--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff