JAL-1894 source formatting

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 05e844c..898e4f7 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -228,8 +228,8 @@ public class AlignmentUtils
    * @param cdnaAlignment
    * @return
    */
-  public static boolean mapProteinAlignmentToCdna(final AlignmentI proteinAlignment,
-          final AlignmentI cdnaAlignment)
+  public static boolean mapProteinAlignmentToCdna(
+          final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment)
   {
     if (proteinAlignment == null || cdnaAlignment == null)
     {
@@ -429,8 +429,7 @@ public class AlignmentUtils
     {
       return null;
     }
-    if (!translatesAs(cdnaSeqChars, startOffset,
-            aaSeqChars))
+    if (!translatesAs(cdnaSeqChars, startOffset, aaSeqChars))
     {
       return null;
     }

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index fce74e3..80ab5d5 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2081,8 +2081,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         infoPanel
                 .add(new Label(MessageManager.getString("warn.delete_all")));
 
-        final JVDialog dialog = new JVDialog(this, title, true, 400,
-                200);
+        final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
         dialog.setMainPanel(infoPanel);
         dialog.ok.setLabel(MessageManager.getString("action.ok"));
         dialog.cancel.setLabel(MessageManager.getString("action.cancel"));

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index efb77e7..36a7cff 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -2404,8 +2404,7 @@ public class JalviewLite extends Applet implements
         return rtn;
       } catch (Exception ex)
       {
-        System.out.println("Exception checking resources: " + f + " "
-                + ex);
+        System.out.println("Exception checking resources: " + f + " " + ex);
         return false;
       }
     }

diff --git a/src/jalview/datamodel/Mapping.java b/src/jalview/datamodel/Mapping.java
index ea08d97..6c619ce 100644 (file)
--- a/src/jalview/datamodel/Mapping.java
+++ b/src/jalview/datamodel/Mapping.java
@@ -253,8 +253,7 @@ public class Mapping
        * allow for offset e.g. treat pos 8 as 2 if sequence starts at 7
        */
       int truePos = sequencePos - (start - 1);
-      while (alignedBases < truePos
-              && alignedColumn < alignedSeq.length)
+      while (alignedBases < truePos && alignedColumn < alignedSeq.length)
       {
         if (alignedSeq[alignedColumn++] != gap)
         {

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index eda4a1c..7908b0c 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2415,7 +2415,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-
   /**
    * DOCUMENT ME!
    * 

diff --git a/src/jalview/io/BioJsHTMLOutput.java b/src/jalview/io/BioJsHTMLOutput.java
index 1f4c53a..ac29d8e 100644 (file)
--- a/src/jalview/io/BioJsHTMLOutput.java
+++ b/src/jalview/io/BioJsHTMLOutput.java
@@ -115,16 +115,15 @@ public class BioJsHTMLOutput
       AlignmentExportData exportData = jalview.gui.AlignFrame
               .getAlignmentForExport(JSONFile.FILE_DESC,
                       ap.getAlignViewport(), exportSettings);
-      String bioJSON = new FormatAdapter(ap,
-              exportData.getSettings()).formatSequences(JSONFile.FILE_DESC,
-              exportData.getAlignment(), exportData.getOmitHidden(),
-              exportData.getStartEndPostions(), ap.getAlignViewport()
-                      .getColumnSelection());
+      String bioJSON = new FormatAdapter(ap, exportData.getSettings())
+              .formatSequences(JSONFile.FILE_DESC, exportData
+                      .getAlignment(), exportData.getOmitHidden(),
+                      exportData.getStartEndPostions(), ap
+                              .getAlignViewport().getColumnSelection());
 
       String bioJSTemplateString = getBioJsTemplateAsString();
       String generatedBioJsWithJalviewAlignmentAsJson = bioJSTemplateString
-              .replaceAll("#sequenceData#", bioJSON)
-              .toString();
+              .replaceAll("#sequenceData#", bioJSON).toString();
 
       PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(
               outputFile));

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index d0960e7..aa5583c 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -123,8 +123,7 @@ public class FeaturesFile extends AlignFile
    *          - process html strings into plain text
    * @return true if features were added
    */
-  public boolean parse(AlignmentI align, Map colours,
-          boolean removeHTML)
+  public boolean parse(AlignmentI align, Map colours, boolean removeHTML)
   {
     return parse(align, colours, null, removeHTML, false);
   }

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 3ac4aa7..aece7a6 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -439,7 +439,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         seqMap.put(seqUniqueId, seq);
       }
 
-
       parseFeatures(jsonSeqArray);
 
       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
@@ -478,8 +477,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
           }
         }
         SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
-                displayBoxes, displayText, colourText,
-                startRes, endRes);
+                displayBoxes, displayText, colourText, startRes, endRes);
         seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
                 seqGrp);
         seqGrp.setShowNonconserved(showNonconserved);

diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java
index 25924f0..67b3a20 100644 (file)
--- a/src/jalview/jbgui/GStructureChooser.java
+++ b/src/jalview/jbgui/GStructureChooser.java
@@ -296,7 +296,7 @@ public abstract class GStructureChooser extends JPanel implements
           {
             if (btn_view.isEnabled())
             {
-            btn_view.requestFocus();
+              btn_view.requestFocus();
             }
             else
             {

diff --git a/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java b/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
index aeab34c..b3422ab 100644 (file)
--- a/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
+++ b/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
@@ -58,6 +58,7 @@ public class ColourSchemeMapper
     csPID = new PIDColourScheme();
     csBlosum62 = new Blosum62ColourScheme();
   }
+
   public static ColourSchemeI getJalviewColourScheme(
           String colourSchemeName, AnnotatedCollectionI annotCol)
   {

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 03632c8..d531fea 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -622,11 +622,10 @@ public class DBRefFetcher implements Runnable
           // absStart = 0;
           // create valid mapping between matching region of local sequence and
           // the mapped sequence
-          mp = new Mapping(null, new int[] {
-              sequenceStart + absStart,
-              sequenceStart + absStart + entrySeq.length() - 1 },
-                  new int[] { entry.getStart(),
-                      entry.getStart() + entrySeq.length() - 1 }, 1, 1);
+          mp = new Mapping(null, new int[] { sequenceStart + absStart,
+              sequenceStart + absStart + entrySeq.length() - 1 }, new int[]
+          { entry.getStart(), entry.getStart() + entrySeq.length() - 1 },
+                  1, 1);
           updateRefFrame = false; // mapping is based on current start/end so
           // don't modify start and end
         }

diff --git a/src/jalview/ws/uimodel/AlignAnalysisUIText.java b/src/jalview/ws/uimodel/AlignAnalysisUIText.java
index 6514d98..9518eaa 100644 (file)
--- a/src/jalview/ws/uimodel/AlignAnalysisUIText.java
+++ b/src/jalview/ws/uimodel/AlignAnalysisUIText.java
@@ -20,7 +20,6 @@
  */
 package jalview.ws.uimodel;
 
-
 public class AlignAnalysisUIText
 {