Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 269ffb3..38ee9ca 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -26,20 +26,20 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
-import java.util.Locale;
-
-import jalview.datamodel.BinaryNode;
-import jalview.datamodel.SequenceNode;
-import jalview.util.MessageManager;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
+import java.util.Locale;
 import java.util.StringTokenizer;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.bin.Jalview;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.SequenceNode;
+import jalview.util.MessageManager;
+
 /**
  * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
  * tree distances and topology are unreliable when they are parsed. TODO: on
@@ -394,7 +394,7 @@ 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.
@@ -488,7 +488,8 @@ public class NewickFile extends FileParse
         {
           try
           {
-            distance = (Double.valueOf(ndist.stringMatched(1))).floatValue();
+            distance = (Double.valueOf(ndist.stringMatched(1)))
+                    .floatValue();
             HasDistances = true;
             nodehasdistance = true;
           } catch (Exception e)
@@ -664,7 +665,7 @@ 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);
           }
@@ -877,20 +878,20 @@ public class NewickFile extends FileParse
       {
         if (root.isDummy())
         {
-          _print(tf,  root.right());
-          _print(tf,  root.left());
+          _print(tf, root.right());
+          _print(tf, root.left());
         }
         else
         {
           tf.append("(");
-          _print(tf,  root.right());
+          _print(tf, root.right());
 
           if (root.left() != null)
           {
             tf.append(",");
           }
 
-          _print(tf,  root.left());
+          _print(tf, root.left());
           tf.append(")" + printRootField(root));
         }
       }
@@ -910,24 +911,24 @@ public class NewickFile extends FileParse
       {
         if (c.isDummy())
         {
-          _print(tf,  c.left());
+          _print(tf, c.left());
           if (c.left() != null)
           {
             tf.append(",");
           }
-          _print(tf,  c.right());
+          _print(tf, c.right());
         }
         else
         {
           tf.append("(");
-          _print(tf,  c.right());
+          _print(tf, c.right());
 
           if (c.left() != null)
           {
             tf.append(",");
           }
 
-          _print(tf,  c.left());
+          _print(tf, c.left());
           tf.append(")" + printNodeField(c));
         }
       }
@@ -945,9 +946,8 @@ public class NewickFile extends FileParse
     {
       if (args == null || args.length != 1)
       {
-        System.err.println(
-                "Takes one argument - file name of a newick tree file.");
-        System.exit(0);
+        Jalview.exit(
+                "Takes one argument - file name of a newick tree file.", 0);
       }
 
       File fn = new File(args[0]);
@@ -962,31 +962,31 @@ 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();
     }
   }