X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=769f9bdb782bc08f02429a310144aa9b378e3ce4;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=372690983598af0aceb00f5ce0442d657883e102;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 3726909..769f9bd 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 // NewickFile.java
 // Tree I/O
@@ -35,10 +34,10 @@ import jalview.datamodel.*;
  * this: NHX codes are appended in comments beginning with &&NHX. The codes are
  * given below (from http://www.phylosoft.org/forester/NHX.html): Element Type
  * Description Corresponding phyloXML element (parent element in parentheses) no
- * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED) <name>(<clade>) :
- * decimal branch length to parent node (MUST BE SECOND, IF ASSIGNED)
- * <branch_length>(<clade>) :GN= string gene name <name>(<sequence>) :AC=
- * string sequence accession <accession>(<sequence>) :ND= string node
+ * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED)
+ * <name>(<clade>) : decimal branch length to parent node (MUST BE SECOND, IF
+ * ASSIGNED) <branch_length>(<clade>) :GN= string gene name <name>(<sequence>)
+ * :AC= string sequence accession <accession>(<sequence>) :ND= string node
  * identifier - if this is being used, it has to be unique within each phylogeny
  * <node_id>(<clade>) :B= decimal confidence value for parent branch
  * <confidence>(<clade>) :D= 'T', 'F', or '?' 'T' if this node represents a
@@ -97,10 +96,10 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param inStr
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @throws IOException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public NewickFile(String inStr) throws IOException
   {
@@ -111,12 +110,12 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param inFile
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param type
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @throws IOException
-   *                 DOCUMENT ME!
+   *           DOCUMENT ME!
    */
   public NewickFile(String inFile, String type) throws IOException
   {
@@ -132,7 +131,7 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param newtree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public NewickFile(SequenceNode newtree)
   {
@@ -143,9 +142,9 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param newtree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param bootstrap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public NewickFile(SequenceNode newtree, boolean bootstrap)
   {
@@ -157,11 +156,11 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param newtree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param bootstrap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param distances
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public NewickFile(SequenceNode newtree, boolean bootstrap,
           boolean distances)
@@ -175,13 +174,13 @@ public class NewickFile extends FileParse
    * Creates a new NewickFile object.
    * 
    * @param newtree
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param bootstrap
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param distances
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param rootdistance
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public NewickFile(SequenceNode newtree, boolean bootstrap,
           boolean distances, boolean rootdistance)
@@ -196,15 +195,15 @@ public class NewickFile extends FileParse
    * DOCUMENT ME!
    * 
    * @param Error
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param Er
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param r
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param p
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -216,8 +215,8 @@ public class NewickFile extends FileParse
             + " at position "
             + p
             + " ( "
-            + s.substring(((p - r) < 0) ? 0 : (p - r), ((p + r) > s
-                    .length()) ? s.length() : (p + r)) + " )\n";
+            + s.substring(((p - r) < 0) ? 0 : (p - r),
+                    ((p + r) > s.length()) ? s.length() : (p + r)) + " )\n";
   }
 
   // @tree annotations
@@ -246,8 +245,8 @@ public class NewickFile extends FileParse
    * parse the filesource as a newick file (new hampshire and/or extended)
    * 
    * @throws IOException
-   *                 with a line number and character position for badly
-   *                 formatted NH strings
+   *           with a line number and character position for badly formatted NH
+   *           strings
    */
   public void parse() throws IOException
   {
@@ -471,8 +470,8 @@ public class NewickFile extends FileParse
             } catch (Exception e)
             {
               Error = ErrorStringrange(Error,
-                      "Can't parse bootstrap value", 4, ncp
-                              + nbootstrap.matchedFrom(), nf);
+                      "Can't parse bootstrap value", 4,
+                      ncp + nbootstrap.matchedFrom(), nf);
             }
           }
         }
@@ -489,8 +488,8 @@ public class NewickFile extends FileParse
           } catch (Exception e)
           {
             Error = ErrorStringrange(Error,
-                    "Can't parse node distance value", 7, ncp
-                            + ndist.matchedFrom(), nf);
+                    "Can't parse node distance value", 7,
+                    ncp + ndist.matchedFrom(), nf);
           }
         }
 
@@ -699,7 +698,7 @@ public class NewickFile extends FileParse
    * root distances and user specificied writing of bootstraps.
    * 
    * @param withbootstraps
-   *                controls if bootstrap values are explicitly written.
+   *          controls if bootstrap values are explicitly written.
    * 
    * @return new hampshire tree in a single line
    */
@@ -723,9 +722,9 @@ public class NewickFile extends FileParse
    * node distances.
    * 
    * @param withbootstraps
-   *                explicitly write bootstrap values
+   *          explicitly write bootstrap values
    * @param withdists
-   *                explicitly write distances
+   *          explicitly write distances
    * 
    * @return new hampshire tree in a single line
    */
@@ -747,11 +746,11 @@ public class NewickFile extends FileParse
    * Generate newick format tree according to user specified flags
    * 
    * @param withbootstraps
-   *                explicitly write bootstrap values
+   *          explicitly write bootstrap values
    * @param withdists
-   *                explicitly write distances
+   *          explicitly write distances
    * @param printRootInfo
-   *                explicitly write root distance
+   *          explicitly write root distance
    * 
    * @return new hampshire tree in a single line
    */
@@ -784,7 +783,7 @@ public class NewickFile extends FileParse
    * DOCUMENT ME!
    * 
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -800,7 +799,7 @@ public class NewickFile extends FileParse
    * DOCUMENT ME!
    * 
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -820,7 +819,7 @@ public class NewickFile extends FileParse
    * DOCUMENT ME!
    * 
    * @param c
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -837,7 +836,7 @@ public class NewickFile extends FileParse
    * DOCUMENT ME!
    * 
    * @param root
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */