JAL-1551 spotlessApply

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ddf2afd..913dffe 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -1523,7 +1523,7 @@ public class Jalview2XML
                 ov.getCanvas().getResidueColour().getRGB());
         overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB());
         view.setOverview(overview);
-      } 
+      }
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
         view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
@@ -2304,22 +2304,24 @@ public class Jalview2XML
           line.setColour(annotation.getThreshold().colour.getRGB());
           an.setThresholdLine(line);
         }
-        if (annotation.graph==AlignmentAnnotation.CONTACT_MAP)
+        if (annotation.graph == AlignmentAnnotation.CONTACT_MAP)
         {
-          if (annotation.sequenceRef.getContactMaps()!=null)
+          if (annotation.sequenceRef.getContactMaps() != null)
           {
-            ContactMatrixI cm = annotation.sequenceRef.getContactMatrixFor(annotation);
-            if (cm!=null)
+            ContactMatrixI cm = annotation.sequenceRef
+                    .getContactMatrixFor(annotation);
+            if (cm != null)
             {
               MatrixType xmlmat = new MatrixType();
               xmlmat.setType(cm.getType());
               xmlmat.setRows(BigInteger.valueOf(cm.getWidth()));
               xmlmat.setCols(BigInteger.valueOf(cm.getHeight()));
-              // consider using an opaque to/from -> allow instance to control its representation ?
+              // consider using an opaque to/from -> allow instance to control
+              // its representation ?
               xmlmat.setElements(ContactMatrix.contactToFloatString(cm));
               if (cm.hasGroups())
               {
-                for (BitSet gp: cm.getGroups())
+                for (BitSet gp : cm.getGroups())
                 {
                   BigInteger val = new BigInteger(gp.toByteArray());
                   xmlmat.getGroups().add(val.toString());
@@ -2335,7 +2337,7 @@ public class Jalview2XML
               {
                 xmlmat.setCutHeight(cm.getCutHeight());
               }
-              
+
               // set/get properties
               an.getContactmatrix().add(xmlmat);
             }
@@ -3948,7 +3950,8 @@ public class Jalview2XML
         jaa.setCalcId(annotation.getCalcId());
         if (annotation.getProperty().size() > 0)
         {
-          for (jalview.xml.binding.jalview.Property prop : annotation.getProperty())
+          for (jalview.xml.binding.jalview.Property prop : annotation
+                  .getProperty())
           {
             jaa.setProperty(prop.getName(), prop.getValue());
           }
@@ -3975,29 +3978,37 @@ public class Jalview2XML
 
                   PAEContactMatrix newpae = new PAEContactMatrix(
                           jaa.sequenceRef, elements);
-                  List<BitSet> newgroups=new ArrayList<BitSet>();
-                  if (xmlmat.getGroups().size()>0)
+                  List<BitSet> newgroups = new ArrayList<BitSet>();
+                  if (xmlmat.getGroups().size() > 0)
                   {
-                    for (String sgroup:xmlmat.getGroups())
+                    for (String sgroup : xmlmat.getGroups())
                     {
-                      try {
+                      try
+                      {
                         BigInteger group = new BigInteger(sgroup);
                         newgroups.add(BitSet.valueOf(group.toByteArray()));
                       } catch (NumberFormatException nfe)
                       {
-                        Console.error("Problem parsing groups for a contact matrix (\""+sgroup+"\"",nfe);
+                        Console.error(
+                                "Problem parsing groups for a contact matrix (\""
+                                        + sgroup + "\"",
+                                nfe);
                       }
                     }
                   }
-                  String nwk=xmlmat.getNewick().size()>0 ? xmlmat.getNewick().get(0):null;
-                  if  (xmlmat.getNewick().size()>1)
+                  String nwk = xmlmat.getNewick().size() > 0
+                          ? xmlmat.getNewick().get(0)
+                          : null;
+                  if (xmlmat.getNewick().size() > 1)
                   {
                     Console.log.info(
                             "Ignoring additional clusterings for contact matrix");
                   }
-                  
+
                   String treeMethod = xmlmat.getTreeMethod();
-                  double thresh = xmlmat.getCutHeight()!=null ? xmlmat.getCutHeight() : 0;
+                  double thresh = xmlmat.getCutHeight() != null
+                          ? xmlmat.getCutHeight()
+                          : 0;
                   newpae.restoreGroups(newgroups, treeMethod, nwk, thresh);
                   jaa.sequenceRef.addContactListFor(jaa, newpae);
                 }
@@ -4246,8 +4257,8 @@ public class Jalview2XML
    */
   protected void loadOverview(Viewport view, String version, AlignFrame af)
   {
-    if (!isVersionStringLaterThan("2.11.3",
-            version) && view.getOverview()==null)
+    if (!isVersionStringLaterThan("2.11.3", version)
+            && view.getOverview() == null)
     {
       return;
     }
@@ -4394,8 +4405,8 @@ public class Jalview2XML
         {
           if (tree.isColumnWise())
           {
-            AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds.get(tree
-                    .getColumnReference());
+            AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds
+                    .get(tree.getColumnReference());
             if (aa == null)
             {
               Console.warn(
@@ -4953,10 +4964,11 @@ public class Jalview2XML
     viewport.setIncrement(safeInt(view.getConsThreshold()));
     viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
     viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
-    viewport.setFont(new Font(view.getFontName(),
-            safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
-            (view.getCharWidth()!=null) ? false : true);
-    if (view.getCharWidth()!=null)
+    viewport.setFont(
+            new Font(view.getFontName(), safeInt(view.getFontStyle()),
+                    safeInt(view.getFontSize())),
+            (view.getCharWidth() != null) ? false : true);
+    if (view.getCharWidth() != null)
     {
       viewport.setCharWidth(view.getCharWidth());
       viewport.setCharHeight(view.getCharHeight());
@@ -5283,7 +5295,7 @@ public class Jalview2XML
               + annotationId);
       return null;
     }
-    // belt-and-braces create a threshold line if the 
+    // belt-and-braces create a threshold line if the
     // colourscheme needs one but the matchedAnnotation doesn't have one
     if (safeInt(viewAnnColour.getAboveThreshold()) != 0
             && matchedAnnotation.getThreshold() == null)