X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=888435e432cfc8ddeec701e198c4278f4bace3c3;hb=a4a4122f1a7b0c615d6780197456c811db6b8a2f;hp=8dc23891bb712243e645ccf9cf1569bff0142ec4;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 8dc2389..888435e 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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 .
*/
// 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) () :
- * decimal branch length to parent node (MUST BE SECOND, IF ASSIGNED)
- * () :GN= string gene name () :AC=
- * string sequence accession () :ND= string node
+ * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED)
+ * () : decimal branch length to parent node (MUST BE SECOND, IF
+ * ASSIGNED) () :GN= string gene name ()
+ * :AC= string sequence accession () :ND= string node
* identifier - if this is being used, it has to be unique within each phylogeny
* () :B= decimal confidence value for parent branch
* () :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!
*/
@@ -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
{
@@ -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!
*/