X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=8bc5a986ebf291db9c8185324e7d24a1b347efa9;hb=a7a16a1cc2d9b2c840d50b02163cbc6327bd28bb;hp=18d8e05555d4101a2d9c101badf9c3f164609ea7;hpb=75aa2f504257f5564e3a88c3677905d7c392f24e;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 18d8e05..8bc5a98 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -20,6 +20,8 @@
  */
 package jalview.ext.jmol;
 
+import java.util.Locale;
+
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
@@ -115,9 +117,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       // }
       // ;
       // instead, we distinguish .cif from non-.cif by filename
-      setStructureFileType(getDataName().toLowerCase().endsWith(".cif")
-              ? PDBEntry.Type.MMCIF.toString()
-              : "PDB");
+      setStructureFileType(
+              getDataName().toLowerCase(Locale.ROOT).endsWith(".cif")
+                      ? PDBEntry.Type.MMCIF.toString()
+                      : "PDB");
 
       transformJmolModelToJalview(jmolModel.ms);
     }
@@ -138,7 +141,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
          * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
          * see http://wiki.jmol.org/index.php/Jmol_Application
          */
-        
+
         viewer = JalviewJmolBinding.getJmolData(this);
         // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
         viewer.setBooleanProperty("defaultStructureDSSP", true);
@@ -152,28 +155,32 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     }
     return viewer;
   }
-  
+
   public static Regex getNewAlphafoldValidator()
   {
-    Regex validator =  new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+    Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
     validator.setIgnoreCase(true);
     return validator;
   }
 
-  PDBEntry.Type jmolFiletype=null;
+  PDBEntry.Type jmolFiletype = null;
+
   /**
-   * resolve a jmol filetype string and update the jmolFiletype field accordingly
+   * resolve a jmol filetype string and update the jmolFiletype field
+   * accordingly
+   * 
    * @param jmolIdentifiedFileType
    * @return true if filetype was identified as MMCIF, PDB
    */
   public boolean updateFileType(String jmolIdentifiedFileType)
   {
-    if (jmolIdentifiedFileType == null 
+    if (jmolIdentifiedFileType == null
             || jmolIdentifiedFileType.trim().equals(""))
     {
       return false;
     }
-    if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType)) {
+    if ("mmcif".equalsIgnoreCase(jmolIdentifiedFileType))
+    {
       jmolFiletype = PDBEntry.Type.MMCIF;
       return true;
     }
@@ -181,10 +188,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     {
       jmolFiletype = PDBEntry.Type.PDB;
       return true;
-    } 
+    }
     return false;
   }
-  
+
   public void transformJmolModelToJalview(ModelSet ms) throws IOException
   {
     try
@@ -201,9 +208,9 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setStructureFileType(jmolFiletype.toString());
       }
-      
+
       isMMCIF = PDBEntry.Type.MMCIF.equals(jmolFiletype);
-      
+
       if (pdbId == null)
       {
         setId(safeName(getDataName()));
@@ -213,7 +220,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setId(pdbId);
         setPDBIdAvailable(true);
-        alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;  
+        alphaFoldModel = alphaFold.search(pdbId) && isMMCIF;
 
       }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
@@ -228,15 +235,16 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         if (tmpchain != null)
         {
           tmpchain.atoms.addElement(tmpatom);
-        } else
+        }
+        else
         {
-          String tempFString=null;
+          String tempFString = null;
           if (isAlphafoldModel())
           {
             tempFString = "Alphafold Reliability";
           }
 
-          tmpchain = new PDBChain(getId(), tmpatom.chain,tempFString);
+          tmpchain = new PDBChain(getId(), tmpatom.chain, tempFString);
           getChains().add(tmpchain);
           tmpchain.atoms.addElement(tmpatom);
         }
@@ -426,7 +434,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   {
     int length = sq.getLength();
     boolean ssFound = false;
-    Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+    Annotation asecstr[] = new Annotation[length + (firstResNum-sq.getStart())];
     for (int p = 0; p < length; p++)
     {
       if (secstr[p] >= 'A' && secstr[p] <= 'z')