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JAL-3990 gradle spotlessApply
author
Jim Procter
<j.procter@dundee.ac.uk>
Tue, 5 Apr 2022 17:14:52 +0000
(18:14 +0100)
committer
Jim Procter
<j.procter@dundee.ac.uk>
Tue, 5 Apr 2022 17:14:52 +0000
(18:14 +0100)
src/jalview/gui/structurechooser/TDBResultAnalyser.java
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src/jalview/io/SequenceAnnotationReport.java
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test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
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test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
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diff --git
a/src/jalview/gui/structurechooser/TDBResultAnalyser.java
b/src/jalview/gui/structurechooser/TDBResultAnalyser.java
index
02d4bda
..
2408d7a
100644
(file)
--- a/
src/jalview/gui/structurechooser/TDBResultAnalyser.java
+++ b/
src/jalview/gui/structurechooser/TDBResultAnalyser.java
@@
-131,7
+131,8
@@
public class TDBResultAnalyser
// ignore anything outside the sequence region
for (FTSData row : collectedResults)
{
// ignore anything outside the sequence region
for (FTSData row : collectedResults)
{
- if (row.getSummaryData() != null && row.getSummaryData()[idx_ups]!=null)
+ if (row.getSummaryData() != null
+ && row.getSummaryData()[idx_ups] != null)
{
int up_s = (Integer) row.getSummaryData()[idx_ups];
int up_e = (Integer) row.getSummaryData()[idx_upe];
{
int up_s = (Integer) row.getSummaryData()[idx_ups];
int up_e = (Integer) row.getSummaryData()[idx_upe];
diff --git
a/src/jalview/io/SequenceAnnotationReport.java
b/src/jalview/io/SequenceAnnotationReport.java
index
7fc04e1
..
c831366
100644
(file)
--- a/
src/jalview/io/SequenceAnnotationReport.java
+++ b/
src/jalview/io/SequenceAnnotationReport.java
@@
-539,7
+539,7
@@
public class SequenceAnnotationReport
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
protected int appendDbRefs(final StringBuilder sb, SequenceI ds,
boolean summary)
{
- List<DBRefEntry> dbrefs,dbrefset = ds.getDBRefs();
+ List<DBRefEntry> dbrefs, dbrefset = ds.getDBRefs();
if (dbrefset == null)
{
if (dbrefset == null)
{
@@
-549,9
+549,9
@@
public class SequenceAnnotationReport
// PATCH for JAL-3980 defensive copy
dbrefs = new ArrayList<DBRefEntry>();
// PATCH for JAL-3980 defensive copy
dbrefs = new ArrayList<DBRefEntry>();
-
+
dbrefs.addAll(dbrefset);
dbrefs.addAll(dbrefset);
-
+
// note this sorts the refs held on the sequence!
dbrefs.sort(comparator);
boolean ellipsis = false;
// note this sorts the refs held on the sequence!
dbrefs.sort(comparator);
boolean ellipsis = false;
diff --git
a/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
b/test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
index
b91466b
..
355eae5
100644
(file)
--- a/
test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
+++ b/
test/jalview/fts/service/pdb/PDBFTSRestClientTest.java
@@
-736,10
+736,10
@@
public class PDBFTSRestClientTest
new String[]
{ readJsonStringFromFile(
"test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt")
new String[]
{ readJsonStringFromFile(
"test/jalview/fts/threedbeacons/p01308_pdbfts_query.txt")
- .trim(),
+ .trim(),
readJsonStringFromFile(
"test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt")
readJsonStringFromFile(
"test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt")
- .trim() });
+ .trim() });
for (int i = 1; i < 5; i++)
{
mocks.add(
for (int i = 1; i < 5; i++)
{
mocks.add(
@@
-747,12
+747,10
@@
public class PDBFTSRestClientTest
new String[]
{ readJsonStringFromFile(
"test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt"
new String[]
{ readJsonStringFromFile(
"test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt"
- + i + ".txt")
- .trim(),
+ + i + ".txt").trim(),
readJsonStringFromFile(
"test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt"
readJsonStringFromFile(
"test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt"
- + i + "_resp.txt")
- .trim() });
+ + i + "_resp.txt").trim() });
}
} catch (Throwable e)
{
}
} catch (Throwable e)
{
diff --git
a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
index
73ba4df
..
7107448
100644
(file)
--- a/
test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
+++ b/
test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
@@
-239,8
+239,7
@@
public class StructureChooserQuerySourceTest
}
@SuppressWarnings("deprecation")
}
@SuppressWarnings("deprecation")
- @Test(groups =
- { "Functional" })
+ @Test(groups = { "Functional" })
public void buildPDBQueryTest()
{
System.out.println("seq >>>> " + seq);
public void buildPDBQueryTest()
{
System.out.println("seq >>>> " + seq);
@@
-288,8
+287,7
@@
public class StructureChooserQuerySourceTest
}
@SuppressWarnings("deprecation")
}
@SuppressWarnings("deprecation")
- @Test(groups =
- { "Functional" })
+ @Test(groups = { "Functional" })
public void buildThreeDBQueryTest()
{
System.out.println("seq >>>> " + upSeq);
public void buildThreeDBQueryTest()
{
System.out.println("seq >>>> " + upSeq);