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Coverage Report

  1. Project Clover database Wed Sep 17 2025 10:52:37 BST
  2. Package jalview.io

File NewickFile.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
29% of files have more coverage

Code metrics

140
272
27
1
1,017
614
114
0.42
10.07
27
4.22

Classes

Class Line # Actions
NewickFile 81 272 114
0.621867962.2%
 

Contributing tests

This file is covered by 16 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 java.io.BufferedReader;
30    import java.io.File;
31    import java.io.FileReader;
32    import java.io.IOException;
33    import java.util.Locale;
34    import java.util.StringTokenizer;
35   
36    import com.stevesoft.pat.Regex;
37   
38    import jalview.bin.Jalview;
39    import jalview.bin.Jalview.ExitCode;
40    import jalview.datamodel.BinaryNode;
41    import jalview.datamodel.SequenceNode;
42    import jalview.util.MessageManager;
43   
44    /**
45    * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
46    * tree distances and topology are unreliable when they are parsed. TODO: on
47    * this: NHX codes are appended in comments beginning with &&NHX. The codes are
48    * given below (from http://www.phylosoft.org/forester/NHX.html): Element Type
49    * Description Corresponding phyloXML element (parent element in parentheses) no
50    * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED)
51    * <name>(<clade>) : decimal branch length to parent node (MUST BE SECOND, IF
52    * ASSIGNED) <branch_length>(<clade>) :GN= string gene name <name>(<sequence>)
53    * :AC= string sequence accession <accession>(<sequence>) :ND= string node
54    * identifier - if this is being used, it has to be unique within each phylogeny
55    * <node_id>(<clade>) :B= decimal confidence value for parent branch
56    * <confidence>(<clade>) :D= 'T', 'F', or '?' 'T' if this node represents a
57    * duplication event - 'F' if this node represents a speciation event, '?' if
58    * this node represents an unknown event (D= tag should be replaced by Ev= tag)
59    * n/a :Ev=duplications>speciations>gene losses>event type>duplication type int
60    * int int string string event (replaces the =D tag), number of duplication,
61    * speciation, and gene loss events, type of event (transfer, fusion, root,
62    * unknown, other, speciation_duplication_loss, unassigned) <events>(<clade>)
63    * :E= string EC number at this node <annotation>(<sequence>) :Fu= string
64    * function at this node <annotation>(<sequence>)
65    * :DS=protein-length>from>to>support>name>from>... int int int double string
66    * int ... domain structure at this node <domain_architecture>(<sequence>) :S=
67    * string species name of the species/phylum at this node <taxonomy>(<clade>)
68    * :T= integer taxonomy ID of the species/phylum at this node <id>(<taxonomy>)
69    * :W= integer width of parent branch <width>(<clade>) :C=rrr.ggg.bbb
70    * integer.integer.integer color of parent branch <color>(<clade>) :Co= 'Y' or
71    * 'N' collapse this node when drawing the tree (default is not to collapse) n/a
72    * :XB= string custom data associated with a branch <property>(<clade>) :XN=
73    * string custom data associated with a node <property>(<clade>) :O= integer
74    * orthologous to this external node n/a :SN= integer subtree neighbors n/a :SO=
75    * integer super orthologous (no duplications on paths) to this external node
76    * n/a
77    *
78    * @author Jim Procter
79    * @version $Revision$
80    */
 
81    public class NewickFile extends FileParse
82    {
83    BinaryNode root;
84   
85    private boolean HasBootstrap = false;
86   
87    private boolean HasDistances = false;
88   
89    private boolean RootHasDistance = false;
90   
91    // File IO Flags
92    boolean ReplaceUnderscores = false;
93   
94    boolean printRootInfo = true;
95   
96    private Regex[] NodeSafeName = new Regex[] {
97    new Regex().perlCode("m/[\\[,:'()]/"), // test for
98    // requiring
99    // quotes
100    new Regex().perlCode("s/'/''/"), // escaping quote
101    // characters
102    new Regex().perlCode("s/\\/w/_/") // unqoted whitespace
103    // transformation
104    };
105   
106    char QuoteChar = '\'';
107   
108    /**
109    * Creates a new NewickFile object.
110    *
111    * @param inStr
112    * DOCUMENT ME!
113    *
114    * @throws IOException
115    * DOCUMENT ME!
116    */
 
