Merge branch 'develop' into feature/JAL-1713_overviewInProject

[jalview.git] / src / jalview / ws / datamodel / alphafold / PAEContactMatrix.java

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
new file mode 100644 (file)
index 0000000..0ac3e00
--- /dev/null
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -0,0 +1,189 @@
+package jalview.ws.datamodel.alphafold;
+
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactListImpl;
+import jalview.datamodel.ContactListProviderI;
+import jalview.datamodel.ContactMatrixI;
+import jalview.datamodel.SequenceI;
+
+public class PAEContactMatrix implements ContactMatrixI
+{
+
+  SequenceI refSeq = null;
+
+  /**
+   * the length that refSeq is expected to be (excluding gaps, of course)
+   */
+  int length;
+
+  int maxrow = 0, maxcol = 0;
+
+  int[] indices1, indices2;
+
+  float[][] elements;
+
+  float maxscore;
+
+  @SuppressWarnings("unchecked")
+  public PAEContactMatrix(SequenceI _refSeq, Map<String, Object> pae_obj)
+          throws Exception
+  {
+    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"))
+    {
+      parse_version_1_pAE(pae_obj);
+      return;
+    }
+    else
+    {
+      parse_version_2_pAE(pae_obj);
+    }
+  }
+
+  /**
+   * parse a sane JSON representation of the pAE
+   * 
+   * @param pae_obj
+   */
+  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();
+    int row = 0, col = 0;
+    while (scoreRows.hasNext())
+    {
+      Iterator<Long> scores = scoreRows.next().iterator();
+      while (scores.hasNext())
+      {
+        elements[row][col++] = scores.next();
+      }
+      row++;
+      col = 0;
+    }
+    maxcol = length;
+    maxrow = length;
+  }
+
+  /**
+   * v1 format got ditched 28th July 2022 see
+   * https://alphafold.ebi.ac.uk/faq#:~:text=We%20updated%20the%20PAE%20JSON%20file%20format%20on%2028th%20July%202022
+   * 
+   * @param pae_obj
+   */
+  private void parse_version_1_pAE(Map<String, Object> pae_obj)
+  {
+    // assume indices are with respect to range defined by _refSeq on the
+    // dataset refSeq
+    Iterator<Long> rows = ((List<Long>) pae_obj.get("residue1")).iterator();
+    Iterator<Long> cols = ((List<Long>) pae_obj.get("residue2")).iterator();
+    Iterator<Double> scores = ((List<Double>) pae_obj.get("distance"))
+            .iterator();
+
+    elements = new float[length][length];
+    while (scores.hasNext())
+    {
+      float escore = scores.next().floatValue();
+      int row = rows.next().intValue();
+      int col = cols.next().intValue();
+      if (maxrow < row)
+      {
+        maxrow = row;
+      }
+      if (maxcol < col)
+      {
+        maxcol = col;
+      }
+      elements[row - 1][col - 1] = escore;
+    }
+
+    maxscore = ((Double) pae_obj.get("max_predicted_aligned_error"))
+            .floatValue();
+  }
+
+  @Override
+  public ContactListI getContactList(final int _column)
+  {
+    if (_column < 0 || _column >= elements.length)
+    {
+      return null;
+    }
+
+    return new ContactListImpl(new ContactListProviderI()
+    {
+      @Override
+      public int getPosition()
+      {
+        return _column;
+      }
+
+      @Override
+      public int getContactHeight()
+      {
+        return maxcol - 1;
+      }
+
+      @Override
+      public double getContactAt(int column)
+      {
+        if (column < 0 || column >= elements[_column].length)
+        {
+          return -1;
+        }
+        // TODO Auto-generated method stub
+        return elements[_column][column];
+      }
+    });
+  }
+
+  @Override
+  public float getMin()
+  {
+    return 0;
+  }
+
+  @Override
+  public float getMax()
+  {
+    return maxscore;
+  }
+
+  @Override
+  public boolean hasReferenceSeq()
+  {
+    return (refSeq != null);
+  }
+
+  @Override
+  public SequenceI getReferenceSeq()
+  {
+    return refSeq;
+  }
+
+  @Override
+  public String getAnnotDescr()
+  {
+    return "Predicted Alignment Error for " + refSeq.getName();
+  }
+
+  @Override
+  public String getAnnotLabel()
+  {
+    return "pAE Matrix";
+
+  }
+}