+ @Override
+ public String getAnnotDescr()
+ {
+ return "Predicted Alignment Error"
+ + ((refSeq == null) ? "" : (" for " + refSeq.getName()));
+ }
+
+ @Override
+ public String getAnnotLabel()
+ {
+ StringBuilder label = new StringBuilder("PAE Matrix");
+ // if (this.getReferenceSeq() != null)
+ // {
+ // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+ // }
+ return label.toString();
+ }
+
+ public static final String PAEMATRIX = "PAE_MATRIX";
+
+ @Override
+ public String getType()
+ {
+ return PAEMATRIX;
+ }
+
+ @Override
+ public int getWidth()
+ {
+ return length;
+ }
+
+ @Override
+ public int getHeight()
+ {
+ return length;
+ }
+
+ List<BitSet> groups = null;
+
+ @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;
+
+ double thresh;
+
+ String treeType = null;
+
+ public void makeGroups(float thresh, boolean abs)
+ {
+ AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
+ this);
+ double height = clusterer.findHeight(clusterer.getTopNode());
+ newick = new jalview.io.NewickFile(clusterer.getTopNode(), false, true)
+ .print();
+ treeType = "UPGMA";
+ Console.trace("Newick string\n" + newick);
+
+ List<BinaryNode> nodegroups;
+ if (abs ? height > thresh : 0 < thresh && thresh < 1)
+ {
+ float cut = abs ? (float) (thresh / height) : thresh;
+ Console.debug("Threshold " + cut + " for height=" + height);
+
+ nodegroups = clusterer.groupNodes(cut);
+ }
+ else
+ {
+ nodegroups = new ArrayList<BinaryNode>();
+ nodegroups.add(clusterer.getTopNode());
+ }
+ this.abs = abs;
+ this.thresh = thresh;
+ 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);
+ }
+ }
+
+ @Override
+ public void updateGroups(List<BitSet> colGroups)
+ {
+ if (colGroups != null)
+ {
+ groups = colGroups;
+ }
+ }
+
+ @Override
+ public BitSet getGroupsFor(int column)
+ {
+ for (BitSet gp : groups)
+ {
+ if (gp.get(column))
+ {
+ return gp;
+ }
+ }
+ return ContactMatrixI.super.getGroupsFor(column);
+ }
+
+ 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);
+ }
+
+ 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;
+ }