117  15 toggle public NewickFile(String inStr) throws IOException
118    {
119  15 super(inStr, DataSourceType.PASTE);
120    }
121   
122    /**
123    * Creates a new NewickFile object.
124    *
125    * @param inFile
126    * DOCUMENT ME!
127    * @param protocol
128    * DOCUMENT ME!
129    *
130    * @throws IOException
131    * DOCUMENT ME!
132    */
 
133  8 toggle public NewickFile(String inFile, DataSourceType protocol)
134    throws IOException
135    {
136  8 super(inFile, protocol);
137    }
138   
 
139  0 toggle public NewickFile(FileParse source) throws IOException
140    {
141  0 super(source);
142    }
143   
144    /**
145    * Creates a new NewickFile object.
146    *
147    * @param newtree
148    * DOCUMENT ME!
149    */
 
150  9 toggle public NewickFile(BinaryNode newtree)
151    {
152  9 root = newtree;
153    }
154   
155    /**
156    * Creates a new NewickFile object.
157    *
158    * @param newtree
159    * DOCUMENT ME!
160    * @param bootstrap
161    * DOCUMENT ME!
162    */
 
163  0 toggle public NewickFile(SequenceNode newtree, boolean bootstrap)
164    {
165  0 HasBootstrap = bootstrap;
166  0 root = newtree;
167    }
168   
169    /**
170    * Creates a new NewickFile object.
171    *
172    * @param newtree
173    * DOCUMENT ME!
174    * @param bootstrap
175    * DOCUMENT ME!
176    * @param distances
177    * DOCUMENT ME!
178    */
 
179  3 toggle public NewickFile(BinaryNode newtree, boolean bootstrap,
180    boolean distances)
181    {
182  3 root = newtree;
183  3 HasBootstrap = bootstrap;
184  3 HasDistances = distances;
185    }
186   
187    /**
188    * Creates a new NewickFile object.
189    *
190    * @param newtree
191    * DOCUMENT ME!
192    * @param bootstrap
193    * DOCUMENT ME!
194    * @param distances
195    * DOCUMENT ME!
196    * @param rootdistance
197    * DOCUMENT ME!
198    */
 
199  0 toggle public NewickFile(BinaryNode newtree, boolean bootstrap,
200    boolean distances, boolean rootdistance)
201    {
202  0 root = newtree;
203  0 HasBootstrap = bootstrap;
204  0 HasDistances = distances;
205  0 RootHasDistance = rootdistance;
206    }
207   
208    /**
209    * DOCUMENT ME!
210    *
211    * @param Error
212    * DOCUMENT ME!
213    * @param Er
214    * DOCUMENT ME!
215    * @param r
216    * DOCUMENT ME!
217    * @param p
218    * DOCUMENT ME!
219    * @param s
220    * DOCUMENT ME!
221    *
222    * @return DOCUMENT ME!
223    */
 
224  0 toggle private String ErrorStringrange(String Error, String Er, int r, int p,
225    String s)
226    {
227  0 return ((Error == null) ? "" : Error) + Er + " at position " + p + " ( "
228  0 + s.substring(((p - r) < 0) ? 0 : (p - r),
229  0 ((p + r) > s.length()) ? s.length() : (p + r))
230    + " )\n";
231    }
232   
233    // @tree annotations
234    // These are set automatically by the reader
 
235  43 toggle public boolean HasBootstrap()
236    {
237  43 return HasBootstrap;
238    }
239   
240    /**
241    * DOCUMENT ME!
242    *
243    * @return DOCUMENT ME!
244    */
 
245  43 toggle public boolean HasDistances()
246    {
247  43 return HasDistances;
248    }
249   
 
250  23 toggle public boolean HasRootDistance()
251    {
252  23 return RootHasDistance;
253    }
254   
255    /**
256    * parse the filesource as a newick file (new hampshire and/or extended)
257    *
258    * @throws IOException
259    * with a line number and character position for badly formatted NH
260    * strings
261    */
 
