X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FNewickFile.java;h=8e374ac0d722eab205ae4112b8f53545ac4059f2;hb=11cce1c1e065d4430400ad414460ae643b51fbfe;hp=9a7f6fb9ff0dae4dccaa96bec65f06b94f141b74;hpb=ab9e5bf849afd2f41102db0bf9893de1df0512f6;p=jalview.git
diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 9a7f6fb..8e374ac 100755
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -1,22 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, 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 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.
- *
- * 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 - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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.
+ *
+ * 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
// http://evolution.genetics.washington.edu/phylip/newick_doc.html
@@ -36,10 +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
@@ -84,12 +82,12 @@ public class NewickFile extends FileParse
private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[]
{ new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for
- // requiring
- // quotes
+ // requiring
+ // quotes
new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote
- // characters
+ // characters
new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace
- // transformation
+ // transformation
};
char QuoteChar = '\'';
@@ -98,10 +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
{
@@ -112,12 +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
{
@@ -133,7 +131,7 @@ public class NewickFile extends FileParse
* Creates a new NewickFile object.
*
* @param newtree
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public NewickFile(SequenceNode newtree)
{
@@ -144,9 +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)
{
@@ -158,11 +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)
@@ -176,13 +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)
@@ -197,15 +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!
*/
@@ -247,8 +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
{
@@ -280,14 +278,14 @@ public class NewickFile extends FileParse
String commentString2 = null; // comments after simple node props
float DefDistance = (float) 0.001; // @param Default distance for a node -
- // very very small
+ // very very small
int DefBootstrap = -1; // @param Default bootstrap for a node
float distance = DefDistance;
int bootstrap = DefBootstrap;
boolean ascending = false; // flag indicating that we are leaving the
- // current node
+ // current node
com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
"[(\\['),;]");
@@ -430,7 +428,7 @@ public class NewickFile extends FileParse
if (uqnodename.search(fstring)
&& ((uqnodename.matchedFrom(1) == 0) || (fstring
.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
- // HACK!
+ // HACK!
{
if (nodename == null)
{
@@ -506,8 +504,8 @@ public class NewickFile extends FileParse
if (c == realroot)
{
RootHasDistance = nodehasdistance; // JBPNote This is really
- // UGLY!!! Ensure root node gets
- // its given distance
+ // UGLY!!! Ensure root node gets
+ // its given distance
}
parseNHXNodeProps(c, commentString2);
commentString2 = null;
@@ -585,7 +583,7 @@ public class NewickFile extends FileParse
nodename = null;
distance = DefDistance;
bootstrap = DefBootstrap;
- commentString2=null;
+ commentString2 = null;
}
if (nextcp == 0)
{
@@ -630,39 +628,40 @@ public class NewickFile extends FileParse
// tree is output
if (commentString != null && commentString.startsWith("&&NHX"))
{
- StringTokenizer st = new StringTokenizer(commentString.substring(5),":");
+ StringTokenizer st = new StringTokenizer(commentString.substring(5),
+ ":");
while (st.hasMoreTokens())
{
String tok = st.nextToken();
- int colpos=tok.indexOf("=");
+ int colpos = tok.indexOf("=");
- if (colpos>-1)
+ if (colpos > -1)
{
String code = tok.substring(0, colpos);
- String value = tok.substring(colpos+1);
- try {
+ String value = tok.substring(colpos + 1);
+ try
+ {
// parse out code/value pairs
if (code.toLowerCase().equals("b"))
{
- int v=-1;
+ int v = -1;
Float iv = new Float(value);
v = iv.intValue(); // jalview only does integer bootstraps
- // currently
+ // currently
c.setBootstrap(v);
HasBootstrap = true;
}
// more codes here.
- }
- catch (Exception e)
+ } catch (Exception e)
{
- System.err.println("Couldn't parse code '"+code+"' = '"+value+"'");
+ System.err.println("Couldn't parse code '" + code + "' = '"
+ + value + "'");
e.printStackTrace(System.err);
}
}
}
}
-
-
+
}
/**
@@ -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!
*/