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JAL-4083 Use jmolViewer.scriptWait instead of jmolViewer.evalStringQuiet whilst highl...
[jalview.git]
/
src
/
jalview
/
urls
/
IdentifiersUrlProvider.java
diff --git
a/src/jalview/urls/IdentifiersUrlProvider.java
b/src/jalview/urls/IdentifiersUrlProvider.java
index
0dab719
..
850a230
100644
(file)
--- a/
src/jalview/urls/IdentifiersUrlProvider.java
+++ b/
src/jalview/urls/IdentifiersUrlProvider.java
@@
-63,7
+63,7
@@
public class IdentifiersUrlProvider extends UrlProviderImpl
public IdentifiersUrlProvider(String cachedUrlList)
{
urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
public IdentifiersUrlProvider(String cachedUrlList)
{
urls = readIdentifiers(IdOrgSettings.getDownloadLocation());
- selectedUrls = new ArrayList<String>();
+ selectedUrls = new ArrayList<>();
checkSelectionMatchesUrls(cachedUrlList);
}
checkSelectionMatchesUrls(cachedUrlList);
}
@@
-75,19
+75,20
@@
public class IdentifiersUrlProvider extends UrlProviderImpl
* @return hashmap of identifiers.org data, keyed by MIRIAM id
*/
@SuppressWarnings("unchecked")
* @return hashmap of identifiers.org data, keyed by MIRIAM id
*/
@SuppressWarnings("unchecked")
-private HashMap<String, UrlLink> readIdentifiers(String idFileName)
+ private HashMap<String, UrlLink> readIdentifiers(String idFileName)
{
// identifiers.org data
{
// identifiers.org data
- HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
+ HashMap<String, UrlLink> idData = new HashMap<>();
String errorMessage = null;
try
{
String errorMessage = null;
try
{
- // NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER
-
+ // NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER
+
FileReader reader = new FileReader(idFileName);
String key = "";
FileReader reader = new FileReader(idFileName);
String key = "";
- Map<String, Object> obj = (Map<String, Object>) JSONUtils.parse(reader);
+ Map<String, Object> obj = (Map<String, Object>) JSONUtils
+ .parse(reader);
if (obj.containsKey(ID_ORG_KEY))
{
key = ID_ORG_KEY;
if (obj.containsKey(ID_ORG_KEY))
{
key = ID_ORG_KEY;
@@
-119,16
+120,21
@@
private HashMap<String, UrlLink> readIdentifiers(String idFileName)
} catch (IOException | ParseException e)
{
// unnecessary e.printStackTrace();
} catch (IOException | ParseException e)
{
// unnecessary e.printStackTrace();
- // Note how in JavaScript we can grab the first bytes from any file reader.
+ // Note how in JavaScript we can grab the first bytes from any file
+ // reader.
// Typical report here is "NetworkError" because the file does not exist.
// Typical report here is "NetworkError" because the file does not exist.
- // "https://." is coming from System.getProperty("user.home"), but this could
+ // "https://." is coming from System.getProperty("user.home"), but this
+ // could
// be set by the page developer to anything, of course.
// be set by the page developer to anything, of course.
- errorMessage = (/** @j2sNative String.fromCharCode.apply(null, reader.$in.is.buf.slice(0,12)) || */e.toString());
+ errorMessage = e.toString();
idData.clear();
}
// BH 2018 -- added more valuable report
if (errorMessage != null)
idData.clear();
}
// BH 2018 -- added more valuable report
if (errorMessage != null)
- System.err.println("IdentifiersUrlProvider: cannot read " + idFileName + ": " + errorMessage);
+ {
+ System.err.println("IdentifiersUrlProvider: cannot read " + idFileName
+ + ": " + errorMessage);
+ }
return idData;
}
return idData;
}
@@
-193,7
+199,7
@@
private HashMap<String, UrlLink> readIdentifiers(String idFileName)
@Override
public List<String> getLinksForMenu()
{
@Override
public List<String> getLinksForMenu()
{
- List<String> links = new ArrayList<String>();
+ List<String> links = new ArrayList<>();
for (String key : selectedUrls)
{
links.add(urls.get(key).toStringWithTarget());
for (String key : selectedUrls)
{
links.add(urls.get(key).toStringWithTarget());
@@
-210,7
+216,7
@@
private HashMap<String, UrlLink> readIdentifiers(String idFileName)
@Override
public void setUrlData(List<UrlLinkDisplay> links)
{
@Override
public void setUrlData(List<UrlLinkDisplay> links)
{
- selectedUrls = new ArrayList<String>();
+ selectedUrls = new ArrayList<>();
Iterator<UrlLinkDisplay> it = links.iterator();
while (it.hasNext())
Iterator<UrlLinkDisplay> it = links.iterator();
while (it.hasNext())