262  23 toggle public void parse() throws IOException
263    {
264  23 String nf;
265   
266    { // fill nf with complete tree file
267   
268  23 StringBuffer file = new StringBuffer();
269   
270  ? while ((nf = nextLine()) != null)
271    {
272  23 file.append(nf);
273    }
274   
275  23 nf = file.toString();
276    }
277   
278  23 root = new SequenceNode();
279   
280  23 BinaryNode realroot = null;
281  23 BinaryNode c = root;
282   
283  23 int d = -1;
284  23 int cp = 0;
285    // int flen = nf.length();
286   
287  23 String Error = null;
288  23 String nodename = null;
289  23 String commentString2 = null; // comments after simple node props
290   
291  23 double DefDistance = (float) 0.001; // @param Default distance for a node -
292    // very very small
293  23 int DefBootstrap = -1; // @param Default bootstrap for a node
294   
295  23 double distance = DefDistance;
296  23 int bootstrap = DefBootstrap;
297   
298  23 boolean ascending = false; // flag indicating that we are leaving the
299    // current node
300   
301  23 Regex majorsyms = new Regex("[(\\['),;]");
302   
303  23 int nextcp = 0;
304  23 int ncp = cp;
305  23 boolean parsednodename = false;
306  801 while (majorsyms.searchFrom(nf, cp) && (Error == null))
307    {
308  778 int fcp = majorsyms.matchedFrom();
309  778 char schar;
310  778 switch (schar = nf.charAt(fcp))
311    {
312  249 case '(':
313   
314    // ascending should not be set
315    // New Internal node
316  249 if (ascending)
317    {
318  0 Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
319   
320  0 continue;
321    }
322  249 d++;
323   
324  249 if (c.right() == null)
325    {
326  113 c.setRight(new SequenceNode(null, c, null, DefDistance,
327    DefBootstrap, false));
328  113 c = c.right();
329    }
330    else
331    {
332  136 if (c.left() != null)
333    {
334    // Dummy node for polytomy - keeps c.left free for new node
335  0 BinaryNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
336  0 tmpn.SetChildren(c.left(), c.right());
337  0 c.setRight(tmpn);
338    }
339   
340  136 c.setLeft(new SequenceNode(null, c, null, DefDistance,
341    DefBootstrap, false));
342  136 c = c.left();
343    }
344   
345  249 if (realroot == null)
346    {
347  23 realroot = c;
348    }
349   
350  249 nodename = null;
351  249 distance = DefDistance;
352  249 bootstrap = DefBootstrap;
353  249 cp = fcp + 1;
354   
355  249 break;
356   
357    // Deal with quoted fields
358  8 case '\'':
359   
360  8 Regex qnodename = new Regex("'([^']|'')+'");
361   
362  8 if (qnodename.searchFrom(nf, fcp))
363    {
364  8 int nl = qnodename.stringMatched().length();
365  8 nodename = new String(
366    qnodename.stringMatched().substring(1, nl - 1));
367    // unpack any escaped colons
368  8 Regex xpandquotes = Regex.perlCode("s/''/'/");
369  8 String widernodename = xpandquotes.replaceAll(nodename);
370  8 nodename = widernodename;
371    // jump to after end of quoted nodename
372  8 nextcp = fcp + nl + 1;
373  8 parsednodename = true;
374    }
375    else
376    {
377  0 Error = ErrorStringrange(Error,
378    "Unterminated quotes for nodename", 7, fcp, nf);
379    }
380   
381  8 break;
382   
383  521 default:
384  521 if (schar == ';')
385    {
386  23 if (d != -1)
387    {
388  0 Error = ErrorStringrange(Error,
389    "Wayward semicolon (depth=" + d + ")", 7, fcp, nf);
390    }
391    // cp advanced at the end of default
392    }
393  521 if (schar == '[')
394    {
395    // node string contains Comment or structured/extended NH format info
396    /*
397    * if ((fcp-cp>1 && nf.substring(cp,fcp).trim().length()>1)) { // will
398    * process in remains jalview.bin.Console.errPrintln("skipped text:
399    * '"+nf.substring(cp,fcp)+"'"); }
400    */
401    // verify termination.
402  0 Regex comment = new Regex("]");
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    // Parse simpler field strings
420  521 String fstring = nf.substring(ncp, fcp);
421    // remove any comments before we parse the node info
422    // TODO: test newick file with quoted square brackets in node name (is
423    // this allowed?)
424  521 while (fstring.indexOf(']') > -1)
425    {
426  0 int cstart = fstring.indexOf('[');
427  0 int cend = fstring.indexOf(']');
428  0 commentString2 = fstring.substring(cstart + 1, cend);
429  0 fstring = fstring.substring(0, cstart)
430    + fstring.substring(cend + 1);
431   
432    }
433  521 Regex uqnodename = new Regex("\\b([^' :;\\](),]+)");
434  521 Regex nbootstrap = new Regex("\\s*([0-9+]+)\\s*:");
435  521 Regex ndist = new Regex(":([-0-9Ee.+]+)");
436   
437  521 if (!parsednodename && uqnodename.search(fstring)
438    && ((uqnodename.matchedFrom(1) == 0) || (fstring
439    .charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
440    // HACK!
441    {
442  264 if (nodename == null)
443    {
444  264 if (ReplaceUnderscores)
445    {
446  0 nodename = uqnodename.stringMatched(1).replace('_', ' ');
447    }
448    else
449    {
450  264 nodename = uqnodename.stringMatched(1);
451    }
452    }
453    else
454    {
455  0 Error = ErrorStringrange(Error,
456    "File has broken algorithm - overwritten nodename", 10,
457    fcp, nf);
458    }
459    }
460    // get comment bootstraps
461   
462  521 if (nbootstrap.search(fstring))
463    {
464  36 if (nbootstrap.stringMatched(1)
465    .equals(uqnodename.stringMatched(1)))
466    {
467  0 nodename = null; // no nodename here.
468    }
469  36 if (nodename == null || nodename.length() == 0
470    || nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1)
471    + uqnodename.stringMatched().length()))
472    {
473  0 try
474    {
475  0 bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
476    .intValue();
477  0 HasBootstrap = true;
478    } catch (Exception e)
479    {
480  0 Error = ErrorStringrange(Error, "Can't parse bootstrap value",
481    4, ncp + nbootstrap.matchedFrom(), nf);
482    }
483    }
484    }
485   
486  521 boolean nodehasdistance = false;
487   
488  521 if (ndist.search(fstring))
489    {
490  498 try
491    {
492  498 distance = (Double.valueOf(ndist.stringMatched(1)))
493    .floatValue();
494  498 HasDistances = true;
495  498 nodehasdistance = true;
496    } catch (Exception e)
497    {
498  0 Error = ErrorStringrange(Error,
499    "Can't parse node distance value", 7,
500    ncp + ndist.matchedFrom(), nf);
501    }
502    }
503   
504  521 if (ascending)
505    {
506    // Write node info here
507  249 c.setName(nodename);
508    // Trees without distances still need a render distance
509  249 c.dist = (HasDistances) ? distance : DefDistance;
510    // be consistent for internal bootstrap defaults too
511  249 c.setBootstrap((HasBootstrap) ? bootstrap : DefBootstrap);
512  249 if (c == realroot)
513    {
514  23 RootHasDistance = nodehasdistance; // JBPNote This is really
515    // UGLY!!! Ensure root node gets
516    // its given distance
517    }
518  249 parseNHXNodeProps(c, commentString2);
519  249 commentString2 = null;
520    }
521    else
522    {
523    // Find a place to put the leaf
524  272 BinaryNode newnode = new SequenceNode(null, c, nodename,
525  272 (HasDistances) ? distance : DefDistance,
526  272 (HasBootstrap) ? bootstrap : DefBootstrap, false);
527  272 parseNHXNodeProps(c, commentString2);
528  272 commentString2 = null;
529   
530  272 if (c.right() == null)
531    {
532  159 c.setRight(newnode);
533    }
534    else
535    {
536  113 if (c.left() == null)
537    {
538  113 c.setLeft(newnode);
539    }
540    else
541    {
542    // Insert a dummy node for polytomy
543    // dummy nodes have distances
544  0 BinaryNode newdummy = new SequenceNode(null, c, null,
545  0 (HasDistances ? 0 : DefDistance), 0, true);
546  0 newdummy.SetChildren(c.left(), newnode);
547  0 c.setLeft(newdummy);
548    }
549    }
550    }
551   
552  521 if (ascending)
553    {
554    // move back up the tree from preceding closure
555  249 c = c.AscendTree();
556   
557  249 if ((d > -1) && (c == null))
558    {
559  0 Error = ErrorStringrange(Error,
560    "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
561    7, fcp, nf);
562    }
563    }
564   
565  521 if (nf.charAt(fcp) == ')')
566    {
567  249 d--;
568  249 ascending = true;
569    }
570    else
571    {
572  272 if (nf.charAt(fcp) == ',')
573    {
574  249 if (ascending)
575    {
576  90 ascending = false;
577    }
578    else
579    {
580    // Just advance focus, if we need to
581  159 if ((c.left() != null) && (!c.left().isLeaf()))
582    {
583  0 c = c.left();
584    }
585    }
586    }
587    }
588   
589    // Reset new node properties to obvious fakes
590  521 nodename = null;
591  521 distance = DefDistance;
592  521 bootstrap = DefBootstrap;
593  521 commentString2 = null;
594  521 parsednodename = false;
595    }
596  778 if (nextcp == 0)
597    {
598  770 ncp = cp = fcp + 1;
599    }
600    else
601    {
602  8 cp = nextcp;
603  8 nextcp = 0;
604    }
605    }
606   
607  23 if (Error != null)
608    {
609  0 throw (new IOException(
610    MessageManager.formatMessage("exception.newfile", new String[]
611    { Error.toString() })));
612    }
613  23 if (root == null)
614    {
615  0 throw (new IOException(
616    MessageManager.formatMessage("exception.newfile", new String[]
617    { MessageManager.getString("label.no_tree_read_in") })));
618    }
619    // THe next line is failing for topali trees - not sure why yet. if
620    // (root.right()!=null && root.isDummy())
621  23 root = root.right().detach(); // remove the imaginary root.
622   
623  23 if (!RootHasDistance)
624    {
625  23 root.dist = (HasDistances) ? 0 : DefDistance;
626    }
627    }
628   
629    /**
630    * parse NHX codes in comment strings and update NewickFile state flags for
631    * distances and bootstraps, and add any additional properties onto the node.
632    *
633    * @param c
634    * @param commentString
635    * @param commentString2
636    */
 
