X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=a43dc42ad400bddad9197261b064d74a5762268f;hb=b72ed01b68a8572022f912687db5be60b53c15cf;hp=027390a1e8fc6facd4f7ae1e5852df515acacf38;hpb=c6977851625f96831a95b45901aa1d84bd7774fe;p=jalview.git

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 027390a..a43dc42 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -26,19 +26,21 @@
 // TODO: Extended SequenceNodeI to hold parsed NHX strings
 package jalview.io;
 
-import java.util.Locale;
-
-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.bin.Jalview.ExitCode;
+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
@@ -78,7 +80,7 @@ import com.stevesoft.pat.Regex;
  */
 public class NewickFile extends FileParse
 {
-  SequenceNode root;
+  BinaryNode root;
 
   private boolean HasBootstrap = false;
 
@@ -145,7 +147,7 @@ public class NewickFile extends FileParse
    * @param newtree
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree)
+  public NewickFile(BinaryNode newtree)
   {
     root = newtree;
   }
@@ -174,7 +176,7 @@ public class NewickFile extends FileParse
    * @param distances
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree, boolean bootstrap,
+  public NewickFile(BinaryNode newtree, boolean bootstrap,
           boolean distances)
   {
     root = newtree;
@@ -194,7 +196,7 @@ public class NewickFile extends FileParse
    * @param rootdistance
    *          DOCUMENT ME!
    */
-  public NewickFile(SequenceNode newtree, boolean bootstrap,
+  public NewickFile(BinaryNode newtree, boolean bootstrap,
           boolean distances, boolean rootdistance)
   {
     root = newtree;
@@ -275,8 +277,8 @@ public class NewickFile extends FileParse
 
     root = new SequenceNode();
 
-    SequenceNode realroot = null;
-    SequenceNode c = root;
+    BinaryNode realroot = null;
+    BinaryNode c = root;
 
     int d = -1;
     int cp = 0;
@@ -323,21 +325,21 @@ public class NewickFile extends FileParse
         {
           c.setRight(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (SequenceNode) c.right();
+          c = c.right();
         }
         else
         {
           if (c.left() != null)
           {
             // Dummy node for polytomy - keeps c.left free for new node
-            SequenceNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
+            BinaryNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
             tmpn.SetChildren(c.left(), c.right());
             c.setRight(tmpn);
           }
 
           c.setLeft(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (SequenceNode) c.left();
+          c = c.left();
         }
 
         if (realroot == null)
@@ -393,7 +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.
@@ -487,7 +489,8 @@ 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)
@@ -518,7 +521,7 @@ public class NewickFile extends FileParse
         else
         {
           // Find a place to put the leaf
-          SequenceNode newnode = new SequenceNode(null, c, nodename,
+          BinaryNode newnode = new SequenceNode(null, c, nodename,
                   (HasDistances) ? distance : DefDistance,
                   (HasBootstrap) ? bootstrap : DefBootstrap, false);
           parseNHXNodeProps(c, commentString2);
@@ -538,7 +541,7 @@ public class NewickFile extends FileParse
             {
               // Insert a dummy node for polytomy
               // dummy nodes have distances
-              SequenceNode newdummy = new SequenceNode(null, c, null,
+              BinaryNode newdummy = new SequenceNode(null, c, null,
                       (HasDistances ? 0 : DefDistance), 0, true);
               newdummy.SetChildren(c.left(), newnode);
               c.setLeft(newdummy);
@@ -577,7 +580,7 @@ public class NewickFile extends FileParse
               // Just advance focus, if we need to
               if ((c.left() != null) && (!c.left().isLeaf()))
               {
-                c = (SequenceNode) c.left();
+                c = c.left();
               }
             }
           }
@@ -615,7 +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)
     {
@@ -631,7 +634,7 @@ public class NewickFile extends FileParse
    * @param commentString
    * @param commentString2
    */
-  private void parseNHXNodeProps(SequenceNode c, String commentString)
+  private void parseNHXNodeProps(BinaryNode c, String commentString)
   {
     // TODO: store raw comment on the sequenceNode so it can be recovered when
     // tree is output
@@ -663,7 +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);
           }
@@ -678,7 +681,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  public SequenceNode getTree()
+  public BinaryNode getTree()
   {
     return root;
   }
@@ -832,7 +835,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  private String printNodeField(SequenceNode c)
+  private String printNodeField(BinaryNode c)
   {
     return ((c.getName() == null) ? "" : nodeName(c.getName()))
             + ((HasBootstrap) ? ((c.getBootstrap() > -1)
@@ -849,7 +852,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  private String printRootField(SequenceNode root)
+  private String printRootField(BinaryNode root)
   {
     return (printRootInfo)
             ? (((root.getName() == null) ? "" : nodeName(root.getName()))
@@ -864,7 +867,7 @@ public class NewickFile extends FileParse
   }
 
   // Non recursive call deals with root node properties
-  public void print(StringBuffer tf, SequenceNode root)
+  public void print(StringBuffer tf, BinaryNode root)
   {
     if (root != null)
     {
@@ -876,20 +879,20 @@ public class NewickFile extends FileParse
       {
         if (root.isDummy())
         {
-          _print(tf, (SequenceNode) root.right());
-          _print(tf, (SequenceNode) root.left());
+          _print(tf, root.right());
+          _print(tf, root.left());
         }
         else
         {
           tf.append("(");
-          _print(tf, (SequenceNode) root.right());
+          _print(tf, root.right());
 
           if (root.left() != null)
           {
             tf.append(",");
           }
 
-          _print(tf, (SequenceNode) root.left());
+          _print(tf, root.left());
           tf.append(")" + printRootField(root));
         }
       }
@@ -897,7 +900,7 @@ public class NewickFile extends FileParse
   }
 
   // Recursive call for non-root nodes
-  public void _print(StringBuffer tf, SequenceNode c)
+  public void _print(StringBuffer tf, BinaryNode c)
   {
     if (c != null)
     {
@@ -909,24 +912,24 @@ public class NewickFile extends FileParse
       {
         if (c.isDummy())
         {
-          _print(tf, (SequenceNode) c.left());
+          _print(tf, c.left());
           if (c.left() != null)
           {
             tf.append(",");
           }
-          _print(tf, (SequenceNode) c.right());
+          _print(tf, c.right());
         }
         else
         {
           tf.append("(");
-          _print(tf, (SequenceNode) c.right());
+          _print(tf, c.right());
 
           if (c.left() != null)
           {
             tf.append(",");
           }
 
-          _print(tf, (SequenceNode) c.left());
+          _print(tf, c.left());
           tf.append(")" + printNodeField(c));
         }
       }
@@ -944,9 +947,9 @@ 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.",
+                ExitCode.INVALID_ARGUMENT);
       }
 
       File fn = new File(args[0]);
@@ -961,31 +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();
     }
   }