Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
NewickFile	75	272	112	182	0.582568858.3%	Show methods

Class NewickFile

Class NewickFile	Line # 75	Total Statements 272	Complexity 112	Uncovered Elements 182	TOTAL Coverage 0.582568858.3%
NewickFile(String)   NewickFile(String)	111111	1.01	1.01	0.00	1.0 1.0100%
NewickFile(String,DataSourceType)   NewickFile(String,DataSourceType)	127127	1.01	1.01	0.00	1.0 1.0100%
NewickFile(FileParse)   NewickFile(FileParse)	133133	1.01	1.01	1.01	0.0 0.00%
NewickFile(SequenceNode)   NewickFile(SequenceNode)	144144	1.01	1.01	0.00	1.0 1.0100%
NewickFile(SequenceNode,boolean)   NewickFile(SequenceNode,boolean)	157157	2.02	1.01	2.02	0.0 0.00%
NewickFile(SequenceNode,boolean,boolean)   NewickFile(SequenceNode,boolean,boolean)	173173	3.03	1.01	3.03	0.0 0.00%
NewickFile(SequenceNode,boolean,boolean,boolean)   NewickFile(SequenceNode,boolean,boolean,boolean)	193193	4.04	1.01	4.04	0.0 0.00%
ErrorStringrange(String,String,int,int,String) : String   ErrorStringrange(String,String,int,int,String) : String	218218	1.01	4.04	7.07	0.0 0.00%
HasBootstrap() : boolean   HasBootstrap() : boolean	229229	1.01	1.01	0.00	1.0 1.0100%
HasDistances() : boolean   HasDistances() : boolean	239239	1.01	1.01	0.00	1.0 1.0100%
HasRootDistance() : boolean   HasRootDistance() : boolean	244244	1.01	1.01	0.00	1.0 1.0100%
parse() : void   parse() : void	256256	148.0148	52.052	65.065	0.7123894 0.712389471.2%
parseNHXNodeProps(SequenceNode,String) : void   parseNHXNodeProps(SequenceNode,String) : void	641641	17.017	7.07	23.023	0.08 0.088%
getTree() : SequenceNode   getTree() : SequenceNode	688688	1.01	1.01	0.00	1.0 1.0100%
print() : String   print() : String	699699	4.04	1.01	0.00	1.0 1.0100%
print(boolean) : String   print(boolean) : String	721721	6.06	1.01	0.00	1.0 1.0100%
print(boolean,boolean) : String   print(boolean,boolean) : String	747747	6.06	1.01	0.00	1.0 1.0100%
print(boolean,boolean,boolean) : String   print(boolean,boolean,boolean) : String	773773	6.06	1.01	0.00	1.0 1.0100%
getQuoteChar() : char   getQuoteChar() : char	793793	1.01	1.01	1.01	0.0 0.00%
setQuoteChar(char) : char   setQuoteChar(char) : char	806806	3.03	1.01	3.03	0.0 0.00%
nodeName(String) : String   nodeName(String) : String	822822	3.03	2.02	0.00	1.0 1.0100%
printNodeField(SequenceNode) : String   printNodeField(SequenceNode) : String	842842	1.01	6.06	6.06	0.45454547 0.4545454745.5%
printRootField(SequenceNode) : String   printRootField(SequenceNode) : String	859859	1.01	7.07	7.07	0.46153846 0.4615384646.2%
print(StringBuffer,SequenceNode) : void   print(StringBuffer,SequenceNode) : void	874874	12.012	6.06	7.07	0.65 0.6565%
_print(StringBuffer,SequenceNode) : void   _print(StringBuffer,SequenceNode) : void	907907	14.014	6.06	9.09	0.625 0.62562.5%
main(String[]) : void   main(String[]) : void	944944	32.032	5.05	36.036	0.0 0.00%

 

Contributing tests

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
7		* Jalview is free software: you can redistribute it and/or
8		* modify it under the terms of the GNU General Public License
9		* as published by the Free Software Foundation, either version 3
10		* of the License, or (at your option) any later version.
11		*
12		* Jalview is distributed in the hope that it will be useful, but
13		* WITHOUT ANY WARRANTY; without even the implied warranty
14		* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15		* PURPOSE. See the GNU General Public License for more details.
16		*
17		* You should have received a copy of the GNU General Public License
18		* along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19		* The Jalview Authors are detailed in the 'AUTHORS' file.
