Merge branch 'develop' into patch/JAL-4110_stdout_for_tests

[jalview.git] / src / jalview / io / NewickFile.java

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index b3c0011..a43dc42 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -36,6 +36,7 @@ import java.util.StringTokenizer;
 import com.stevesoft.pat.Regex;
 
 import jalview.bin.Jalview;
+import jalview.bin.Jalview.ExitCode;
 import jalview.datamodel.BinaryNode;
 import jalview.datamodel.SequenceNode;
 import jalview.util.MessageManager;
@@ -324,7 +325,7 @@ public class NewickFile extends FileParse
         {
           c.setRight(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (BinaryNode) c.right();
+          c = c.right();
         }
         else
         {
@@ -338,7 +339,7 @@ public class NewickFile extends FileParse
 
           c.setLeft(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (BinaryNode) c.left();
+          c = c.left();
         }
 
         if (realroot == null)
@@ -394,7 +395,7 @@ public class NewickFile extends FileParse
           // node string contains Comment or structured/extended NH format info
           /*
            * if ((fcp-cp>1 && nf.substring(cp,fcp).trim().length()>1)) { // will
-           * process in remains System.err.println("skipped text:
+           * process in remains jalview.bin.Console.errPrintln("skipped text:
            * '"+nf.substring(cp,fcp)+"'"); }
            */
           // verify termination.
@@ -579,7 +580,7 @@ public class NewickFile extends FileParse
               // Just advance focus, if we need to
               if ((c.left() != null) && (!c.left().isLeaf()))
               {
-                c = (BinaryNode) c.left();
+                c = c.left();
               }
             }
           }
@@ -617,7 +618,7 @@ public class NewickFile extends FileParse
     }
     // THe next line is failing for topali trees - not sure why yet. if
     // (root.right()!=null && root.isDummy())
-    root = (SequenceNode) root.right().detach(); // remove the imaginary root.
+    root = root.right().detach(); // remove the imaginary root.
 
     if (!RootHasDistance)
     {
@@ -665,7 +666,7 @@ public class NewickFile extends FileParse
             // more codes here.
           } catch (Exception e)
           {
-            System.err.println(
+            jalview.bin.Console.errPrintln(
                     "Couldn't parse code '" + code + "' = '" + value + "'");
             e.printStackTrace(System.err);
           }
@@ -947,7 +948,8 @@ public class NewickFile extends FileParse
       if (args == null || args.length != 1)
       {
         Jalview.exit(
-                "Takes one argument - file name of a newick tree file.", 0);
+                "Takes one argument - file name of a newick tree file.",
+                ExitCode.INVALID_ARGUMENT);
       }
 
       File fn = new File(args[0]);
@@ -962,31 +964,35 @@ public class NewickFile extends FileParse
       }
 
       treefile.close();
-      System.out.println("Read file :\n");
+      jalview.bin.Console.outPrintln("Read file :\n");
 
       NewickFile trf = new NewickFile(args[0], DataSourceType.FILE);
       trf.parse();
-      System.out.println("Original file :\n");
+      jalview.bin.Console.outPrintln("Original file :\n");
 
       Regex nonl = new Regex("\n+", "");
-      System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
-
-      System.out.println("Parsed file.\n");
-      System.out.println("Default output type for original input.\n");
-      System.out.println(trf.print());
-      System.out.println("Without bootstraps.\n");
-      System.out.println(trf.print(false));
-      System.out.println("Without distances.\n");
-      System.out.println(trf.print(true, false));
-      System.out.println("Without bootstraps but with distanecs.\n");
-      System.out.println(trf.print(false, true));
-      System.out.println("Without bootstraps or distanecs.\n");
-      System.out.println(trf.print(false, false));
-      System.out.println("With bootstraps and with distances.\n");
-      System.out.println(trf.print(true, true));
+      jalview.bin.Console
+              .outPrintln(nonl.replaceAll(newickfile.toString()) + "\n");
+
+      jalview.bin.Console.outPrintln("Parsed file.\n");
+      jalview.bin.Console
+              .outPrintln("Default output type for original input.\n");
+      jalview.bin.Console.outPrintln(trf.print());
+      jalview.bin.Console.outPrintln("Without bootstraps.\n");
+      jalview.bin.Console.outPrintln(trf.print(false));
+      jalview.bin.Console.outPrintln("Without distances.\n");
+      jalview.bin.Console.outPrintln(trf.print(true, false));
+      jalview.bin.Console
+              .outPrintln("Without bootstraps but with distanecs.\n");
+      jalview.bin.Console.outPrintln(trf.print(false, true));
+      jalview.bin.Console.outPrintln("Without bootstraps or distanecs.\n");
+      jalview.bin.Console.outPrintln(trf.print(false, false));
+      jalview.bin.Console
+              .outPrintln("With bootstraps and with distances.\n");
+      jalview.bin.Console.outPrintln(trf.print(true, true));
     } catch (java.io.IOException e)
     {
-      System.err.println("Exception\n" + e);
+      jalview.bin.Console.errPrintln("Exception\n" + e);
       e.printStackTrace();
     }
   }