637  521 toggle private void parseNHXNodeProps(BinaryNode c, String commentString)
638    {
639    // TODO: store raw comment on the sequenceNode so it can be recovered when
640    // tree is output
641  521 if (commentString != null && commentString.startsWith("&&NHX"))
642    {
643  0 StringTokenizer st = new StringTokenizer(commentString.substring(5),
644    ":");
645  0 while (st.hasMoreTokens())
646    {
647  0 String tok = st.nextToken();
648  0 int colpos = tok.indexOf("=");
649   
650  0 if (colpos > -1)
651    {
652  0 String code = tok.substring(0, colpos);
653  0 String value = tok.substring(colpos + 1);
654  0 try
655    {
656    // parse out code/value pairs
657  0 if (code.toLowerCase(Locale.ROOT).equals("b"))
658    {
659  0 int v = -1;
660  0 Float iv = Float.valueOf(value);
661  0 v = iv.intValue(); // jalview only does integer bootstraps
662    // currently
663  0 c.setBootstrap(v);
664  0 HasBootstrap = true;
665    }
666    // more codes here.
667    } catch (Exception e)
668    {
669  0 jalview.bin.Console.errPrintln(
670    "Couldn't parse code '" + code + "' = '" + value + "'");
671  0 e.printStackTrace(System.err);
672    }
673    }
674    }
675    }
676   
677    }
678   
679    /**
680    * DOCUMENT ME!
681    *
682    * @return DOCUMENT ME!
683    */
 
