Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh...

[jalview.git] / src / jalview / io / NewickFile.java

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 4a30d73..a283691 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -80,14 +80,14 @@ public class NewickFile extends FileParse
 {
   SequenceNode root;
 
-  private boolean HasBootstrap = false;
+  private boolean hasBootstrap = false;
 
-  private boolean HasDistances = false;
+  private boolean hasDistances = false;
 
-  private boolean RootHasDistance = false;
+  private boolean rootHasDistance = false;
 
   // File IO Flags
-  boolean ReplaceUnderscores = false;
+  boolean replaceUnderscores = false;
 
   boolean printRootInfo = true;
 
@@ -160,7 +160,7 @@ public class NewickFile extends FileParse
    */
   public NewickFile(SequenceNode newtree, boolean bootstrap)
   {
-    HasBootstrap = bootstrap;
+    hasBootstrap = bootstrap;
     root = newtree;
   }
 
@@ -178,8 +178,8 @@ public class NewickFile extends FileParse
           boolean distances)
   {
     root = newtree;
-    HasBootstrap = bootstrap;
-    HasDistances = distances;
+    hasBootstrap = bootstrap;
+    hasDistances = distances;
   }
 
   /**
@@ -198,9 +198,9 @@ public class NewickFile extends FileParse
           boolean distances, boolean rootdistance)
   {
     root = newtree;
-    HasBootstrap = bootstrap;
-    HasDistances = distances;
-    RootHasDistance = rootdistance;
+    hasBootstrap = bootstrap;
+    hasDistances = distances;
+    rootHasDistance = rootdistance;
   }
 
   /**
@@ -230,9 +230,9 @@ public class NewickFile extends FileParse
 
   // @tree annotations
   // These are set automatically by the reader
-  public boolean HasBootstrap()
+  public boolean hasBootstrap()
   {
-    return HasBootstrap;
+    return hasBootstrap;
   }
 
   /**
@@ -240,14 +240,14 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  public boolean HasDistances()
+  public boolean hasDistances()
   {
-    return HasDistances;
+    return hasDistances;
   }
 
-  public boolean HasRootDistance()
+  public boolean hasRootDistance()
   {
-    return RootHasDistance;
+    return rootHasDistance;
   }
 
   /**
@@ -439,7 +439,7 @@ public class NewickFile extends FileParse
         {
           if (nodename == null)
           {
-            if (ReplaceUnderscores)
+            if (replaceUnderscores)
             {
               nodename = uqnodename.stringMatched(1).replace('_', ' ');
             }
@@ -472,7 +472,7 @@ public class NewickFile extends FileParse
             {
               bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
                       .intValue();
-              HasBootstrap = true;
+              hasBootstrap = true;
             } catch (Exception e)
             {
               Error = ErrorStringrange(Error, "Can't parse bootstrap value",
@@ -503,12 +503,12 @@ public class NewickFile extends FileParse
           // Write node info here
           c.setName(nodename);
           // Trees without distances still need a render distance
-          c.dist = (HasDistances) ? distance : DefDistance;
+          c.dist = (hasDistances) ? distance : DefDistance;
           // be consistent for internal bootstrap defaults too
-          c.setBootstrap((HasBootstrap) ? bootstrap : DefBootstrap);
+          c.setBootstrap((hasBootstrap) ? bootstrap : DefBootstrap);
           if (c == realroot)
           {
-            RootHasDistance = nodehasdistance; // JBPNote This is really
+            rootHasDistance = nodehasdistance; // JBPNote This is really
             // UGLY!!! Ensure root node gets
             // its given distance
           }
@@ -519,8 +519,8 @@ public class NewickFile extends FileParse
         {
           // Find a place to put the leaf
           SequenceNode newnode = new SequenceNode(null, c, nodename,
-                  (HasDistances) ? distance : DefDistance,
-                  (HasBootstrap) ? bootstrap : DefBootstrap, false);
+                  (hasDistances) ? distance : DefDistance,
+                  (hasBootstrap) ? bootstrap : DefBootstrap, false);
           parseNHXNodeProps(c, commentString2);
           commentString2 = null;
 
@@ -539,7 +539,7 @@ public class NewickFile extends FileParse
               // Insert a dummy node for polytomy
               // dummy nodes have distances
               SequenceNode newdummy = new SequenceNode(null, c, null,
-                      (HasDistances ? 0 : DefDistance), 0, true);
+                      (hasDistances ? 0 : DefDistance), 0, true);
               newdummy.SetChildren(c.left(), newnode);
               c.setLeft(newdummy);
             }
@@ -617,9 +617,9 @@ public class NewickFile extends FileParse
     // (root.right()!=null && root.isDummy())
     root = (SequenceNode) root.right().detach(); // remove the imaginary root.
 
-    if (!RootHasDistance)
+    if (!rootHasDistance)
     {
-      root.dist = (HasDistances) ? 0 : DefDistance;
+      root.dist = (hasDistances) ? 0 : DefDistance;
     }
   }
 
@@ -658,7 +658,7 @@ public class NewickFile extends FileParse
               v = iv.intValue(); // jalview only does integer bootstraps
               // currently
               c.setBootstrap(v);
-              HasBootstrap = true;
+              hasBootstrap = true;
             }
             // more codes here.
           } catch (Exception e)
@@ -715,11 +715,11 @@ public class NewickFile extends FileParse
   {
     synchronized (this)
     {
-      boolean boots = this.HasBootstrap;
-      this.HasBootstrap = withbootstraps;
+      boolean boots = this.hasBootstrap;
+      this.hasBootstrap = withbootstraps;
 
       String rv = print();
-      this.HasBootstrap = boots;
+      this.hasBootstrap = boots;
 
       return rv;
     }
@@ -741,11 +741,11 @@ public class NewickFile extends FileParse
   {
     synchronized (this)
     {
-      boolean dists = this.HasDistances;
-      this.HasDistances = withdists;
+      boolean dists = this.hasDistances;
+      this.hasDistances = withdists;
 
       String rv = print(withbootstraps);
-      this.HasDistances = dists;
+      this.hasDistances = dists;
 
       return rv;
     }
@@ -835,10 +835,10 @@ public class NewickFile extends FileParse
   private String printNodeField(SequenceNode c)
   {
     return ((c.getName() == null) ? "" : nodeName(c.getName()))
-            + ((HasBootstrap) ? ((c.getBootstrap() > -1)
+            + ((hasBootstrap) ? ((c.getBootstrap() > -1)
                     ? ((c.getName() != null ? " " : "") + c.getBootstrap())
                     : "") : "")
-            + ((HasDistances) ? (":" + c.dist) : "");
+            + ((hasDistances) ? (":" + c.dist) : "");
   }
 
   /**
@@ -853,13 +853,13 @@ public class NewickFile extends FileParse
   {
     return (printRootInfo)
             ? (((root.getName() == null) ? "" : nodeName(root.getName()))
-                    + ((HasBootstrap)
+                    + ((hasBootstrap)
                             ? ((root.getBootstrap() > -1)
                                     ? ((root.getName() != null ? " " : "")
                                             + +root.getBootstrap())
                                     : "")
                             : "")
-                    + ((RootHasDistance) ? (":" + root.dist) : ""))
+                    + ((rootHasDistance) ? (":" + root.dist) : ""))
             : "";
   }