X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;fp=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=92c762bb861bb38ca1d5e712587aa278eb4e8ce9;hb=e83ce5d8ef826fc0b509a51f154abdf734501077;hp=57b406e16d29d6f9db5b88e7387c140dfc381b15;hpb=786475501a15799d7c4058dbf74e4bf896d03736;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 57b406e..92c762b 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -92,6 +92,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   {
     super(fp, doXferSettings);
   }
+
   public JmolParser(FileParse fp) throws IOException
   {
     super(fp);
@@ -338,7 +339,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       }
     } catch (OutOfMemoryError er)
     {
-      System.out.println(
+      jalview.bin.Console.outPrintln(
               "OUT OF MEMORY LOADING TRANSFORMING JMOL MODEL TO JALVIEW MODEL");
       throw new IOException(MessageManager
               .getString("exception.outofmemory_loading_mmcif_file"));
@@ -391,7 +392,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           org.jmol.modelset.Atom prevAtom,
           HashMap<String, org.jmol.modelset.Atom> chainTerMap)
   {
-    // System.out.println("Atom: " + curAtom.getAtomNumber()
+    // jalview.bin.Console.outPrintln("Atom: " + curAtom.getAtomNumber()
     // + " Last atom index " + curAtom.group.lastAtomIndex);
     if (chainTerMap == null || prevAtom == null)
     {
@@ -488,7 +489,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
   {
     int length = sq.getLength();
     boolean ssFound = false;
-    Annotation asecstr[] = new Annotation[length + (firstResNum-sq.getStart())];
+    Annotation asecstr[] = new Annotation[length
+            + (firstResNum - sq.getStart())];
     for (int p = 0; p < length; p++)
     {
       if (secstr[p] >= 'A' && secstr[p] <= 'z')