From: James Procter <j.procter@dundee.ac.uk>
Date: Wed, 22 Feb 2023 14:24:04 +0000 (+0000)
Subject: JAL-1551 source formatting
X-Git-Tag: Release_2_11_3_0~18^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9d9ad2a9237a50e305349a63eb01bb5548d028d0;p=jalview.git

JAL-1551 source formatting
---

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 84af3e4..6281c29 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -600,9 +600,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase
      * test for patch release versions
      */
     assertFalse(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.2"));
-    assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0","2.11.4"));
-    assertFalse(Jalview2XML.isVersionStringLaterThan("2.12.2.0b1","2.12.2.0"));
-    assertFalse(Jalview2XML.isVersionStringLaterThan("2.12.2.3","2.12.2.2"));
+    assertTrue(Jalview2XML.isVersionStringLaterThan("2.11.3.0", "2.11.4"));
+    assertFalse(
+            Jalview2XML.isVersionStringLaterThan("2.12.2.0b1", "2.12.2.0"));
+    assertFalse(
+            Jalview2XML.isVersionStringLaterThan("2.12.2.3", "2.12.2.2"));
 
   }
 
@@ -870,8 +872,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     acg.setPredefinedColours(true);
     af.changeColour(acg);
     Color seqcol[] = new Color[3];
-    for (int iStart=fsq.findIndex(fsq.getStart()),i=0;i<3;i++) {
-      seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
+    for (int iStart = fsq.findIndex(fsq.getStart()), i = 0; i < 3; i++)
+    {
+      seqcol[i] = af.alignPanel.getSeqPanel().seqCanvas
+              .getSequenceRenderer()
+              .getResidueColour(fsq, iStart + i, null);
     }
     /*
      * save project, close windows, reload project, verify
@@ -880,7 +885,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             "testStoreAndRecoverAnnotRowElemColors", ".jvp");
     tfile.deleteOnExit();
     new Jalview2XML(false).saveState(tfile);
-    //Desktop.instance.closeAll_actionPerformed(null);
+    // Desktop.instance.closeAll_actionPerformed(null);
     af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);
     Assert.assertNotNull(af, "Failed to reload project");
@@ -888,9 +893,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase
      * verify alignment annotation has colors
      */
     av = af.getViewport();
-    
+
     ColourSchemeI loadedCscheme = av.getGlobalColourScheme();
-    Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,"Didn't apply Annotation colour gradient");
+    Assert.assertTrue(loadedCscheme instanceof AnnotationColourGradient,
+            "Didn't apply Annotation colour gradient");
     acg = (AnnotationColourGradient) loadedCscheme;
     assertTrue(acg.isSeqAssociated());
     assertTrue(acg.isPredefinedColours());
@@ -903,13 +909,16 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     for (int iStart = al.getSequenceAt(0)
             .findIndex(al.getSequenceAt(0).getStart()), i = 0; i < 3; i++)
     {
-      Assert.assertTrue(ala.annotations[i].colour!=null);
+      Assert.assertTrue(ala.annotations[i].colour != null);
       Assert.assertTrue(ala.annotations[i].colour.equals(annots[i].colour));
-      Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer().getResidueColour(fsq, iStart+i, null);
-      Assert.assertTrue(seqcol[i].equals(newseqcol),"Sequence shading is different");
+      Color newseqcol = af.alignPanel.getSeqPanel().seqCanvas
+              .getSequenceRenderer()
+              .getResidueColour(fsq, iStart + i, null);
+      Assert.assertTrue(seqcol[i].equals(newseqcol),
+              "Sequence shading is different");
 
     }
-    
+
   }
 
   /**
@@ -1490,7 +1499,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   }
 
   /**
-   * Test that a view from an older version of Jalview is restored with Overview automatically shown when the preference is set
+   * Test that a view from an older version of Jalview is restored with Overview
+   * automatically shown when the preference is set
    * 
    * @throws Exception
    */
@@ -1515,7 +1525,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
    * 
    * @throws Exception
    */
-  @Test(groups = {"Functional"}, enabled=false)
+  @Test(groups = { "Functional" }, enabled = false)
   public void testReloadActuallyReloads() throws Exception
   {
     Desktop.instance.closeAll_actionPerformed(null);