JAL-4059 update Jmol and JSmol to 15.2.69 - revised Jalview classes interating with...

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

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 70fda66..e854247 100755 (executable)
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -20,6 +20,11 @@
  */
 package mc_view;
 
+import java.awt.Color;
+import java.util.List;
+import java.util.Locale;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -33,10 +38,6 @@ import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureMapping;
 import jalview.util.Comparison;
 
-import java.awt.Color;
-import java.util.List;
-import java.util.Vector;
-
 public class PDBChain
 {
   public static final String RESNUM_FEATURE = "RESNUM";
@@ -80,25 +81,28 @@ public class PDBChain
 
   String tfacName = "Temperature Factor";
 
-
-  public PDBChain(String thePdbid, String theId, String tempFactorColumnName)
+  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;
-    if (tempFactorColumnName!=null && tempFactorColumnName.length()>0)
+    if (tempFactorColumnName != null && tempFactorColumnName.length() > 0)
     {
       tfacName = tempFactorColumnName;
     }
   }
 
   /**
-   * import chain data assuming Temperature Factor is in the Temperature Factor column
+   * 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);
+    this(thePdbid, theId, null);
   }
 
   /**
@@ -210,8 +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)
@@ -229,11 +233,18 @@ 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)
+   * 
+   * @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)
     {
@@ -261,12 +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,
-                pdbid, feature.getScore());
+                altPDBID, feature.getScore());
         tx.setStatus(status
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0)
                         ? ""
@@ -411,8 +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);
       }
@@ -424,12 +436,12 @@ 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);
-        resAnnotation.addElement(new Annotation(tmpat.tfactor));
+        resAnnotation.addElement(new Annotation((float) tmpat.tfactor));
         // Keep totting up the sequence
 
         if ((symbol = ResidueProperties.getAA3Hash()
@@ -508,10 +520,10 @@ public class PDBChain
         min = Math.min(min, annots[i].value);
         resAnnotation.setElementAt(null, i);
       }
-      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);
@@ -519,7 +531,6 @@ public class PDBChain
     }
   }
 
-
   /**
    * Colour start/end of bonds by charge
    * <ul>
@@ -683,8 +694,8 @@ public class PDBChain
         // Useful for debugging mappings - adds annotation for mapped position
         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++)
+        for (int i = sq.getStart(), j = sq.getEnd(),
+                k = 0; i <= j; i++, k++)
         {
           int prn = mapping.getPDBResNum(k + 1);