Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / datamodel / GroupSet.java

diff --git a/src/jalview/datamodel/GroupSet.java b/src/jalview/datamodel/GroupSet.java
new file mode 100644 (file)
index 0000000..db38e7b
--- /dev/null
+++ b/src/jalview/datamodel/GroupSet.java
@@ -0,0 +1,221 @@
+package jalview.datamodel;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.List;
+
+import jalview.analysis.AverageDistanceEngine;
+import jalview.bin.Console;
+
+public class GroupSet implements GroupSetI
+{
+  List<BitSet> groups = Arrays.asList();
+
+  public GroupSet(GroupSet grps)
+  {
+    abs = grps.abs;
+    colorMap = new HashMap<BitSet, Color>(grps.colorMap);
+    groups = new ArrayList<BitSet>(grps.groups);
+    newick = grps.newick;
+    thresh = grps.thresh;
+    treeType = grps.treeType;
+  }
+
+  public GroupSet()
+  {
+    // TODO Auto-generated constructor stub
+  }
+
+  public GroupSet(boolean abs2, float thresh2, List<BitSet> groups2,
+          String treeType2, String newick2)
+  {
+    abs = abs2;
+    thresh = thresh2;
+    groups = groups2;
+    treeType = treeType2;
+    newick = newick2;
+  }
+
+  @Override
+  public boolean hasGroups()
+  {
+    return groups != null;
+  }
+
+  String newick = null;
+
+  @Override
+  public String getNewick()
+  {
+    return newick;
+  }
+
+  @Override
+  public boolean hasTree()
+  {
+    return newick != null && newick.length() > 0;
+  }
+
+  boolean abs = false;
+
+  double thresh = 0;
+
+  String treeType = null;
+
+  @Override
+  public void updateGroups(List<BitSet> colGroups)
+  {
+    if (colGroups != null)
+    {
+      groups = colGroups;
+    }
+  }
+
+  @Override
+  public BitSet getGroupsFor(int column)
+  {
+    if (groups != null)
+    {
+      for (BitSet gp : groups)
+      {
+        if (gp.get(column))
+        {
+          return gp;
+        }
+      }
+    }
+    // return singleton set;
+    BitSet bs = new BitSet();
+    bs.set(column);
+    return bs;
+  }
+
+  HashMap<BitSet, Color> colorMap = new HashMap<>();
+
+  @Override
+  public Color getColourForGroup(BitSet bs)
+  {
+    if (bs == null)
+    {
+      return Color.white;
+    }
+    Color groupCol = colorMap.get(bs);
+    if (groupCol == null)
+    {
+      return Color.white;
+    }
+    return groupCol;
+  }
+
+  @Override
+  public void setColorForGroup(BitSet bs, Color color)
+  {
+    colorMap.put(bs, color);
+  }
+
+  @Override
+  public void restoreGroups(List<BitSet> newgroups, String treeMethod,
+          String tree, double thresh2)
+  {
+    treeType = treeMethod;
+    groups = newgroups;
+    thresh = thresh2;
+    newick = tree;
+
+  }
+
+  @Override
+  public boolean hasCutHeight()
+  {
+    return groups != null && thresh != 0;
+  }
+
+  @Override
+  public double getCutHeight()
+  {
+    return thresh;
+  }
+
+  @Override
+  public String getTreeMethod()
+  {
+    return treeType;
+  }
+
+  public static GroupSet makeGroups(ContactMatrixI matrix, boolean autoCut)
+  {
+    return makeGroups(matrix, autoCut, 0, autoCut);
+  }
+  public static GroupSet makeGroups(ContactMatrixI matrix, boolean auto, float thresh,
+          boolean abs)
+  {
+    AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
+            matrix, true);
+    double height = clusterer.findHeight(clusterer.getTopNode());
+    Console.debug("Column tree height: " + height);
+    String newick = new jalview.io.NewickFile(clusterer.getTopNode(), false,
+            true).print();
+    String treeType = "UPGMA";
+    Console.trace("Newick string\n" + newick);
+
+    List<BinaryNode> nodegroups;
+    float cut = -1f;
+    if (auto)
+    {
+      double rootw = 0;
+      int p = 2;
+      BinaryNode bn = clusterer.getTopNode();
+      while (p-- > 0 & bn.left() != null)
+      {
+        if (bn.left() != null)
+        {
+          bn = bn.left();
+        }
+        if (bn.left() != null)
+        {
+          rootw = bn.height;
+        }
+      }
+      thresh = Math.max((float) (rootw / height) - 0.01f, 0);
+      cut = thresh;
+      nodegroups = clusterer.groupNodes(thresh);
+    }
+    else
+    {
+      if (abs ? (height > thresh) : (0 < thresh && thresh < 1))
+      {
+        cut = abs ? thresh : (float) (thresh * height);
+        Console.debug("Threshold " + cut + " for height=" + height);
+        nodegroups = clusterer.groupNodes(cut);
+      }
+      else
+      {
+        nodegroups = new ArrayList<BinaryNode>();
+        nodegroups.add(clusterer.getTopNode());
+      }
+    }
+    
+    List<BitSet> groups = new ArrayList<>();
+    for (BinaryNode root : nodegroups)
+    {
+      BitSet gpset = new BitSet();
+      for (BinaryNode leaf : clusterer.findLeaves(root))
+      {
+        gpset.set((Integer) leaf.element());
+      }
+      groups.add(gpset);
+    }
+    GroupSet grps = new GroupSet(abs, (cut == -1f) ? thresh : cut, groups,
+            treeType, newick);
+    return grps;
+  }
+
+  @Override
+  public List<BitSet> getGroups()
+  {
+    return groups;
+  }
+}