20		*/
21		// NewickFile.java
22		// Tree I/O
23		// http://evolution.genetics.washington.edu/phylip/newick_doc.html
24		// TODO: Implement Basic NHX tag parsing and preservation
25		// TODO: http://evolution.genetics.wustl.edu/eddy/forester/NHX.html
26		// TODO: Extended SequenceNodeI to hold parsed NHX strings
27		package jalview.io;
28
29		import jalview.datamodel.SequenceNode;
30		import jalview.util.MessageManager;
31
32		import java.io.BufferedReader;
33		import java.io.File;
34		import java.io.FileReader;
35		import java.io.IOException;
36		import java.util.StringTokenizer;
37
38		/**
39		* Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
40		* tree distances and topology are unreliable when they are parsed. TODO: on
41		* this: NHX codes are appended in comments beginning with &&NHX. The codes are
42		* given below (from http://www.phylosoft.org/forester/NHX.html): Element Type
43		* Description Corresponding phyloXML element (parent element in parentheses) no
44		* tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED)
45		* <name>(<clade>) : decimal branch length to parent node (MUST BE SECOND, IF
46		* ASSIGNED) <branch_length>(<clade>) :GN= string gene name <name>(<sequence>)
47		* :AC= string sequence accession <accession>(<sequence>) :ND= string node
48		* identifier - if this is being used, it has to be unique within each phylogeny
49		* <node_id>(<clade>) :B= decimal confidence value for parent branch
50		* <confidence>(<clade>) :D= 'T', 'F', or '?' 'T' if this node represents a
51		* duplication event - 'F' if this node represents a speciation event, '?' if
52		* this node represents an unknown event (D= tag should be replaced by Ev= tag)
53		* n/a :Ev=duplications>speciations>gene losses>event type>duplication type int
54		* int int string string event (replaces the =D tag), number of duplication,
55		* speciation, and gene loss events, type of event (transfer, fusion, root,
56		* unknown, other, speciation_duplication_loss, unassigned) <events>(<clade>)
57		* :E= string EC number at this node <annotation>(<sequence>) :Fu= string
58		* function at this node <annotation>(<sequence>)
59		* :DS=protein-length>from>to>support>name>from>... int int int double string
60		* int ... domain structure at this node <domain_architecture>(<sequence>) :S=
61		* string species name of the species/phylum at this node <taxonomy>(<clade>)
62		* :T= integer taxonomy ID of the species/phylum at this node <id>(<taxonomy>)
63		* :W= integer width of parent branch <width>(<clade>) :C=rrr.ggg.bbb
64		* integer.integer.integer color of parent branch <color>(<clade>) :Co= 'Y' or
65		* 'N' collapse this node when drawing the tree (default is not to collapse) n/a
66		* :XB= string custom data associated with a branch <property>(<clade>) :XN=
67		* string custom data associated with a node <property>(<clade>) :O= integer
68		* orthologous to this external node n/a :SN= integer subtree neighbors n/a :SO=
69		* integer super orthologous (no duplications on paths) to this external node
70		* n/a
71		*
72		* @author Jim Procter
73		* @version $Revision$
74		*/
		58.3% Uncovered Elements: 182 (436) Complexity: 112 Complexity Density: 0.41
75		public class NewickFile extends FileParse
76		{
77		SequenceNode root;
78
79		private boolean HasBootstrap = false;
80
81		private boolean HasDistances = false;
82
83		private boolean RootHasDistance = false;
84
85		// File IO Flags
86		boolean ReplaceUnderscores = false;
87
88		boolean printRootInfo = true;
89
90		private com.stevesoft.pat.Regex[] NodeSafeName = new com.stevesoft.pat.Regex[] {
91		new com.stevesoft.pat.Regex().perlCode("m/[\\[,:'()]/"), // test for
92		// requiring
93		// quotes
94		new com.stevesoft.pat.Regex().perlCode("s/'/''/"), // escaping quote
95		// characters
96		new com.stevesoft.pat.Regex().perlCode("s/\\/w/_/") // unqoted whitespace
97		// transformation
98		};
99
100		char QuoteChar = '\'';
101
102		/**
103		* Creates a new NewickFile object.
104		*
105		* @param inStr
106		* DOCUMENT ME!
107		*
108		* @throws IOException
109		* DOCUMENT ME!
110		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
111	12	public NewickFile(String inStr) throws IOException...
