package jalview.ws.datamodel.alphafold;
+import java.awt.Color;
import java.util.ArrayList;
import java.util.BitSet;
+import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
}
length = _refSeq.getEnd() - _refSeq.getStart() + 1;
}
+
@SuppressWarnings("unchecked")
public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
{
setRefSeq(_refSeq);
// convert the lists to primitive arrays and store
-
+
if (!MapUtils.containsAKey(pae_obj, "predicted_aligned_error", "pae"))
{
parse_version_1_pAE(pae_obj);
parse_version_2_pAE(pae_obj);
}
}
+
/**
* construct a sequence associated PAE matrix directly from a float array
+ *
* @param _refSeq
* @param matrix
*/
public PAEContactMatrix(SequenceI _refSeq, float[][] matrix)
{
setRefSeq(_refSeq);
- maxcol=0;
- for (float[] row:matrix)
+ maxcol = 0;
+ for (float[] row : matrix)
{
- if (row.length>maxcol)
+ if (row.length > maxcol)
{
- maxcol=row.length;
+ maxcol = row.length;
}
- maxscore=row[0];
- for (float f:row)
+ maxscore = row[0];
+ for (float f : row)
{
- if (maxscore<f) {
- maxscore=f;
+ if (maxscore < f)
+ {
+ maxscore = f;
}
}
}
- maxrow=matrix.length;
+ maxrow = matrix.length;
elements = matrix;
-
+
}
/**
maxscore = ((Double) MapUtils.getFirst(pae_obj,
"max_predicted_aligned_error", "max_pae")).floatValue();
List<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
- .getFirst(pae_obj, "predicted_aligned_error", "pae"))
- ;
+ .getFirst(pae_obj, "predicted_aligned_error", "pae"));
elements = new float[scoreRows.size()][scoreRows.size()];
int row = 0, col = 0;
- for (List<Long> scoreRow:scoreRows)
+ for (List<Long> scoreRow : scoreRows)
{
Iterator<Long> scores = scoreRow.iterator();
while (scores.hasNext())
if (d instanceof Double)
elements[row][col++] = ((Double) d).longValue();
else
- elements[row][col++] = (float) ((Long)d).longValue();
+ elements[row][col++] = (float) ((Long) d).longValue();
}
row++;
col = 0;
@Override
public int getContactHeight()
{
- return maxcol-1;
+ return maxcol - 1;
}
@Override
@Override
public String getAnnotDescr()
{
- return "Predicted Alignment Error for " + refSeq.getName();
+ return "Predicted Alignment Error"
+ + ((refSeq == null) ? "" : (" for " + refSeq.getName()));
}
@Override
public String getAnnotLabel()
{
- return "pAE Matrix";
+ 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";
+ 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;
+
+ List<BitSet> groups = null;
+
@Override
public boolean hasGroups()
{
- return groups!=null;
+ return groups != null;
}
- String newick=null;
- public String getNewickString()
+
+ String newick = null;
+
+ @Override
+ public String getNewick()
{
return newick;
}
- public void makeGroups(float thresh,boolean abs)
+
+ @Override
+ public boolean hasTree()
{
- AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, this);
- double height = clusterer.findHeight(clusterer.getTopNode());
- newick = new jalview.io.NewickFile(clusterer.getTopNode(),false,true).print();
+ return newick != null && newick.length() > 0;
+ }
+
+ boolean abs;
+
+ double thresh;
- Console.trace("Newick string\n"+newick);
+ 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);
+ 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;
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)
+ {
+ 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
+ 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff