JAL-2403 JAL-838 remove unused methods and unneeded public visibility

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index fdadb13..4ee0be9 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -308,8 +308,8 @@ public class NJTree
   {
     jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
 
-    return fout.print(isHasBootstrap(), isHasDistances(),
-            isHasRootDistance()); // output all data available for tree
+    return fout.print(hasBootstrap(), hasDistances(),
+            hasRootDistance()); // output all data available for tree
   }
 
   /**
@@ -319,7 +319,7 @@ public class NJTree
    * @param list
    *          Sequence set to be associated with tree nodes
    */
-  public void UpdatePlaceHolders(List<SequenceI> list)
+  public void updatePlaceHolders(List<SequenceI> list)
   {
     Vector<SequenceNode> leaves = findLeaves(top);
 
@@ -404,7 +404,7 @@ public class NJTree
   /**
    * DOCUMENT ME!
    */
-  public void cluster()
+  void cluster()
   {
     while (noClus > 2)
     {
@@ -466,7 +466,7 @@ public class NJTree
    * 
    * @return DOCUMENT ME!
    */
-  public Cluster joinClusters(int i, int j)
+  Cluster joinClusters(int i, int j)
   {
     double dist = distance.getValue(i, j);
 
@@ -534,7 +534,7 @@ public class NJTree
    * @param dist
    *          DOCUMENT ME!
    */
-  public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
+  void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
           double dist)
   {
 
@@ -562,7 +562,7 @@ public class NJTree
    * @param dist
    *          DOCUMENT ME!
    */
-  public void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
+  void findNewDistances(SequenceNode tmpi, SequenceNode tmpj,
           double dist)
   {
     double ih = 0;
@@ -595,7 +595,7 @@ public class NJTree
    * @param j
    *          DOCUMENT ME!
    */
-  public void findClusterDistance(int i, int j)
+  void findClusterDistance(int i, int j)
   {
     int noi = cluster.elementAt(i).value.length;
     int noj = cluster.elementAt(j).value.length;
@@ -636,7 +636,7 @@ public class NJTree
    * @param j
    *          DOCUMENT ME!
    */
-  public void findClusterNJDistance(int i, int j)
+  void findClusterNJDistance(int i, int j)
   {
 
     // New distances from cluster to others
@@ -676,7 +676,7 @@ public class NJTree
    * 
    * @return DOCUMENT ME!
    */
-  public double findr(int i, int j)
+  double findr(int i, int j)
   {
     double tmp = 1;
 
@@ -702,7 +702,7 @@ public class NJTree
    * 
    * @return DOCUMENT ME!
    */
-  public double findMinNJDistance()
+  double findMinNJDistance()
   {
     double min = Double.MAX_VALUE;
 
@@ -735,7 +735,7 @@ public class NJTree
    * 
    * @return DOCUMENT ME!
    */
-  public double findMinDistance()
+  double findMinDistance()
   {
     double min = Double.MAX_VALUE;
 
@@ -764,7 +764,7 @@ public class NJTree
   /**
    * DOCUMENT ME!
    */
-  public void makeLeaves()
+  void makeLeaves()
   {
     cluster = new Vector<Cluster>();
 
@@ -838,54 +838,12 @@ public class NJTree
   }
 
   /**
-   * Find the leaf node with a particular ycount
-   * 
-   * @param nd
-   *          initial point on tree to search from
-   * @param count
-   *          value to search for
-   * 
-   * @return null or the node with ycound=count
-   */
-  public Object findLeaf(SequenceNode nd, int count)
-  {
-    found = _findLeaf(nd, count);
-
-    return found;
-  }
-
-  /*
-   * #see findLeaf(SequenceNode node, count)
-   */
-  public Object _findLeaf(SequenceNode nd, int count)
-  {
-    if (nd == null)
-    {
-      return null;
-    }
-
-    if (nd.ycount == count)
-    {
-      found = nd.element();
-
-      return found;
-    }
-    else
-    {
-      _findLeaf((SequenceNode) nd.left(), count);
-      _findLeaf((SequenceNode) nd.right(), count);
-    }
-
-    return found;
-  }
-
-  /**
    * printNode is mainly for debugging purposes.
    * 
    * @param nd
    *          SequenceNode
    */
-  public void printNode(SequenceNode nd)
+  void printNode(SequenceNode nd)
   {
     if (nd == null)
     {
@@ -912,7 +870,7 @@ public class NJTree
    * @param nd
    *          DOCUMENT ME!
    */
-  public void findMaxDist(SequenceNode nd)
+  void findMaxDist(SequenceNode nd)
   {
     if (nd == null)
     {
@@ -1034,8 +992,9 @@ public class NJTree
    * 
    * @return DOCUMENT ME!
    */
-  public SequenceNode reRoot()
+  SequenceNode reRoot()
   {
+    // TODO not used - remove?
     if (maxdist != null)
     {
       ycount = 0;
@@ -1109,7 +1068,7 @@ public class NJTree
    * @param nd
    *          DOCUMENT ME!
    */
-  public void printN(SequenceNode nd)
+  void printN(SequenceNode nd)
   {
     if (nd == null)
     {
@@ -1152,7 +1111,7 @@ public class NJTree
    * @param nd
    *          DOCUMENT ME!
    */
-  public void _reCount(SequenceNode nd)
+  void _reCount(SequenceNode nd)
   {
     // if (_lycount<_lylimit)
     // {
@@ -1211,7 +1170,7 @@ public class NJTree
    * @param dir
    *          DOCUMENT ME!
    */
-  public void changeDirection(SequenceNode nd, SequenceNode dir)
+  void changeDirection(SequenceNode nd, SequenceNode dir)
   {
     if (nd == null)
     {
@@ -1290,7 +1249,7 @@ public class NJTree
    * 
    * @return true if tree has real distances
    */
-  public boolean isHasDistances()
+  public boolean hasDistances()
   {
     return hasDistances;
   }
@@ -1299,12 +1258,12 @@ public class NJTree
    * 
    * @return true if tree has real bootstrap values
    */
-  public boolean isHasBootstrap()
+  public boolean hasBootstrap()
   {
     return hasBootstrap;
   }
 
-  public boolean isHasRootDistance()
+  public boolean hasRootDistance()
   {
     return hasRootDistance;
   }

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 0a33ea8..74dd29a 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -160,7 +160,7 @@ public class TreePanel extends GTreePanel
                     .println("new alignment sequences vector value is null");
           }
 
-          tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
+          tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
           treeCanvas.nameHash.clear(); // reset the mapping between canvas
           // rectangles and leafnodes
           repaint();
@@ -367,8 +367,8 @@ public class TreePanel extends GTreePanel
     NewickFile fout = new NewickFile(tree.getTopNode());
     try
     {
-      cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
-              tree.isHasRootDistance()));
+      cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
+              tree.hasRootDistance()));
       Desktop.addInternalFrame(cap, newTitle, 500, 100);
     } catch (OutOfMemoryError oom)
     {
@@ -406,8 +406,8 @@ public class TreePanel extends GTreePanel
       {
         jalview.io.NewickFile fout = new jalview.io.NewickFile(
                 tree.getTopNode());
-        String output = fout.print(tree.isHasBootstrap(),
-                tree.isHasDistances(), tree.isHasRootDistance());
+        String output = fout.print(tree.hasBootstrap(),
+                tree.hasDistances(), tree.hasRootDistance());
         java.io.PrintWriter out = new java.io.PrintWriter(
                 new java.io.FileWriter(choice));
         out.println(output);