X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalviewLite.java;h=7d66f6d9997df9376d595679eaa0d9a127d8593a;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=a60496c4191bc5fd13ac5a59ccfd299d39aea527;hpb=2a66892874abea357a5e5d9ef2f69919453c31d0;p=jalview.git

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index a60496c..7d66f6d 100644
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -20,6 +20,8 @@
  */
 package jalview.bin;
 
+import java.util.Locale;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.appletgui.AlignFrame;
@@ -198,7 +200,7 @@ public class JalviewLite extends Applet
       int apos = -1;
       try
       {
-        apos = new Integer(position).intValue();
+        apos = Integer.valueOf(position).intValue();
         apos--;
       } catch (NumberFormatException ex)
       {
@@ -207,8 +209,9 @@ public class JalviewLite extends Applet
       final StructureSelectionManagerProvider me = this;
       final int pos = apos;
       // use vamsas listener to broadcast to all listeners in scope
-      if (alignedPosition != null && (alignedPosition.trim().length() == 0
-              || alignedPosition.toLowerCase().indexOf("false") > -1))
+      if (alignedPosition != null
+              && (alignedPosition.trim().length() == 0 || alignedPosition
+                      .toLowerCase(Locale.ROOT).indexOf("false") > -1))
       {
         java.awt.EventQueue.invokeLater(new Runnable()
         {
@@ -337,7 +340,7 @@ public class JalviewLite extends Applet
           int from = -1, to = -1;
           try
           {
-            from = new Integer(cl.substring(0, p)).intValue();
+            from = Integer.valueOf(cl.substring(0, p)).intValue();
             from--;
           } catch (NumberFormatException ex)
           {
@@ -348,7 +351,7 @@ public class JalviewLite extends Applet
           }
           try
           {
-            to = new Integer(cl.substring(p + 1)).intValue();
+            to = Integer.valueOf(cl.substring(p + 1)).intValue();
             to--;
           } catch (NumberFormatException ex)
           {
@@ -408,11 +411,11 @@ public class JalviewLite extends Applet
           int r = -1;
           try
           {
-            r = new Integer(cl).intValue();
+            r = Integer.valueOf(cl).intValue();
             r--;
           } catch (NumberFormatException ex)
           {
-            if (cl.toLowerCase().equals("sequence"))
+            if (cl.toLowerCase(Locale.ROOT).equals("sequence"))
             {
               // we are in the dataset sequence's coordinate frame.
               inseqpos = true;
@@ -1176,7 +1179,7 @@ public class JalviewLite extends Applet
         try
         {
           StructureSelectionManager.getStructureSelectionManager(me)
-                  .mouseOverStructure(new Integer(pdbResNum).intValue(),
+                  .mouseOverStructure(Integer.valueOf(pdbResNum).intValue(),
                           chain, pdbfile);
           if (debug)
           {
@@ -1212,8 +1215,8 @@ public class JalviewLite extends Applet
       {
         try
         {
-          alf.scrollTo(new Integer(topRow).intValue(),
-                  new Integer(leftHandColumn).intValue());
+          alf.scrollTo(Integer.valueOf(topRow).intValue(),
+                  Integer.valueOf(leftHandColumn).intValue());
 
         } catch (Exception ex)
         {
@@ -1244,7 +1247,7 @@ public class JalviewLite extends Applet
       {
         try
         {
-          alf.scrollToRow(new Integer(topRow).intValue());
+          alf.scrollToRow(Integer.valueOf(topRow).intValue());
 
         } catch (Exception ex)
         {
@@ -1276,7 +1279,7 @@ public class JalviewLite extends Applet
       {
         try
         {
-          alf.scrollToColumn(new Integer(leftHandColumn).intValue());
+          alf.scrollToColumn(Integer.valueOf(leftHandColumn).intValue());
 
         } catch (Exception ex)
         {
@@ -1333,7 +1336,7 @@ public class JalviewLite extends Applet
   private boolean alignPdbStructures = false;
 
   /**
-   * use an external structure viewer exclusively (no jmols or MCViews will be
+   * use an external structure viewer exclusively (no jmols or mc_views will be
    * opened by JalviewLite itself)
    */
   public boolean useXtrnalSviewer = false;
@@ -1440,7 +1443,8 @@ public class JalviewLite extends Applet
     String externalsviewer = getParameter("externalstructureviewer");
     if (externalsviewer != null)
     {
-      useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
+      useXtrnalSviewer = externalsviewer.trim().toLowerCase(Locale.ROOT)
+              .equals(TRUE);
     }
     /**
      * if true disable the check for jmol
@@ -1798,7 +1802,7 @@ public class JalviewLite extends Applet
           if (!jmolAvailable)
           {
             System.out.println(
-                    "Jmol not available - Using MCview for structures");
+                    "Jmol not available - Using mc_view for structures");
           }
         } catch (java.lang.ClassNotFoundException ex)
         {
@@ -1810,7 +1814,7 @@ public class JalviewLite extends Applet
         if (debug)
         {
           System.err.println(
-                  "Skipping Jmol check. Will use MCView (probably)");
+                  "Skipping Jmol check. Will use mc_view (probably)");
         }
       }
       checkedForJmol = true;
@@ -2691,7 +2695,7 @@ public class JalviewLite extends Applet
           final String groups, boolean state)
   {
     final boolean st = state;// !(state==null || state.equals("") ||
-    // state.toLowerCase().equals("false"));
+    // state.toLowerCase(Locale.ROOT).equals("false"));
     java.awt.EventQueue.invokeLater(new Runnable()
     {
       @Override