JAL-3929 URLencode pdbid to remove problematic characters - propagate urlEncoded...

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

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 2a813d0..70fda66 100755 (executable)
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -78,11 +78,27 @@ 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.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 +108,6 @@ public class PDBChain
 
   public Mapping shadowMap;
 
-  private boolean alphaFoldModel;
-
   public void setNewlineString(String nl)
   {
     newline = nl;
@@ -215,6 +229,7 @@ public class PDBChain
    * @param seq
    * @param status
    *          The Status of the transferred annotation
+   * @param actualGroupId the group id for the features on the destination sequence (e.g. the official accession ID)
    */
   public void transferRESNUMFeatures(SequenceI seq,
           String status)
@@ -251,7 +266,7 @@ public class PDBChain
         int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
                 .elementAt(0).alignmentMapping;
         SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
-                feature.getFeatureGroup(), feature.getScore());
+                pdbid, feature.getScore());
         tx.setStatus(status
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0)
                         ? ""
@@ -493,11 +508,6 @@ 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);
@@ -509,10 +519,6 @@ public class PDBChain
     }
   }
 
-  private boolean isAlphaFoldModel()
-  {
-    return alphaFoldModel;
-  }
 
   /**
    * Colour start/end of bonds by charge