Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / util / GroupUrlLink.java

diff --git a/src/jalview/util/GroupUrlLink.java b/src/jalview/util/GroupUrlLink.java
index a26dfbb..af0b308 100644 (file)
--- a/src/jalview/util/GroupUrlLink.java
+++ b/src/jalview/util/GroupUrlLink.java
@@ -36,6 +36,7 @@ public class GroupUrlLink
 
     public int urlLength;
 
+    @Override
     public String toString()
     {
       return "Generated url is estimated to be too long (" + urlLength
@@ -317,10 +318,12 @@ public class GroupUrlLink
   private String _replaceFor(String token)
   {
     for (int i = 0; i < mtch.length; i++)
+    {
       if (segs[i] > -1 && mtch[i].equals(token))
       {
         return regexReplace[i];
       }
+    }
     return null;
   }
 
@@ -582,7 +585,7 @@ public class GroupUrlLink
               // debug
               /*
                * for (int s = 0; s <= rg.numSubs(); s++) {
-               * System.err.println("Sub " + s + " : " + rg.matchedFrom(s) +
+               * jalview.bin.Console.errPrintln("Sub " + s + " : " + rg.matchedFrom(s) +
                * " : " + rg.matchedTo(s) + " : '" + rg.stringMatched(s) + "'");
                * }
                */
@@ -744,6 +747,7 @@ public class GroupUrlLink
     return r;
   }
 
+  @Override
   public String toString()
   {
     StringBuffer result = new StringBuffer();
@@ -783,35 +787,41 @@ public class GroupUrlLink
 
     if (url == null)
     {
-      System.out.println("Created NO urls.");
+      jalview.bin.Console.outPrintln("Created NO urls.");
     }
     else
     {
-      System.out.println("Created a url from " + ((int[]) url[0])[0]
-              + "out of " + idstring[0].length + " sequences.");
-      System.out.println("Sequences that did not match:");
+      jalview.bin.Console
+              .outPrintln("Created a url from " + ((int[]) url[0])[0]
+                      + "out of " + idstring[0].length + " sequences.");
+      jalview.bin.Console.outPrintln("Sequences that did not match:");
       for (int sq = 0; sq < idstring[0].length; sq++)
       {
         if (!((boolean[]) url[1])[sq])
         {
-          System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "
-                  + idstring[1][sq]);
+          jalview.bin.Console.outPrintln("Seq " + sq + ": "
+                  + idstring[0][sq] + "\t: " + idstring[1][sq]);
         }
       }
-      System.out.println("Sequences that DID match:");
+      jalview.bin.Console.outPrintln("Sequences that DID match:");
       for (int sq = 0; sq < idstring[0].length; sq++)
       {
         if (((boolean[]) url[1])[sq])
         {
-          System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "
-                  + idstring[1][sq]);
+          jalview.bin.Console.outPrintln("Seq " + sq + ": "
+                  + idstring[0][sq] + "\t: " + idstring[1][sq]);
         }
       }
-      System.out.println("The generated URL:");
-      System.out.println(((String[]) url[3])[0]);
+      jalview.bin.Console.outPrintln("The generated URL:");
+      jalview.bin.Console.outPrintln(((String[]) url[3])[0]);
     }
   }
 
+  /**
+   * 
+   * @param argv
+   * @j2sIgnore
+   */
   public static void main(String argv[])
   {
     // note - JAL-1383 - these services are all dead
@@ -840,15 +850,17 @@ public class GroupUrlLink
       GroupUrlLink ul = new GroupUrlLink(links[i]);
       if (ul.isValid())
       {
-        System.out.println("\n\n\n");
-        System.out.println(
+        jalview.bin.Console.outPrintln("\n\n\n");
+        jalview.bin.Console.outPrintln(
                 "Link " + i + " " + links[i] + " : " + ul.toString());
-        System.out.println(" pref : " + ul.getUrl_prefix());
-        System.out.println(" IdReplace : " + ul.getIDRegexReplace());
-        System.out.println(" SeqReplace : " + ul.getSeqRegexReplace());
-        System.out.println(" Suffixes : " + ul.getUrl_suffix());
-
-        System.out.println(
+        jalview.bin.Console.outPrintln(" pref : " + ul.getUrl_prefix());
+        jalview.bin.Console
+                .outPrintln(" IdReplace : " + ul.getIDRegexReplace());
+        jalview.bin.Console
+                .outPrintln(" SeqReplace : " + ul.getSeqRegexReplace());
+        jalview.bin.Console.outPrintln(" Suffixes : " + ul.getUrl_suffix());
+
+        jalview.bin.Console.outPrintln(
                 "<insert input id and sequence strings here> Without onlyIfMatches:");
         Object[] urls;
         try
@@ -858,9 +870,9 @@ public class GroupUrlLink
           testUrls(ul, seqsandids, urls);
         } catch (UrlStringTooLongException ex)
         {
-          System.out.println("too long exception " + ex);
+          jalview.bin.Console.outPrintln("too long exception " + ex);
         }
-        System.out.println(
+        jalview.bin.Console.outPrintln(
                 "<insert input id and sequence strings here> With onlyIfMatches set:");
         try
         {
@@ -869,13 +881,13 @@ public class GroupUrlLink
           testUrls(ul, seqsandids, urls);
         } catch (UrlStringTooLongException ex)
         {
-          System.out.println("too long exception " + ex);
+          jalview.bin.Console.outPrintln("too long exception " + ex);
         }
       }
       else
       {
-        System.err.println("Invalid URLLink : " + links[i] + " : "
-                + ul.getInvalidMessage());
+        jalview.bin.Console.errPrintln("Invalid URLLink : " + links[i]
+                + " : " + ul.getInvalidMessage());
       }
     }
   }