transfer of residue numbering as alignment annotation

[jalview.git] / src / MCview / PDBChain.java

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index dc3743e..33944fd 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -25,6 +25,7 @@ import java.awt.*;
 import jalview.analysis.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.structure.StructureMapping;
 
 public class PDBChain
 {
@@ -65,7 +66,7 @@ public class PDBChain
     return tmp;
   }
 
-  void makeExactMapping(AlignSeq as, Sequence s1)
+  public void makeExactMapping(AlignSeq as, SequenceI s1)
   {
     int pdbpos = as.getSeq2Start() - 2;
     int alignpos = s1.getStart() + as.getSeq1Start() - 3;
@@ -94,7 +95,6 @@ public class PDBChain
       }
     }
   }
-
   /**
    * copy over the RESNUM seqfeatures from the internal chain sequence to the mapped sequence
    * @param seq
@@ -104,13 +104,13 @@ public class PDBChain
   public SequenceFeature[] transferRESNUMFeatures(SequenceI seq, String status)
   {
     SequenceI sq = seq;
-    while (sq != null)
+    while (sq!=null && sq.getDatasetSequence()!=null)
     {
+      sq = sq.getDatasetSequence();
       if (sq == sequence)
       {
         return null;
       }
-      sq = sq.getDatasetSequence();
     }
     /**
      * Remove any existing features for this chain if they exist ?
@@ -138,7 +138,8 @@ public class PDBChain
         tx.setStatus(status +
                      ( (tx.getStatus() == null || tx.getStatus().length() == 0) ?
                       "" : ":" + tx.getStatus()));
-        seq.addSequenceFeature(tx);
+        if (tx.begin!=0 && tx.end!=0)
+          sq.addSequenceFeature(tx);
       }
     }
     return features;
@@ -188,6 +189,7 @@ public class PDBChain
     int count = 0;
     StringBuffer seq = new StringBuffer();
     Vector resFeatures = new Vector();
+    Vector resAnnotation = new Vector();
     int i, iSize = atoms.size() - 1;
     int resNumber = -1;
     for (i = 0; i <= iSize; i++)
@@ -235,6 +237,7 @@ public class PDBChain
                               "", offset + count, offset + count,
                               MCview.PDBChain.PDBFILEFEATURE);
       resFeatures.addElement(sf);
+      resAnnotation.addElement(new Annotation(tmpat.tfactor));
       // Keep totting up the sequence
       if (ResidueProperties.getAA3Hash().get(tmpat.resName) == null)
       {
@@ -252,9 +255,9 @@ public class PDBChain
       count++;
     }
 
-    if (id.length() < 1 || id.equals(" "))
+    if (id.length() < 1)
     {
-      id = "_";
+      id = " ";
     }
 
     sequence = new Sequence(id, seq.toString(), offset, resNumber - 1); // Note: resNumber-offset ~= seq.size()
@@ -265,6 +268,19 @@ public class PDBChain
       sequence.addSequenceFeature( (SequenceFeature) resFeatures.elementAt(i));
       resFeatures.setElementAt(null, i);
     }
+    Annotation[] annots = new Annotation[resAnnotation.size()];
+    float max=0;
+    for (i=0,iSize=annots.length; i<iSize; i++)
+    {
+      annots[i] = (Annotation) resAnnotation.elementAt(i);
+      if (annots[i].value>max)
+        max = annots[i].value;
+      resAnnotation.setElementAt(null, i);
+    }
+    AlignmentAnnotation tfactorann = new AlignmentAnnotation("PDB.CATempFactor","CA Temperature Factor for "+sequence.getName(), 
+            annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
+    tfactorann.setSequenceRef(sequence);
+    sequence.addAlignmentAnnotation(tfactorann);
   }
 
   public void setChargeColours()
@@ -359,4 +375,51 @@ public class PDBChain
       tmp.endCol = col;
     }
   }
+
+  public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq, String status)
+  {
+    AlignmentAnnotation[] transferred = null;
+    
+    return transferred;
+    
+  }
+
+  /**
+   * copy any sequence annotation onto the sequence mapped using the provided StructureMapping
+   * @param mapping
+   */
+  public void transferResidueAnnotation(StructureMapping mapping)
+  {
+    SequenceI sq = mapping.getSequence();
+    if (sq!=null)
+    {
+      if (sequence!=null && sequence.getAnnotation()!=null)
+      {
+        
+      }
+      float min=-1,max=0;
+      Annotation[] an=new Annotation[sq.getEnd()-sq.getStart()+1];
+      for (int i=sq.getStart(),j=sq.getEnd(),k=0; i<=j; i++,k++)
+      {
+        int prn = mapping.getPDBResNum(k+1);
+
+        an[k] = new Annotation((float)prn);
+        if (min==-1)
+        {
+          min=k;
+          max=k;
+        } else {
+          if (min>k)
+          {
+            min=k;
+          } else 
+            if (max<k)
+            {
+              max=k;
+            }
+        }
+      }
+      sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM", "PDB Residue Numbering for "+this.pdbid+":"+this.id, an, (float)min,(float)max, AlignmentAnnotation.LINE_GRAPH));
+    }
+  }
 }