From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 20 Aug 2021 14:12:11 +0000 (+0100)
Subject: JAL-3855 JAL-2349 (d0h) class for holding and accessing PAE as a contact matrix
X-Git-Tag: Release_2_11_4_0~562^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b5ea0bbb85bef19c50fb4341bda9e9da9ef09b13;p=jalview.git

JAL-3855 JAL-2349 (d0h) class for holding and accessing PAE as a contact matrix
---

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
new file mode 100644
index 0000000..e61af44
--- /dev/null
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -0,0 +1,107 @@
+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.ContactRange;
+import jalview.datamodel.SequenceI;
+
+public class PAEContactMatrix implements ContactMatrixI
+{
+
+  SequenceI refSeq=null;
+  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
+    int length = _refSeq.getEnd()-_refSeq.getStart()+1;
+    
+    // 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)
+  {
+    
+    return new ContactListImpl(new ContactListProviderI() 
+    {
+      @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;
+  }
+
+}