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

[jalview.git] / src / jalview / analysis / NJTree.java

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 5f268ae..4ee0be9 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -21,6 +21,7 @@
 package jalview.analysis;
 
 import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.analysis.DistanceScoreModelI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityScoreModelI;
@@ -231,6 +232,10 @@ public class NJTree
   {
     this.sequence = sqs;
     this.node = new Vector<SequenceNode>();
+    if (!(treeType.equals(NEIGHBOUR_JOINING)))
+    {
+      treeType = AVERAGE_DISTANCE;
+    }
     this.type = treeType;
     this.pwtype = modelType;
     if (seqView != null)
@@ -248,11 +253,6 @@ public class NJTree
       sdata.addOperation(CigarArray.M, end - start + 1);
       this.seqData = new AlignmentView(sdata, start);
     }
-    // System.err.println("Made seqData");// dbg
-    if (!(treeType.equals(NEIGHBOUR_JOINING)))
-    {
-      treeType = AVERAGE_DISTANCE;
-    }
 
     if (sm == null && !(modelType.equals("PID")))
     {
@@ -274,31 +274,28 @@ public class NJTree
 
     noseqs = i++;
 
+    // TODO pass choice of params from GUI in constructo
     if (sm instanceof DistanceScoreModelI)
     {
-      distance = ((DistanceScoreModelI) sm).findDistances(seqData);
+      distance = ((DistanceScoreModelI) sm).findDistances(seqData,
+              SimilarityParams.Jalview);
     }
     else if (sm instanceof SimilarityScoreModelI)
     {
       /*
        * compute similarity and invert it to give a distance measure
        */
-      MatrixI result = ((SimilarityScoreModelI) sm)
-              .findSimilarities(seqData);
-      double maxScore = result.getMaxValue();
-      result.subtractAllFrom(maxScore);
+      MatrixI result = ((SimilarityScoreModelI) sm).findSimilarities(
+              seqData, SimilarityParams.Jalview);
+      result.reverseRange(true);
       distance = result;
     }
 
-    // System.err.println("Made distances");// dbg
     makeLeaves();
-    // System.err.println("Made leaves");// dbg
 
     noClus = cluster.size();
 
     cluster();
-    // System.err.println("Made clusters");// dbg
-
   }
 
   /**
@@ -311,8 +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
   }
 
   /**
@@ -322,7 +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);
 
@@ -407,7 +404,7 @@ public class NJTree
   /**
    * DOCUMENT ME!
    */
-  public void cluster()
+  void cluster()
   {
     while (noClus > 2)
     {
@@ -469,7 +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);
 
@@ -537,7 +534,7 @@ public class NJTree
    * @param dist
    *          DOCUMENT ME!
    */
-  public void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
+  void findNewNJDistances(SequenceNode tmpi, SequenceNode tmpj,
           double dist)
   {
 
@@ -565,7 +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;
@@ -598,7 +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;
@@ -639,7 +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
@@ -679,7 +676,7 @@ public class NJTree
    * 
    * @return DOCUMENT ME!
    */
-  public double findr(int i, int j)
+  double findr(int i, int j)
   {
     double tmp = 1;
 
@@ -705,7 +702,7 @@ public class NJTree
    * 
    * @return DOCUMENT ME!
    */
-  public double findMinNJDistance()
+  double findMinNJDistance()
   {
     double min = Double.MAX_VALUE;
 
@@ -738,7 +735,7 @@ public class NJTree
    * 
    * @return DOCUMENT ME!
    */
-  public double findMinDistance()
+  double findMinDistance()
   {
     double min = Double.MAX_VALUE;
 
@@ -765,50 +762,9 @@ public class NJTree
   }
 
   /**
-   * Calculate a distance matrix given the sequence input data and score model
-   * 
-   * @return
-   */
-  public MatrixI findDistances(ScoreModelI scoreModel)
-  {
-    MatrixI result = null;
-
-    if (scoreModel == null)
-    {
-      // Resolve substitution model
-      scoreModel = ScoreModels.getInstance().forName(pwtype);
-      if (scoreModel == null)
-      {
-        scoreModel = ScoreModels.getInstance().forName("BLOSUM62");
-      }
-    }
-    if (scoreModel instanceof DistanceScoreModelI)
-    {
-      result = ((DistanceScoreModelI) scoreModel).findDistances(seqData);
-    }
-    else if (scoreModel instanceof SimilarityScoreModelI)
-    {
-      /*
-       * compute similarity and invert it to give a distance measure
-       */
-      result = ((SimilarityScoreModelI) scoreModel)
-              .findSimilarities(seqData);
-      double maxScore = result.getMaxValue();
-      result.subtractAllFrom(maxScore);
-    }
-    else
-    {
-      System.err
-              .println("Unexpected type of score model, can't compute distances");
-    }
-
-    return result;
-  }
-
-  /**
    * DOCUMENT ME!
    */
-  public void makeLeaves()
+  void makeLeaves()
   {
     cluster = new Vector<Cluster>();
 
@@ -882,54 +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)
     {
@@ -956,7 +870,7 @@ public class NJTree
    * @param nd
    *          DOCUMENT ME!
    */
-  public void findMaxDist(SequenceNode nd)
+  void findMaxDist(SequenceNode nd)
   {
     if (nd == null)
     {
@@ -1078,8 +992,9 @@ public class NJTree
    * 
    * @return DOCUMENT ME!
    */
-  public SequenceNode reRoot()
+  SequenceNode reRoot()
   {
+    // TODO not used - remove?
     if (maxdist != null)
     {
       ycount = 0;
@@ -1153,7 +1068,7 @@ public class NJTree
    * @param nd
    *          DOCUMENT ME!
    */
-  public void printN(SequenceNode nd)
+  void printN(SequenceNode nd)
   {
     if (nd == null)
     {
@@ -1196,7 +1111,7 @@ public class NJTree
    * @param nd
    *          DOCUMENT ME!
    */
-  public void _reCount(SequenceNode nd)
+  void _reCount(SequenceNode nd)
   {
     // if (_lycount<_lylimit)
     // {
@@ -1255,7 +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)
     {
@@ -1334,7 +1249,7 @@ public class NJTree
    * 
    * @return true if tree has real distances
    */
-  public boolean isHasDistances()
+  public boolean hasDistances()
   {
     return hasDistances;
   }
@@ -1343,12 +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;
   }