112		{
113	12	super(inStr, DataSourceType.PASTE);
114		}
115
116		/**
117		* Creates a new NewickFile object.
118		*
119		* @param inFile
120		* DOCUMENT ME!
121		* @param protocol
122		* DOCUMENT ME!
123		*
124		* @throws IOException
125		* DOCUMENT ME!
126		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
127	6	public NewickFile(String inFile, DataSourceType protocol)...
128		throws IOException
129		{
130	6	super(inFile, protocol);
131		}
132
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
133	0	public NewickFile(FileParse source) throws IOException...
134		{
135	0	super(source);
136		}
137
138		/**
139		* Creates a new NewickFile object.
140		*
141		* @param newtree
142		* DOCUMENT ME!
143		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
144	5	public NewickFile(SequenceNode newtree)...
145		{
146	5	root = newtree;
147		}
148
149		/**
150		* Creates a new NewickFile object.
151		*
152		* @param newtree
153		* DOCUMENT ME!
154		* @param bootstrap
155		* DOCUMENT ME!
156		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
157	0	public NewickFile(SequenceNode newtree, boolean bootstrap)...
158		{
159	0	HasBootstrap = bootstrap;
160	0	root = newtree;
161		}
162
163		/**
164		* Creates a new NewickFile object.
165		*
166		* @param newtree
167		* DOCUMENT ME!
168		* @param bootstrap
169		* DOCUMENT ME!
170		* @param distances
171		* DOCUMENT ME!
172		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
173	0	public NewickFile(SequenceNode newtree, boolean bootstrap,...
174		boolean distances)
175		{
176	0	root = newtree;
177	0	HasBootstrap = bootstrap;
178	0	HasDistances = distances;
179		}
180
181		/**
182		* Creates a new NewickFile object.
183		*
184		* @param newtree
185		* DOCUMENT ME!
186		* @param bootstrap
187		* DOCUMENT ME!
188		* @param distances
189		* DOCUMENT ME!
190		* @param rootdistance
191		* DOCUMENT ME!
192		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
193	0	public NewickFile(SequenceNode newtree, boolean bootstrap,...
194		boolean distances, boolean rootdistance)
195		{
196	0	root = newtree;
197	0	HasBootstrap = bootstrap;
198	0	HasDistances = distances;
199	0	RootHasDistance = rootdistance;
200		}
201
202		/**
203		* DOCUMENT ME!
204		*
205		* @param Error
206		* DOCUMENT ME!
207		* @param Er
208		* DOCUMENT ME!
209		* @param r
210		* DOCUMENT ME!
211		* @param p
212		* DOCUMENT ME!
213		* @param s
214		* DOCUMENT ME!
215		*
216		* @return DOCUMENT ME!
217		*/
		0% Uncovered Elements: 7 (7) Complexity: 4 Complexity Density: 4
218	0	private String ErrorStringrange(String Error, String Er, int r, int p,...
219		String s)
220		{
221	0	return ((Error == null) ? "" : Error) + Er + " at position " + p + " ( "
222	0	+ s.substring(((p - r) < 0) ? 0 : (p - r),
223	0	((p + r) > s.length()) ? s.length() : (p + r))
224		+ " )\n";
225		}
226
227		// @tree annotations
228		// These are set automatically by the reader
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
229	33	public boolean HasBootstrap()...
230		{
231	33	return HasBootstrap;
232		}
233
234		/**
235		* DOCUMENT ME!
236		*
237		* @return DOCUMENT ME!
238		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
239	33	public boolean HasDistances()...
240		{
241	33	return HasDistances;
242		}
243
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
244	18	public boolean HasRootDistance()...
245		{
246	18	return RootHasDistance;
247		}
248
249		/**
250		* parse the filesource as a newick file (new hampshire and/or extended)
251		*
252		* @throws IOException
253		* with a line number and character position for badly formatted NH
254		* strings
255		*/
		71.2% Uncovered Elements: 65 (226) Complexity: 52 Complexity Density: 0.35
256	18	public void parse() throws IOException...
