X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdatamodel%2Falphafold%2FPAEContactMatrix.java;h=cefdbd21b7a68edc6d24bcd9f2fa5d1d1ef3b9b5;hb=d42b7588a34477b24ce97ba75788536e74e6cf86;hp=3a8e26a0654006453073739ab8cb9c9c1807ba91;hpb=71b8b157747abb849fb50316450a22d4559873da;p=jalview.git

diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
index 3a8e26a..cefdbd2 100644
--- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java
@@ -9,6 +9,7 @@ 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
 {
@@ -28,19 +29,23 @@ 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;
@@ -52,25 +57,60 @@ public class PAEContactMatrix implements ContactMatrixI
   }
 
   /**
+   * 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;
@@ -85,6 +125,7 @@ public class PAEContactMatrix implements ContactMatrixI
    * 
    * @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
@@ -93,7 +134,7 @@ public class PAEContactMatrix implements ContactMatrixI
     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())
     {
@@ -111,8 +152,8 @@ public class PAEContactMatrix implements ContactMatrixI
       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
@@ -126,6 +167,12 @@ public class PAEContactMatrix implements ContactMatrixI
     return new ContactListImpl(new ContactListProviderI()
     {
       @Override
+      public int getPosition()
+      {
+        return _column;
+      }
+
+      @Override
       public int getContactHeight()
       {
         return maxcol - 1;
@@ -138,7 +185,6 @@ public class PAEContactMatrix implements ContactMatrixI
         {
           return -1;
         }
-        // TODO Auto-generated method stub
         return elements[_column][column];
       }
     });
@@ -168,4 +214,38 @@ public class PAEContactMatrix implements ContactMatrixI
     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;
+  }
 }