JAL-2164 create RESNUM features with padding the same as for pre 2.10 features

[jalview.git] / src / jalview / ext / jmol / JmolParser.java

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 7c3ff42..ddb4492 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -22,11 +22,13 @@ package jalview.ext.jmol;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureImportSettings;
+import jalview.util.Format;
 import jalview.util.MessageManager;
 
 import java.io.IOException;
@@ -97,6 +99,18 @@ public class JmolParser extends StructureFile implements JmolStatusListener
      */
     if (jmolModel.ms.mc > 0)
     {
+      // ideally we do this
+      // try
+      // {
+      // setStructureFileType(jmolModel.evalString("show _fileType"));
+      // } catch (Exception q)
+      // {
+      // }
+      // ;
+      // instead, we distinguish .cif from non-.cif by filename
+      setStructureFileType(getDataName().toLowerCase().endsWith(".cif") ? PDBEntry.Type.MMCIF
+              .toString() : "PDB");
+
       transformJmolModelToJalview(jmolModel.ms);
     }
   }
@@ -217,8 +231,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         curAtom.resNumber = atom.getResno();
         curAtom.occupancy = ms.occupancies != null ? ms.occupancies[atom
                 .getIndex()] : Float.valueOf(atom.getOccupancy100());
-        curAtom.resNumIns = ("" + curAtom.resNumber + curAtom.insCode)
-                .trim();
+        String fmt = new Format("%4i").form(curAtom.resNumber);
+        curAtom.resNumIns = (fmt + curAtom.insCode);
         curAtom.tfactor = atom.getBfactor100() / 100f;
         curAtom.type = 0;
         // significantAtoms.add(curAtom);