257		{
258	18	String nf;
259
260		{ // fill nf with complete tree file
261
262	18	StringBuffer file = new StringBuffer();
263
264	?	while ((nf = nextLine()) != null)
265		{
266	18	file.append(nf);
267		}
268
269	18	nf = file.toString();
270		}
271
272	18	root = new SequenceNode();
273
274	18	SequenceNode realroot = null;
275	18	SequenceNode c = root;
276
277	18	int d = -1;
278	18	int cp = 0;
279		// int flen = nf.length();
280
281	18	String Error = null;
282	18	String nodename = null;
283	18	String commentString2 = null; // comments after simple node props
284
285	18	float DefDistance = (float) 0.001; // @param Default distance for a node -
286		// very very small
287	18	int DefBootstrap = -1; // @param Default bootstrap for a node
288
289	18	float distance = DefDistance;
290	18	int bootstrap = DefBootstrap;
291
292	18	boolean ascending = false; // flag indicating that we are leaving the
293		// current node
294
295	18	com.stevesoft.pat.Regex majorsyms = new com.stevesoft.pat.Regex(
296		"[(\\['),;]");
297
298	18	int nextcp = 0;
299	18	int ncp = cp;
300	18	boolean parsednodename = false;
301	464	while (majorsyms.searchFrom(nf, cp) && (Error == null))
302		{
303	446	int fcp = majorsyms.matchedFrom();
304	446	char schar;
305	446	switch (schar = nf.charAt(fcp))
306		{
307	140	case '(':
308
309		// ascending should not be set
310		// New Internal node
311	140	if (ascending)
312		{
313	0	Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
314
315	0	continue;
316		}
317
318	140	;
319	140	d++;
320
321	140	if (c.right() == null)
322		{
323	68	c.setRight(new SequenceNode(null, c, null, DefDistance,
324		DefBootstrap, false));
325	68	c = (SequenceNode) c.right();
326		}
327		else
328		{
329	72	if (c.left() != null)
330		{
331		// Dummy node for polytomy - keeps c.left free for new node
332	0	SequenceNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
333	0	tmpn.SetChildren(c.left(), c.right());
334	0	c.setRight(tmpn);
335		}
336
337	72	c.setLeft(new SequenceNode(null, c, null, DefDistance,
338		DefBootstrap, false));
339	72	c = (SequenceNode) c.left();
340		}
341
342	140	if (realroot == null)
343		{
344	18	realroot = c;
345		}
346
347	140	nodename = null;
348	140	distance = DefDistance;
349	140	bootstrap = DefBootstrap;
350	140	cp = fcp + 1;
351
352	140	break;
353
354		// Deal with quoted fields
355	8	case '\'':
356
357	8	com.stevesoft.pat.Regex qnodename = new com.stevesoft.pat.Regex(
358		"'([^']|'')+'");
359
360	8	if (qnodename.searchFrom(nf, fcp))
361		{
362	8	int nl = qnodename.stringMatched().length();
363	8	nodename = new String(
364		qnodename.stringMatched().substring(1, nl - 1));
365		// unpack any escaped colons
366	8	com.stevesoft.pat.Regex xpandquotes = com.stevesoft.pat.Regex
367		.perlCode("s/''/'/");
368	8	String widernodename = xpandquotes.replaceAll(nodename);
369	8	nodename = widernodename;
370		// jump to after end of quoted nodename
371	8	nextcp = fcp + nl + 1;
372	8	parsednodename = true;
373		}
374		else
375		{
376	0	Error = ErrorStringrange(Error,
377		"Unterminated quotes for nodename", 7, fcp, nf);
378		}
379
380	8	break;
381
382	298	default:
383	298	if (schar == ';')
384		{
385	18	if (d != -1)
386		{
387	0	Error = ErrorStringrange(Error,
388		"Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
389		}
390		// cp advanced at the end of default
391		}
392	298	if (schar == '[')
393		{
394		// node string contains Comment or structured/extended NH format info
395		/*
396		* if ((fcp-cp>1 && nf.substring(cp,fcp).trim().length()>1)) { // will
397		* process in remains System.err.println("skipped text:
398		* '"+nf.substring(cp,fcp)+"'"); }
399		*/
400		// verify termination.
401	0	com.stevesoft.pat.Regex comment = new com.stevesoft.pat.Regex(
402		"]");
403	0	if (comment.searchFrom(nf, fcp))
404		{
405		// Skip the comment field
406	0	nextcp = comment.matchedFrom() + 1;
407	0	warningMessage = "Tree file contained comments which may confuse input algorithm.";
408	0	break;
409
410		// cp advanced at the end of default to nextcp, ncp is unchanged so
411		// any node info can be read.
