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 ddb4492..ca45d7b 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -61,15 +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);
   }
@@ -126,6 +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
@@ -353,9 +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();