From 5a352aa2f3330ae269d9b70c4a7374c2518bfb2e Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 5 Apr 2022 18:14:52 +0100 Subject: [PATCH] JAL-3990 gradle spotlessApply --- src/jalview/gui/structurechooser/TDBResultAnalyser.java | 3 ++- src/jalview/io/SequenceAnnotationReport.java | 6 +++--- test/jalview/fts/service/pdb/PDBFTSRestClientTest.java | 10 ++++------ .../structurechooser/StructureChooserQuerySourceTest.java | 6 ++---- 4 files changed, 11 insertions(+), 14 deletions(-) diff --git a/src/jalview/gui/structurechooser/TDBResultAnalyser.java b/src/jalview/gui/structurechooser/TDBResultAnalyser.java index 02d4bda..2408d7a 100644 --- 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) { - 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]; diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java index 7fc04e1..c831366 100644 --- 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) { - List dbrefs,dbrefset = ds.getDBRefs(); + List dbrefs, dbrefset = ds.getDBRefs(); if (dbrefset == null) { @@ -549,9 +549,9 @@ public class SequenceAnnotationReport // PATCH for JAL-3980 defensive copy dbrefs = new ArrayList(); - + dbrefs.addAll(dbrefset); - + // 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 --- 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") - .trim(), + .trim(), readJsonStringFromFile( "test/jalview/fts/threedbeacons/p01308_pdbfts_resp.txt") - .trim() }); + .trim() }); 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" - + i + ".txt") - .trim(), + + i + ".txt").trim(), readJsonStringFromFile( "test/jalview/fts/threedbeacons/p0dtd1_pdbfts_fts_query_pt" - + i + "_resp.txt") - .trim() }); + + i + "_resp.txt").trim() }); } } catch (Throwable e) { diff --git a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java index 73ba4df..7107448 100644 --- a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java +++ b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java @@ -239,8 +239,7 @@ public class StructureChooserQuerySourceTest } @SuppressWarnings("deprecation") - @Test(groups = - { "Functional" }) + @Test(groups = { "Functional" }) public void buildPDBQueryTest() { System.out.println("seq >>>> " + seq); @@ -288,8 +287,7 @@ public class StructureChooserQuerySourceTest } @SuppressWarnings("deprecation") - @Test(groups = - { "Functional" }) + @Test(groups = { "Functional" }) public void buildThreeDBQueryTest() { System.out.println("seq >>>> " + upSeq); -- 1.7.10.2