412		}
413		else
414		{
415	0	Error = ErrorStringrange(Error, "Unterminated comment", 3, fcp,
416		nf);
417		}
418
419	0	;
420		}
421		// Parse simpler field strings
422	298	String fstring = nf.substring(ncp, fcp);
423		// remove any comments before we parse the node info
424		// TODO: test newick file with quoted square brackets in node name (is
425		// this allowed?)
426	298	while (fstring.indexOf(']') > -1)
427		{
428	0	int cstart = fstring.indexOf('[');
429	0	int cend = fstring.indexOf(']');
430	0	commentString2 = fstring.substring(cstart + 1, cend);
431	0	fstring = fstring.substring(0, cstart)
432		+ fstring.substring(cend + 1);
433
434		}
435	298	com.stevesoft.pat.Regex uqnodename = new com.stevesoft.pat.Regex(
436		"\\b([^' :;\\](),]+)");
437	298	com.stevesoft.pat.Regex nbootstrap = new com.stevesoft.pat.Regex(
438		"\\s*([0-9+]+)\\s*:");
439	298	com.stevesoft.pat.Regex ndist = new com.stevesoft.pat.Regex(
440		":([-0-9Ee.+]+)");
441
442	298	if (!parsednodename && uqnodename.search(fstring)
443		&& ((uqnodename.matchedFrom(1) == 0) || (fstring
444		.charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
445		// HACK!
446		{
447	150	if (nodename == null)
448		{
449	150	if (ReplaceUnderscores)
450		{
451	0	nodename = uqnodename.stringMatched(1).replace('_', ' ');
452		}
453		else
454		{
455	150	nodename = uqnodename.stringMatched(1);
456		}
457		}
458		else
459		{
460	0	Error = ErrorStringrange(Error,
461		"File has broken algorithm - overwritten nodename", 10,
462		fcp, nf);
463		}
464		}
465		// get comment bootstraps
466
467	298	if (nbootstrap.search(fstring))
468		{
469	0	if (nbootstrap.stringMatched(1)
470		.equals(uqnodename.stringMatched(1)))
471		{
472	0	nodename = null; // no nodename here.
473		}
474	0	if (nodename == null || nodename.length() == 0
475		|| nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1)
476		+ uqnodename.stringMatched().length()))
477		{
478	0	try
479		{
480	0	bootstrap = (new Integer(nbootstrap.stringMatched(1)))
481		.intValue();
482	0	HasBootstrap = true;
483		} catch (Exception e)
484		{
485	0	Error = ErrorStringrange(Error, "Can't parse bootstrap value",
486		4, ncp + nbootstrap.matchedFrom(), nf);
487		}
488		}
489		}
490
491	298	boolean nodehasdistance = false;
492
493	298	if (ndist.search(fstring))
494		{
495	280	try
496		{
497	280	distance = (new Float(ndist.stringMatched(1))).floatValue();
498	280	HasDistances = true;
499	280	nodehasdistance = true;
500		} catch (Exception e)
501		{
502	0	Error = ErrorStringrange(Error,
503		"Can't parse node distance value", 7,
504		ncp + ndist.matchedFrom(), nf);
505		}
506		}
507
508	298	if (ascending)
509		{
510		// Write node info here
511	140	c.setName(nodename);
512		// Trees without distances still need a render distance
513	140	c.dist = (HasDistances) ? distance : DefDistance;
514		// be consistent for internal bootstrap defaults too
515	140	c.setBootstrap((HasBootstrap) ? bootstrap : DefBootstrap);
516	140	if (c == realroot)
517		{
518	18	RootHasDistance = nodehasdistance; // JBPNote This is really
519		// UGLY!!! Ensure root node gets
520		// its given distance
521		}
522	140	parseNHXNodeProps(c, commentString2);
523	140	commentString2 = null;
524		}
525		else
526		{
527		// Find a place to put the leaf
528	158	SequenceNode newnode = new SequenceNode(null, c, nodename,
529	158	(HasDistances) ? distance : DefDistance,
530	158	(HasBootstrap) ? bootstrap : DefBootstrap, false);
531	158	parseNHXNodeProps(c, commentString2);
532	158	commentString2 = null;
533
534	158	if (c.right() == null)
535		{
536	90	c.setRight(newnode);
537		}
538		else
539		{
540	68	if (c.left() == null)
541		{
542	68	c.setLeft(newnode);
543		}
544		else
545		{
546		// Insert a dummy node for polytomy
547		// dummy nodes have distances
548	0	SequenceNode newdummy = new SequenceNode(null, c, null,
549	0	(HasDistances ? 0 : DefDistance), 0, true);
550	0	newdummy.SetChildren(c.left(), newnode);
551	0	c.setLeft(newdummy);
552		}
553		}
554		}
555
556	298	if (ascending)
557		{
558		// move back up the tree from preceding closure
559	140	c = c.AscendTree();
560
561	140	if ((d > -1) && (c == null))
562		{
563	0	Error = ErrorStringrange(Error,
564		"File broke algorithm: Lost place in tree (is there an extra ')' ?)",
565		7, fcp, nf);
566		}
567		}
568
569	298	if (nf.charAt(fcp) == ')')
570		{
571	140	d--;
572	140	ascending = true;
573		}
574		else
575		{
576	158	if (nf.charAt(fcp) == ',')
577		{
578	140	if (ascending)
579		{
580	50	ascending = false;
581		}
582		else
583		{
584		// Just advance focus, if we need to
585	90	if ((c.left() != null) && (!c.left().isLeaf()))
586		{
587	0	c = (SequenceNode) c.left();
588		}
589		}
590		}
591		}
592
593		// Reset new node properties to obvious fakes
594	298	nodename = null;
595	298	distance = DefDistance;
596	298	bootstrap = DefBootstrap;
597	298	commentString2 = null;
598	298	parsednodename = false;
599		}
600	446	if (nextcp == 0)
601		{
602	438	ncp = cp = fcp + 1;
603		}
604		else
605		{
606	8	cp = nextcp;
607	8	nextcp = 0;
608		}
609		}
610
611	18	if (Error != null)
612		{
613	0	throw (new IOException(
614		MessageManager.formatMessage("exception.newfile", new String[]
615		{ Error.toString() })));
616		}
617	18	if (root == null)
618		{
619	0	throw (new IOException(
620		MessageManager.formatMessage("exception.newfile", new String[]
621		{ MessageManager.getString("label.no_tree_read_in") })));
622		}
623		// THe next line is failing for topali trees - not sure why yet. if
624		// (root.right()!=null && root.isDummy())
625	18	root = (SequenceNode) root.right().detach(); // remove the imaginary root.
626
627	18	if (!RootHasDistance)
628		{
629	18	root.dist = (HasDistances) ? 0 : DefDistance;
630		}
631		}
632
633		/**
634		* parse NHX codes in comment strings and update NewickFile state flags for
635		* distances and bootstraps, and add any additional properties onto the node.
636		*
637		* @param c
638		* @param commentString
639		* @param commentString2
640		*/
		8% Uncovered Elements: 23 (25) Complexity: 7 Complexity Density: 0.41
641	298	private void parseNHXNodeProps(SequenceNode c, String commentString)...
642		{
643		// TODO: store raw comment on the sequenceNode so it can be recovered when
644		// tree is output
645	298	if (commentString != null && commentString.startsWith("&&NHX"))
646		{
647	0	StringTokenizer st = new StringTokenizer(commentString.substring(5),
648		":");
649	0	while (st.hasMoreTokens())
650		{
651	0	String tok = st.nextToken();
652	0	int colpos = tok.indexOf("=");
653
654	0	if (colpos > -1)
655		{
656	0	String code = tok.substring(0, colpos);
657	0	String value = tok.substring(colpos + 1);
658	0	try
659		{
660		// parse out code/value pairs
661	0	if (code.toLowerCase().equals("b"))
662		{
663	0	int v = -1;
664	0	Float iv = new Float(value);
665	0	v = iv.intValue(); // jalview only does integer bootstraps
666		// currently
667	0	c.setBootstrap(v);
668	0	HasBootstrap = true;
669		}
670		// more codes here.
671		} catch (Exception e)
672		{
673	0	System.err.println(
674		"Couldn't parse code '" + code + "' = '" + value + "'");
675	0	e.printStackTrace(System.err);
676		}
677		}
678		}
679		}
680
681		}
682
683		/**
684		* DOCUMENT ME!
685		*
686		* @return DOCUMENT ME!
687		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
688	42	public SequenceNode getTree()...
689		{
690	42	return root;
691		}
692
693		/**
694		* Generate a newick format tree according to internal flags for bootstraps,
695		* distances and root distances.
696		*
697		* @return new hampshire tree in a single line
698		*/
		100% Uncovered Elements: 0 (4) Complexity: 1 Complexity Density: 0.25
699	5	public String print()...
