X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fmc_view%2FPDBChain.java;h=72d276effc349e5481f556ef21ae66fc5eeda635;hb=5d003f492184b893aa4c2f437c6021626b573c45;hp=2a813d0b26da416aff1ca197c6fb27a2147e4bb8;hpb=aeba223cbf5028332d3b1a8fcfad7857bd840409;p=jalview.git

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 2a813d0..72d276e 100755
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -35,6 +35,7 @@ import jalview.util.Comparison;
 
 import java.awt.Color;
 import java.util.List;
+import java.util.Locale;
 import java.util.Vector;
 
 public class PDBChain
@@ -78,11 +79,30 @@ public class PDBChain
 
   public String pdbid = "";
 
-  public PDBChain(String thePdbid, String theId, boolean isAlphaFoldModel)
+  String tfacName = "Temperature Factor";
+
+  public PDBChain(String thePdbid, String theId,
+          String tempFactorColumnName)
   {
-    this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
+    this.pdbid = thePdbid == null ? thePdbid
+            : thePdbid.toLowerCase(Locale.ROOT);
     this.id = theId;
-    this.alphaFoldModel = isAlphaFoldModel;
+    if (tempFactorColumnName != null && tempFactorColumnName.length() > 0)
+    {
+      tfacName = tempFactorColumnName;
+    }
+  }
+
+  /**
+   * import chain data assuming Temperature Factor is in the Temperature Factor
+   * column
+   * 
+   * @param thePdbid
+   * @param theId
+   */
+  public PDBChain(String thePdbid, String theId)
+  {
+    this(thePdbid, theId, null);
   }
 
   /**
@@ -92,8 +112,6 @@ public class PDBChain
 
   public Mapping shadowMap;
 
-  private boolean alphaFoldModel;
-
   public void setNewlineString(String nl)
   {
     newline = nl;
@@ -196,8 +214,8 @@ public class PDBChain
       }
       char seqchar = ds.getCharAt(seqpos - ds.getStart());
 
-      boolean sameResidue = Comparison.isSameResidue(
-              seqchar, strchar, false);
+      boolean sameResidue = Comparison.isSameResidue(seqchar, strchar,
+              false);
       if (sameResidue)
       {
         for (Atom atom : res.atoms)
@@ -215,10 +233,18 @@ public class PDBChain
    * @param seq
    * @param status
    *          The Status of the transferred annotation
+   * 
+   * @param altPDBID
+   *          the group id for the features on the destination sequence (e.g.
+   *          the official accession ID)
    */
-  public void transferRESNUMFeatures(SequenceI seq,
-          String status)
+  public void transferRESNUMFeatures(SequenceI seq, String status,
+          String altPDBID)
   {
+    if (altPDBID == null)
+    {
+      altPDBID = pdbid;
+    }
     SequenceI sq = seq;
     while (sq != null && sq.getDatasetSequence() != null)
     {
@@ -246,12 +272,13 @@ public class PDBChain
       if (feature.getFeatureGroup() != null
               && feature.getFeatureGroup().equals(pdbid))
       {
-        int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms
-                .elementAt(0).alignmentMapping;
+        int newBegin = 1
+                + residues.elementAt(feature.getBegin() - offset).atoms
+                        .elementAt(0).alignmentMapping;
         int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
                 .elementAt(0).alignmentMapping;
         SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
-                feature.getFeatureGroup(), feature.getScore());
+                altPDBID, feature.getScore());
         tx.setStatus(status
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0)
                         ? ""
@@ -396,8 +423,8 @@ public class PDBChain
       {
         String desc = currAtom.resName + ":" + currAtom.resNumIns + " "
                 + pdbid + id;
-        SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset
-                + count - 1, offset + count - 1, "PDB_INS");
+        SequenceFeature sf = new SequenceFeature("INSERTION", desc,
+                offset + count - 1, offset + count - 1, "PDB_INS");
         resFeatures.addElement(sf);
         residues.lastElement().atoms.addAll(resAtoms);
       }
@@ -409,8 +436,8 @@ public class PDBChain
         Residue tmpres = residues.lastElement();
         Atom tmpat = tmpres.atoms.get(0);
         // Make A new SequenceFeature for the current residue numbering
-        String desc = tmpat.resName
-                + ":" + tmpat.resNumIns + " " + pdbid + id;
+        String desc = tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid
+                + id;
         SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc,
                 offset + count, offset + count, pdbid);
         resFeatures.addElement(sf);
@@ -493,15 +520,10 @@ public class PDBChain
         min = Math.min(min, annots[i].value);
         resAnnotation.setElementAt(null, i);
       }
-      String tfacName = "Temperature Factor";
-      if (isAlphaFoldModel())
-      {
-        tfacName = "Alphafold Reliability";
-      }
-      AlignmentAnnotation tfactorann = new AlignmentAnnotation(
-              tfacName, tfacName + " for " + pdbid + id,
-              annots, min, max, AlignmentAnnotation.LINE_GRAPH);
-      
+      AlignmentAnnotation tfactorann = new AlignmentAnnotation(tfacName,
+              tfacName + " for " + pdbid + id, annots, min, max,
+              AlignmentAnnotation.LINE_GRAPH);
+
       tfactorann.setCalcId(getClass().getName());
 
       tfactorann.setSequenceRef(sequence);
@@ -509,11 +531,6 @@ public class PDBChain
     }
   }
 
-  private boolean isAlphaFoldModel()
-  {
-    return alphaFoldModel;
-  }
-
   /**
    * Colour start/end of bonds by charge
    * <ul>