}
}
}