JAL-1645 source formatting and organise imports

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index d0c3829..3024e66 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1385,8 +1385,7 @@ public class JalviewLite extends Applet implements
     String externalsviewer = getParameter("externalstructureviewer");
     if (externalsviewer != null)
     {
-      useXtrnalSviewer = externalsviewer.trim().toLowerCase()
-              .equals(TRUE);
+      useXtrnalSviewer = externalsviewer.trim().toLowerCase().equals(TRUE);
     }
     /**
      * if true disable the check for jmol
@@ -1412,7 +1411,9 @@ public class JalviewLite extends Applet implements
       }
       else
       {
-        throw new Error(MessageManager.getString("error.invalid_separator_parameter"));
+        throw new Error(
+                MessageManager
+                        .getString("error.invalid_separator_parameter"));
       }
     }
     int r = 255;
@@ -1921,7 +1922,8 @@ public class JalviewLite extends Applet implements
       AlignmentI al = null;
       try
       {
-        al = new AppletFormatAdapter().readFile(resolvedFile, protocol, format);
+        al = new AppletFormatAdapter().readFile(resolvedFile, protocol,
+                format);
         if ((al != null) && (al.getHeight() > 0))
         {
           dbgMsg("Successfully loaded file.");
@@ -1939,13 +1941,13 @@ public class JalviewLite extends Applet implements
           if (protocol == AppletFormatAdapter.PASTE)
           {
             newAlignFrame.setTitle(MessageManager.formatMessage(
-                    "label.sequences_from", new Object[]
-                    { applet.getDocumentBase().toString() }));
+                    "label.sequences_from", new Object[] { applet
+                            .getDocumentBase().toString() }));
           }
 
           newAlignFrame.statusBar.setText(MessageManager.formatMessage(
-                  "label.successfully_loaded_file", new Object[]
-                  { resolvedFile }));
+                  "label.successfully_loaded_file",
+                  new Object[] { resolvedFile }));
 
           return newAlignFrame;
         }
@@ -2040,10 +2042,9 @@ public class JalviewLite extends Applet implements
             String sequence = applet.getParameter("PDBSEQ");
             if (sequence != null)
             {
-              seqs = new SequenceI[]
-              { matcher == null ? (Sequence) alignFrame.getAlignViewport()
-                      .getAlignment().findName(sequence) : matcher
-                      .findIdMatch(sequence) };
+              seqs = new SequenceI[] { matcher == null ? (Sequence) alignFrame
+                      .getAlignViewport().getAlignment().findName(sequence)
+                      : matcher.findIdMatch(sequence) };
             }
 
           }
@@ -2125,8 +2126,8 @@ public class JalviewLite extends Applet implements
             }
             else
             {
-              pdbs.addElement(new Object[]
-              { pdb, seqs, chains, new String(protocol) });
+              pdbs.addElement(new Object[] { pdb, seqs, chains,
+                  new String(protocol) });
             }
           }
         }
@@ -2401,8 +2402,7 @@ public class JalviewLite extends Applet implements
         if (debug)
         {
           System.err.println("Prepended document base '" + documentBase
-                  + "' to make: '" + url
-                  + "'");
+                  + "' to make: '" + url + "'");
         }
         return url;
       }
@@ -2911,8 +2911,7 @@ public class JalviewLite extends Applet implements
     if (url.indexOf("/") == 0)
     {
       String localfile = localref.getFile();
-      url = codebase.substring(0, codebase.length()
-              - localfile.length())
+      url = codebase.substring(0, codebase.length() - localfile.length())
               + url;
     }
     else