@Override
public String getAnnotDescr()
{
- return "Predicted Alignment Error"+((refSeq==null) ? "" : (" for " + refSeq.getName()));
+ 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));
- //}
+ // if (this.getReferenceSeq() != null)
+ // {
+ // label.append(":").append(this.getReferenceSeq().getDisplayId(false));
+ // }
return label.toString();
}
{
return length;
}
- List<BitSet> groups=null;
+
+ List<BitSet> groups = null;
+
@Override
public boolean hasGroups()
{
- return groups!=null;
+ return groups != null;
}
- String newick=null;
+
+ String newick = null;
+
@Override
public String getNewick()
{
return newick;
}
+
@Override
public boolean hasTree()
{
- return newick!=null && newick.length()>0;
+ return newick != null && newick.length() > 0;
}
+
boolean abs;
+
double thresh;
- String treeType=null;
- public void makeGroups(float thresh,boolean abs)
+
+ String treeType = null;
+
+ public void makeGroups(float thresh, boolean abs)
{
- AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, this);
+ AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null,
+ this);
double height = clusterer.findHeight(clusterer.getTopNode());
- newick = new jalview.io.NewickFile(clusterer.getTopNode(),false,true).print();
+ newick = new jalview.io.NewickFile(clusterer.getTopNode(), false, true)
+ .print();
treeType = "UPGMA";
- Console.trace("Newick string\n"+newick);
+ 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);
+ Console.debug("Threshold " + cut + " for height=" + height);
nodegroups = clusterer.groupNodes(cut);
}
nodegroups = new ArrayList<BinaryNode>();
nodegroups.add(clusterer.getTopNode());
}
- this.abs=abs;
- this.thresh=thresh;
+ this.abs = abs;
+ this.thresh = thresh;
groups = new ArrayList<>();
- for (BinaryNode root:nodegroups)
+ for (BinaryNode root : nodegroups)
{
- BitSet gpset=new BitSet();
- for (BinaryNode leaf:clusterer.findLeaves(root))
+ BitSet gpset = new BitSet();
+ for (BinaryNode leaf : clusterer.findLeaves(root))
{
- gpset.set((Integer)leaf.element());
+ gpset.set((Integer) leaf.element());
}
groups.add(gpset);
}
}
+
@Override
public void updateGroups(List<BitSet> colGroups)
{
- if (colGroups!=null)
+ if (colGroups != null)
{
- groups=colGroups;
- }
+ groups = colGroups;
+ }
}
+
@Override
public BitSet getGroupsFor(int column)
{
- for (BitSet gp:groups) {
+ for (BitSet gp : groups)
+ {
if (gp.get(column))
{
return gp;
return ContactMatrixI.super.getGroupsFor(column);
}
- HashMap<BitSet,Color> colorMap = new HashMap<>();
- @Override
+ HashMap<BitSet, Color> colorMap = new HashMap<>();
+
+ @Override
public Color getColourForGroup(BitSet bs)
{
- if (bs==null) {
+ if (bs == null)
+ {
return Color.white;
}
- Color groupCol=colorMap.get(bs);
- if (groupCol==null)
+ Color groupCol = colorMap.get(bs);
+ if (groupCol == null)
{
return Color.white;
}
return groupCol;
}
- @Override
- public void setColorForGroup(BitSet bs,Color color)
+
+ @Override
+ public void setColorForGroup(BitSet bs, Color color)
{
- colorMap.put(bs,color);
+ colorMap.put(bs, color);
}
+
public void restoreGroups(List<BitSet> newgroups, String treeMethod,
String tree, double thresh2)
{
- treeType=treeMethod;
+ treeType = treeMethod;
groups = newgroups;
- thresh=thresh2;
- newick =tree;
-
+ thresh = thresh2;
+ newick = tree;
+
}
+
@Override
- public boolean hasCutHeight() {
- return groups!=null && thresh!=0;
+ public boolean hasCutHeight()
+ {
+ return groups != null && thresh != 0;
}
+
@Override
public double getCutHeight()
{
return thresh;
}
+
@Override
public String getTreeMethod()
{