JAL-2233 reverted changes to Jmol logging levels

[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..ca45d7b 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;
@@ -59,15 +61,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
-  public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
-          boolean externalSecStr, String inFile, String type)
-          throws IOException
+  public JmolParser(String inFile, String type) throws IOException
   {
     super(inFile, type);
   }
 
-  public JmolParser(boolean addAlignmentAnnotations, boolean predictSecStr,
-          boolean externalSecStr, FileParse fp) throws IOException
+  public JmolParser(FileParse fp) throws IOException
   {
     super(fp);
   }
@@ -97,6 +96,18 @@ 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);
     }
   }
@@ -112,6 +123,10 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     {
       try
       {
+        /*
+         * params -o (output to sysout) -n (nodisplay) -x (exit when finished)
+         * see http://wiki.jmol.org/index.php/Jmol_Application
+         */
         viewer = (Viewer) JmolViewer.allocateViewer(null, null, null, null,
                 null, "-x -o -n", this);
         // ensure the 'new' (DSSP) not 'old' (Ramachandran) SS method is used
@@ -217,8 +232,8 @@ 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);
@@ -339,9 +354,9 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         try
         {
-        asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
-                secstrcode[p], Float.NaN);
-        ssFound = true;
+          asecstr[p] = new Annotation(String.valueOf(secstr[p]), null,
+                  secstrcode[p], Float.NaN);
+          ssFound = true;
         } catch (Exception e)
         {
           // e.printStackTrace();