JAL-4274 comments to help follow the tests

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

diff --git a/src/jalview/bin/JalviewLiteURLRetrieve.java b/src/jalview/bin/JalviewLiteURLRetrieve.java
index 156e146..d38892a 100644 (file)
--- a/src/jalview/bin/JalviewLiteURLRetrieve.java
+++ b/src/jalview/bin/JalviewLiteURLRetrieve.java
@@ -25,6 +25,7 @@ import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
 import jalview.io.FileParse;
 import jalview.io.IdentifyFile;
 
@@ -63,7 +64,7 @@ public class JalviewLiteURLRetrieve extends Applet
     DataSourceType protocol = null;
     try
     {
-      System.out.println("Loading thread started with:\n>>file\n" + file
+      jalview.bin.Console.outPrintln("Loading thread started with:\n>>file\n" + file
               + ">>endfile");
       // This might throw a security exception in certain browsers
       // Netscape Communicator for instance.
@@ -76,7 +77,7 @@ public class JalviewLiteURLRetrieve extends Applet
           rtn = true;
           is.close();
         }
-        System.err.println("Resource '" + file + "' was "
+        jalview.bin.Console.errPrintln("Resource '" + file + "' was "
                 + (rtn ? "" : "not") + " located by classloader.");
         if (rtn)
         {
@@ -85,8 +86,8 @@ public class JalviewLiteURLRetrieve extends Applet
 
       } catch (Exception ex)
       {
-        System.out.println("Exception checking resources: " + file + " "
-                + ex);
+        jalview.bin.Console.outPrintln(
+                "Exception checking resources: " + file + " " + ex);
       }
       if (file.indexOf("://") > -1)
       {
@@ -98,7 +99,7 @@ public class JalviewLiteURLRetrieve extends Applet
         protocol = DataSourceType.FILE;
       }
 
-      System.out.println("Trying to get contents of resource:");
+      jalview.bin.Console.outPrintln("Trying to get contents of resource:");
       FileParse fp = new FileParse(file, protocol);
       if (fp.isValid())
       {
@@ -111,19 +112,20 @@ public class JalviewLiteURLRetrieve extends Applet
       }
       else
       {
-        System.out.println("Resource at " + file
+        jalview.bin.Console.outPrintln("Resource at " + file
                 + " cannot be read with protocol==" + protocol);
         return;
       }
-      FileFormatI format = FileFormat.valueOf(getParameter("format"));
+      FileFormatI format = FileFormats.getInstance()
+              .forName(getParameter("format"));
       if (format == null)
       {
         format = new IdentifyFile().identify(file, protocol);
-        System.out.println("Format is " + format);
+        jalview.bin.Console.outPrintln("Format is " + format);
       }
       else
       {
-        System.out.println("User specified Format is " + format);
+        jalview.bin.Console.outPrintln("User specified Format is " + format);
       }
       AlignmentI al = null;
       try
@@ -131,17 +133,17 @@ public class JalviewLiteURLRetrieve extends Applet
         al = new AppletFormatAdapter().readFile(file, protocol, format);
       } catch (java.io.IOException ex)
       {
-        System.err.println("Failed to open the file.");
+        jalview.bin.Console.errPrintln("Failed to open the file.");
         ex.printStackTrace();
       }
       if (al != null)
       {
-        System.out.println(new AppletFormatAdapter().formatSequences(
-                FileFormat.Fasta, al, false));
+        jalview.bin.Console.outPrintln(new AppletFormatAdapter()
+                .formatSequences(FileFormat.Fasta, al, false));
       }
     } catch (Exception e)
     {
-      System.err.println("bailing out : Unexpected exception:");
+      jalview.bin.Console.errPrintln("bailing out : Unexpected exception:");
       e.printStackTrace();
     }
   }