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;
+ }
+
+ @SuppressWarnings("unchecked")
+ public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
+ {
+ setRefSeq(_refSeq);
+ // convert the lists to primitive arrays and store
- if (!pae_obj.containsKey("predicted_aligned_error"))
+ 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];
}
});
@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";
+
+ @Override
+ public String getType()
+ {
+ return PAEMATRIX;
+ }
+
+ @Override
+ public int getWidth()
+ {
+ return length;
+ }
+ @Override
+ public int getHeight()
+ {
+ return length;
}
}