700		{
701	5	synchronized (this)
702		{
703	5	StringBuffer tf = new StringBuffer();
704	5	print(tf, root);
705
706	5	return (tf.append(";").toString());
707		}
708		}
709
710		/**
711		*
712		*
713		* Generate a newick format tree according to internal flags for distances and
714		* root distances and user specificied writing of bootstraps.
715		*
716		* @param withbootstraps
717		* controls if bootstrap values are explicitly written.
718		*
719		* @return new hampshire tree in a single line
720		*/
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17
721	5	public String print(boolean withbootstraps)...
722		{
723	5	synchronized (this)
724		{
725	5	boolean boots = this.HasBootstrap;
726	5	this.HasBootstrap = withbootstraps;
727
728	5	String rv = print();
729	5	this.HasBootstrap = boots;
730
731	5	return rv;
732		}
733		}
734
735		/**
736		*
737		* Generate newick format tree according to internal flags for writing root
738		* node distances.
739		*
740		* @param withbootstraps
741		* explicitly write bootstrap values
742		* @param withdists
743		* explicitly write distances
744		*
745		* @return new hampshire tree in a single line
746		*/
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17
747	5	public String print(boolean withbootstraps, boolean withdists)...
748		{
749	5	synchronized (this)
750		{
751	5	boolean dists = this.HasDistances;
752	5	this.HasDistances = withdists;
753
754	5	String rv = print(withbootstraps);
755	5	this.HasDistances = dists;
756
757	5	return rv;
758		}
759		}
760
761		/**
762		* Generate newick format tree according to user specified flags
763		*
764		* @param withbootstraps
765		* explicitly write bootstrap values
766		* @param withdists
767		* explicitly write distances
768		* @param printRootInfo
769		* explicitly write root distance
770		*
771		* @return new hampshire tree in a single line
772		*/
		100% Uncovered Elements: 0 (6) Complexity: 1 Complexity Density: 0.17
773	2	public String print(boolean withbootstraps, boolean withdists,...
774		boolean printRootInfo)
775		{
776	2	synchronized (this)
777		{
778	2	boolean rootinfo = printRootInfo;
779	2	this.printRootInfo = printRootInfo;
780
781	2	String rv = print(withbootstraps, withdists);
782	2	this.printRootInfo = rootinfo;
783
784	2	return rv;
785		}
786		}
787
788		/**
789		* DOCUMENT ME!
790		*
791		* @return DOCUMENT ME!
792		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
793	0	char getQuoteChar()...
794		{
795	0	return QuoteChar;
796		}
797
798		/**
799		* DOCUMENT ME!
800		*
801		* @param c
802		* DOCUMENT ME!
803		*
804		* @return DOCUMENT ME!
805		*/
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
806	0	char setQuoteChar(char c)...
807		{
808	0	char old = QuoteChar;
809	0	QuoteChar = c;
810
811	0	return old;
812		}
813
814		/**
815		* DOCUMENT ME!
816		*
817		* @param name
818		* DOCUMENT ME!
819		*
820		* @return DOCUMENT ME!
821		*/
		100% Uncovered Elements: 0 (5) Complexity: 2 Complexity Density: 0.67
822	39	private String nodeName(String name)...
823		{
824	39	if (NodeSafeName[0].search(name))
825		{
826	4	return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
827		}
828		else
829		{
830	35	return NodeSafeName[2].replaceAll(name);
831		}
832		}
833
834		/**
835		* DOCUMENT ME!
836		*
837		* @param c
838		* DOCUMENT ME!
839		*
840		* @return DOCUMENT ME!
841		*/
		45.5% Uncovered Elements: 6 (11) Complexity: 6 Complexity Density: 6
842	68	private String printNodeField(SequenceNode c)...
843		{
844	68	return ((c.getName() == null) ? "" : nodeName(c.getName()))
845	68	+ ((HasBootstrap) ? ((c.getBootstrap() > -1)
846	0	? ((c.getName() != null ? " " : "") + c.getBootstrap())
847		: "") : "")
848	68	+ ((HasDistances) ? (":" + c.dist) : "");
849		}
850
851		/**
852		* DOCUMENT ME!
853		*
854		* @param root
855		* DOCUMENT ME!
856		*
857		* @return DOCUMENT ME!
858		*/
		46.2% Uncovered Elements: 7 (13) Complexity: 7 Complexity Density: 7
859	5	private String printRootField(SequenceNode root)...
