Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppre...

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

diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 425bc18..72d276e 100755 (executable)
--- 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
@@ -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)
@@ -230,12 +234,14 @@ public class PDBChain
    * @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)
+   * @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, String altPDBID)
+  public void transferRESNUMFeatures(SequenceI seq, String status,
+          String altPDBID)
   {
-    if (altPDBID==null)
+    if (altPDBID == null)
     {
       altPDBID = pdbid;
     }
@@ -266,8 +272,9 @@ 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,
@@ -416,8 +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);
       }
@@ -429,8 +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);
@@ -513,10 +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);
@@ -524,7 +531,6 @@ public class PDBChain
     }
   }
 
-
   /**
    * Colour start/end of bonds by charge
    * <ul>