684  52 toggle public BinaryNode getTree()
685    {
686  52 return root;
687    }
688   
689    /**
690    * Generate a newick format tree according to internal flags for bootstraps,
691    * distances and root distances.
692    *
693    * @return new hampshire tree in a single line
694    */
 
695  12 toggle public String print()
696    {
697  12 synchronized (this)
698    {
699  12 StringBuffer tf = new StringBuffer();
700  12 print(tf, root);
701   
702  12 return (tf.append(";").toString());
703    }
704    }
705   
706    /**
707    *
708    *
709    * Generate a newick format tree according to internal flags for distances and
710    * root distances and user specificied writing of bootstraps.
711    *
712    * @param withbootstraps
713    * controls if bootstrap values are explicitly written.
714    *
715    * @return new hampshire tree in a single line
716    */
 
717  9 toggle public String print(boolean withbootstraps)
718    {
719  9 synchronized (this)
720    {
721  9 boolean boots = this.HasBootstrap;
722  9 this.HasBootstrap = withbootstraps;
723   
724  9 String rv = print();
725  9 this.HasBootstrap = boots;
726   
727  9 return rv;
728    }
729    }
730   
731    /**
732    *
733    * Generate newick format tree according to internal flags for writing root
734    * node distances.
735    *
736    * @param withbootstraps
737    * explicitly write bootstrap values
738    * @param withdists
739    * explicitly write distances
740    *
741    * @return new hampshire tree in a single line
742    */
 