860		{
861	5	return (printRootInfo)
862	3	? (((root.getName() == null) ? "" : nodeName(root.getName()))
863	3	+ ((HasBootstrap)
864	0	? ((root.getBootstrap() > -1)
865	0	? ((root.getName() != null ? " " : "")
866		+ +root.getBootstrap())
867		: "")
868		: "")
869	3	+ ((RootHasDistance) ? (":" + root.dist) : ""))
870		: "";
871		}
872
873		// Non recursive call deals with root node properties
		65% Uncovered Elements: 7 (20) Complexity: 6 Complexity Density: 0.5
874	5	public void print(StringBuffer tf, SequenceNode root)...
875		{
876	5	if (root != null)
877		{
878	5	if (root.isLeaf() && printRootInfo)
879		{
880	0	tf.append(printRootField(root));
881		}
882		else
883		{
884	5	if (root.isDummy())
885		{
886	0	_print(tf, (SequenceNode) root.right());
887	0	_print(tf, (SequenceNode) root.left());
888		}
889		else
890		{
891	5	tf.append("(");
892	5	_print(tf, (SequenceNode) root.right());
893
894	5	if (root.left() != null)
895		{
896	5	tf.append(",");
897		}
898
899	5	_print(tf, (SequenceNode) root.left());
900	5	tf.append(")" + printRootField(root));
901		}
902		}
903		}
904		}
905
906		// Recursive call for non-root nodes
		62.5% Uncovered Elements: 9 (24) Complexity: 6 Complexity Density: 0.43
907	68	public void _print(StringBuffer tf, SequenceNode c)...
908		{
909	68	if (c != null)
910		{
911	68	if (c.isLeaf())
912		{
913	39	tf.append(printNodeField(c));
914		}
915		else
916		{
917	29	if (c.isDummy())
918		{
919	0	_print(tf, (SequenceNode) c.left());
920	0	if (c.left() != null)
921		{
922	0	tf.append(",");
923		}
924	0	_print(tf, (SequenceNode) c.right());
925		}
926		else
927		{
928	29	tf.append("(");
929	29	_print(tf, (SequenceNode) c.right());
930
931	29	if (c.left() != null)
932		{
933	29	tf.append(",");
934		}
935
936	29	_print(tf, (SequenceNode) c.left());
937	29	tf.append(")" + printNodeField(c));
938		}
939		}
940		}
941		}
942
943		// Test
		0% Uncovered Elements: 36 (36) Complexity: 5 Complexity Density: 0.16
944	0	public static void main(String[] args)...
945		{
946	0	try
947		{
948	0	if (args == null || args.length != 1)
949		{
950	0	System.err.println(
951		"Takes one argument - file name of a newick tree file.");
952	0	System.exit(0);
953		}
954
955	0	File fn = new File(args[0]);
956
957	0	StringBuffer newickfile = new StringBuffer();
958	0	BufferedReader treefile = new BufferedReader(new FileReader(fn));
959	0	String l;
960
961	0	while ((l = treefile.readLine()) != null)
962		{
963	0	newickfile.append(l);
964		}
965
966	0	treefile.close();
967	0	System.out.println("Read file :\n");
968
969	0	NewickFile trf = new NewickFile(args[0], DataSourceType.FILE);
970	0	trf.parse();
971	0	System.out.println("Original file :\n");
972
973	0	com.stevesoft.pat.Regex nonl = new com.stevesoft.pat.Regex("\n+", "");
974	0	System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
975
976	0	System.out.println("Parsed file.\n");
977	0	System.out.println("Default output type for original input.\n");
978	0	System.out.println(trf.print());
979	0	System.out.println("Without bootstraps.\n");
980	0	System.out.println(trf.print(false));
981	0	System.out.println("Without distances.\n");
982	0	System.out.println(trf.print(true, false));
983	0	System.out.println("Without bootstraps but with distanecs.\n");
984	0	System.out.println(trf.print(false, true));
985	0	System.out.println("Without bootstraps or distanecs.\n");
986	0	System.out.println(trf.print(false, false));
987	0	System.out.println("With bootstraps and with distances.\n");
988	0	System.out.println(trf.print(true, true));
989		} catch (java.io.IOException e)
990		{
991	0	System.err.println("Exception\n" + e);
992	0	e.printStackTrace();
993		}
994		}
995		}