Merge branch 'features/r2_11_2_alphafold/JAL-629' into features/JAL-3858_PAEsInProjects

[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
index 0ac3e00..0349417 100644 (file)
--- 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 +29,22 @@ 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;
@@ -50,27 +54,60 @@ public class PAEContactMatrix implements ContactMatrixI
       parse_version_2_pAE(pae_obj);
     }
   }
+  /**
+   * 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();
+    Iterator<List<Long>> scoreRows = ((List<List<Long>>) MapUtils
+            .getFirst(pae_obj, "predicted_aligned_error", "pae"))
+            .iterator();
     int row = 0, col = 0;
     while (scoreRows.hasNext())
     {
       Iterator<Long> scores = scoreRows.next().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) d;
       }
       row++;
       col = 0;
@@ -85,6 +122,7 @@ 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
@@ -111,8 +149,8 @@ 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
@@ -134,7 +172,7 @@ public class PAEContactMatrix implements ContactMatrixI
       @Override
       public int getContactHeight()
       {
-        return maxcol - 1;
+        return maxcol-1;
       }
 
       @Override
@@ -144,7 +182,6 @@ public class PAEContactMatrix implements ContactMatrixI
         {
           return -1;
         }
-        // TODO Auto-generated method stub
         return elements[_column][column];
       }
     });
@@ -184,6 +221,22 @@ public class PAEContactMatrix implements ContactMatrixI
   public String getAnnotLabel()
   {
     return "pAE Matrix";
+  }
 
+  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;
   }
 }