package jalview.ws.datamodel.alphafold;
+import java.util.ArrayList;
+import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import jalview.analysis.AverageDistanceEngine;
+import jalview.bin.Console;
+import jalview.datamodel.BinaryNode;
import jalview.datamodel.ContactListI;
import jalview.datamodel.ContactListImpl;
import jalview.datamodel.ContactListProviderI;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.SequenceI;
+import jalview.util.MapUtils;
public class PAEContactMatrix implements ContactMatrixI
{
float maxscore;
- @SuppressWarnings("unchecked")
- public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
- throws Exception
+ private void setRefSeq(SequenceI _refSeq)
{
refSeq = _refSeq;
while (refSeq.getDatasetSequence() != null)
{
refSeq = refSeq.getDatasetSequence();
}
- // convert the lists to primitive arrays and store
length = _refSeq.getEnd() - _refSeq.getStart() + 1;
+ }
- if (!pae_obj.containsKey("predicted_aligned_error"))
+ @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);
return;
}
/**
+ * 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)
+ {
+ if (row.length > maxcol)
+ {
+ maxcol = row.length;
+ }
+ maxscore = row[0];
+ for (float f : row)
+ {
+ if (maxscore < f)
+ {
+ maxscore = f;
+ }
+ }
+ }
+ maxrow = matrix.length;
+ elements = matrix;
+
+ }
+
+ /**
* parse a sane JSON representation of the pAE
*
* @param pae_obj
*/
+ @SuppressWarnings("unchecked")
private void parse_version_2_pAE(Map<String, Object> pae_obj)
{
- elements = new float[length][length];
// this is never going to be reached by the integer rounding.. or is it ?
- maxscore = ((Double) pae_obj.get("max_predicted_aligned_error"))
- .floatValue();
- Iterator<List<Long>> scoreRows = ((List<List<Long>>) pae_obj
- .get("predicted_aligned_error")).iterator();
+ 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"));
+ elements = new float[scoreRows.size()][scoreRows.size()];
int row = 0, col = 0;
- while (scoreRows.hasNext())
+ for (List<Long> scoreRow : scoreRows)
{
- Iterator<Long> scores = scoreRows.next().iterator();
+ Iterator<Long> scores = scoreRow.iterator();
while (scores.hasNext())
{
- elements[row][col++] = scores.next();
+ Object d = scores.next();
+ if (d instanceof Double)
+ elements[row][col++] = ((Double) d).longValue();
+ else
+ elements[row][col++] = (float) ((Long) d).longValue();
}
row++;
col = 0;
*
* @param pae_obj
*/
+ @SuppressWarnings("unchecked")
private void parse_version_1_pAE(Map<String, Object> pae_obj)
{
// assume indices are with respect to range defined by _refSeq on the
Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
.iterator();
-
+ // assume square matrix
elements = new float[length][length];
while (scores.hasNext())
{
elements[row - 1][col - 1] = escore;
}
- maxscore = ((Double) pae_obj.get("max_predicted_aligned_error"))
- .floatValue();
+ maxscore = ((Double) MapUtils.getFirst(pae_obj,
+ "max_predicted_aligned_error", "max_pae")).floatValue();
}
@Override
{
return -1;
}
- // TODO Auto-generated method stub
return elements[_column][column];
}
});
return refSeq;
}
+ @Override
+ public String getAnnotDescr()
+ {
+ return "Predicted Alignment Error 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;
+ public String getNewickString()
+ {
+ return newick;
+ }
+ 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 BitSet getGroupsFor(int column)
+ {
+ for (BitSet gp:groups) {
+ if (gp.get(column))
+ {
+ return gp;
+ }
+ }
+ return ContactMatrixI.super.getGroupsFor(column);
+ }
+
+ 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