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JAL-3438 spotless for 2.11.2.0
[jalview.git]
/
src
/
jalview
/
ws
/
DBRefFetcher.java
diff --git
a/src/jalview/ws/DBRefFetcher.java
b/src/jalview/ws/DBRefFetcher.java
index
4705fe5
..
d8858a9
100644
(file)
--- a/
src/jalview/ws/DBRefFetcher.java
+++ b/
src/jalview/ws/DBRefFetcher.java
@@
-306,8
+306,7
@@
public class DBRefFetcher implements Runnable
e.printStackTrace();
}
e.printStackTrace();
}
- Vector<SequenceI> sdataset = new Vector<>(
- Arrays.asList(dataset));
+ Vector<SequenceI> sdataset = new Vector<>(Arrays.asList(dataset));
List<String> warningMessages = new ArrayList<>();
// clear any old feature display settings recorded from past sessions
List<String> warningMessages = new ArrayList<>();
// clear any old feature display settings recorded from past sessions
@@
-365,8
+364,8
@@
public class DBRefFetcher implements Runnable
{
if (Console.isDebugEnabled())
{
{
if (Console.isDebugEnabled())
{
- Console.debug("Querying " + dbsource.getDbName()
- + " with : '" + queryString.toString() + "'");
+ Console.debug("Querying " + dbsource.getDbName() + " with : '"
+ + queryString.toString() + "'");
}
retrieved = dbsource.getSequenceRecords(queryString.toString());
} catch (Exception ex)
}
retrieved = dbsource.getSequenceRecords(queryString.toString());
} catch (Exception ex)
@@
-379,8
+378,8
@@
public class DBRefFetcher implements Runnable
}
if (retrieved != null)
{
}
if (retrieved != null)
{
- transferReferences(sdataset, dbsource, retrieved,
- trimDsSeqs, warningMessages);
+ transferReferences(sdataset, dbsource, retrieved, trimDsSeqs,
+ warningMessages);
}
}
else
}
}
else
@@
-399,7
+398,7
@@
public class DBRefFetcher implements Runnable
{
for (int j = 0, n = uprefs.size(); j < n; j++)
{
{
for (int j = 0, n = uprefs.size(); j < n; j++)
{
- DBRefEntry upref = uprefs.get(j);
+ DBRefEntry upref = uprefs.get(j);
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
upref.getAccessionId().toUpperCase(Locale.ROOT));
addSeqId(sequence, upref.getAccessionId());
queries.addElement(
upref.getAccessionId().toUpperCase(Locale.ROOT));
@@
-407,10
+406,10
@@
public class DBRefFetcher implements Runnable
}
else
{
}
else
{
- Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
+ Pattern possibleIds = Pattern.compile("[A-Za-z0-9_]+");
// generate queries from sequence ID string
Matcher tokens = possibleIds.matcher(sequence.getName());
// generate queries from sequence ID string
Matcher tokens = possibleIds.matcher(sequence.getName());
- int p=0;
+ int p = 0;
while (tokens.find(p))
{
String token = tokens.group();
while (tokens.find(p))
{
String token = tokens.group();
@@
-510,9
+509,8
@@
public class DBRefFetcher implements Runnable
* a list of messages to add to
*/
boolean transferReferences(Vector<SequenceI> sdataset,
* a list of messages to add to
*/
boolean transferReferences(Vector<SequenceI> sdataset,
- DbSourceProxy dbSourceProxy,
- AlignmentI retrievedAl, boolean trimDatasetSeqs,
- List<String> warningMessages)
+ DbSourceProxy dbSourceProxy, AlignmentI retrievedAl,
+ boolean trimDatasetSeqs, List<String> warningMessages)
{
// System.out.println("trimming ? " + trimDatasetSeqs);
if (retrievedAl == null || retrievedAl.getHeight() == 0)
{
// System.out.println("trimming ? " + trimDatasetSeqs);
if (retrievedAl == null || retrievedAl.getHeight() == 0)
@@
-544,7
+542,7
@@
public class DBRefFetcher implements Runnable
}
for (int j = 0, n = entryRefs.size(); j < n; j++)
{
}
for (int j = 0, n = entryRefs.size(); j < n; j++)
{
- DBRefEntry ref = entryRefs.get(j);
+ DBRefEntry ref = entryRefs.get(j);
String accessionId = ref.getAccessionId();
// match up on accessionId
if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
String accessionId = ref.getAccessionId();
// match up on accessionId
if (seqRefs.containsKey(accessionId.toUpperCase(Locale.ROOT)))
@@
-741,7
+739,8
@@
public class DBRefFetcher implements Runnable
.toUpperCase(Locale.ROOT);
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
.toUpperCase(Locale.ROOT);
int oldstrt = alseqs[alsq].getStart();
alseqs[alsq].setStart(sequence.getSequenceAsString()
- .toUpperCase(Locale.ROOT).indexOf(ngAlsq) + sequence.getStart());
+ .toUpperCase(Locale.ROOT).indexOf(ngAlsq)
+ + sequence.getStart());
if (oldstrt != alseqs[alsq].getStart())
{
alseqs[alsq].setEnd(
if (oldstrt != alseqs[alsq].getStart())
{
alseqs[alsq].setEnd(
@@
-782,15
+781,17
@@
public class DBRefFetcher implements Runnable
/**
*
/**
*
- * @return any feature settings associated with sources that have provided sequences
+ * @return any feature settings associated with sources that have provided
+ * sequences
*/
*/
- public List<FeatureSettingsModelI>getFeatureSettingsModels()
+ public List<FeatureSettingsModelI> getFeatureSettingsModels()
{
return featureDisplaySettings == null
? Arrays.asList(new FeatureSettingsModelI[0])
: Arrays.asList(featureDisplaySettings.values()
.toArray(new FeatureSettingsModelI[1]));
}
{
return featureDisplaySettings == null
? Arrays.asList(new FeatureSettingsModelI[0])
: Arrays.asList(featureDisplaySettings.values()
.toArray(new FeatureSettingsModelI[1]));
}
+
/**
* Adds the message to the list unless it already contains it
*
/**
* Adds the message to the list unless it already contains it
*
@@
-813,11
+814,11
@@
public class DBRefFetcher implements Runnable
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
*/
private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
{
- int n;
- if (sequencesArray == null || (n = sequencesArray.length) == 0)
- return sequencesArray;
+ int n;
+ if (sequencesArray == null || (n = sequencesArray.length) == 0)
+ return sequencesArray;
ArrayList<SequenceI> nseq = new ArrayList<>();
ArrayList<SequenceI> nseq = new ArrayList<>();
- for (int i = 0;i < n; i++)
+ for (int i = 0; i < n; i++)
{
nseq.add(sequencesArray[i]);
List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
{
nseq.add(sequencesArray[i]);
List<DBRefEntry> dbr = sequencesArray[i].getDBRefs();
@@
-832,11
+833,12
@@
public class DBRefFetcher implements Runnable
{
nseq.add(map.getTo());
}
{
nseq.add(map.getTo());
}
- }
+ }
}
}
}
}
}
}
- // BH 2019.01.25 question here if this is the right logic. Return the original if nothing found?
+ // BH 2019.01.25 question here if this is the right logic. Return the
+ // original if nothing found?
if (nseq.size() > 0)
{
return nseq.toArray(new SequenceI[nseq.size()]);
if (nseq.size() > 0)
{
return nseq.toArray(new SequenceI[nseq.size()]);