743  9 toggle public String print(boolean withbootstraps, boolean withdists)
744    {
745  9 synchronized (this)
746    {
747  9 boolean dists = this.HasDistances;
748  9 this.HasDistances = withdists;
749   
750  9 String rv = print(withbootstraps);
751  9 this.HasDistances = dists;
752   
753  9 return rv;
754    }
755    }
756   
757    /**
758    * Generate newick format tree according to user specified flags
759    *
760    * @param withbootstraps
761    * explicitly write bootstrap values
762    * @param withdists
763    * explicitly write distances
764    * @param printRootInfo
765    * explicitly write root distance
766    *
767    * @return new hampshire tree in a single line
768    */
 
769  4 toggle public String print(boolean withbootstraps, boolean withdists,
770    boolean printRootInfo)
771    {
772  4 synchronized (this)
773    {
774  4 boolean rootinfo = printRootInfo;
775  4 this.printRootInfo = printRootInfo;
776   
777  4 String rv = print(withbootstraps, withdists);
778  4 this.printRootInfo = rootinfo;
779   
780  4 return rv;
781    }
782    }
783   
784    /**
785    * DOCUMENT ME!
786    *
787    * @return DOCUMENT ME!
788    */
 
789  0 toggle char getQuoteChar()
790    {
791  0 return QuoteChar;
792    }
793   
794    /**
795    * DOCUMENT ME!
796    *
797    * @param c
798    * DOCUMENT ME!
799    *
800    * @return DOCUMENT ME!
801    */
 
802  0 toggle char setQuoteChar(char c)
803    {
804  0 char old = QuoteChar;
805  0 QuoteChar = c;
806   
807  0 return old;
808    }
809   
810    /**
811    * DOCUMENT ME!
812    *
813    * @param name
814    * DOCUMENT ME!
815    *
816    * @return DOCUMENT ME!
817    */
 
818  185 toggle private String nodeName(String name)
819    {
820  185 if (NodeSafeName[0].search(name))
821    {
822  4 return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
823    }
824    else
825    {
826  181 return NodeSafeName[2].replaceAll(name);
827    }
828    }
829   
830    /**
831    * Default method for generating a string for a node in a tree - override if
832    * you need to inject custom strings for nodes in a newick file
833    *
834    * @param c
835    * - binary node - may be null !
836    * @return null - or a string to be used for the given node in the exported
837    * newick file
838    */
 
839  535 toggle public String getNodenameFor(BinaryNode c)
840    {
841  535 if (c == null)
842    {
843  0 return null;
844    }
845  535 return c.getName();
846    }
847   
848    /**
849    * DOCUMENT ME!
850    *
851    * @param c
852    * DOCUMENT ME!
853    *
854    * @return DOCUMENT ME!
855    */
 
856  346 toggle private String printNodeField(BinaryNode c)
857    {
858  346 return ((getNodenameFor(c) == null) ? "" : nodeName(getNodenameFor(c)))
859  116 + ((HasBootstrap) ? ((c.getBootstrap() > -1)
860  116 ? ((getNodenameFor(c) != null ? " " : "")
861    + c.getBootstrap())
862    : "") : "")
863  346 + ((HasDistances) ? (":" + c.dist) : "");
864    }
865   
866    /**
867    * DOCUMENT ME!
868    *
869    * @param root
870    * DOCUMENT ME!
871    *
872    * @return DOCUMENT ME!
873    */
 
874  12 toggle private String printRootField(BinaryNode root)
875    {
876  12 return (printRootInfo)
877  8 ? (((getNodenameFor(root) == null) ? ""
878    : nodeName(getNodenameFor(root)))
879  1 + ((HasBootstrap) ? ((root.getBootstrap() > -1)
880  1 ? ((getNodenameFor(root) != null ? " " : "")
881    + +root.getBootstrap())
882    : "") : "")
883  8 + ((RootHasDistance) ? (":" + root.dist) : ""))
884    : "";
885    }
886   
887    // Non recursive call deals with root node properties
 
888  12 toggle public void print(StringBuffer tf, BinaryNode root)
889    {
890  12 if (root != null)
891    {
892  12 if (root.isLeaf() && printRootInfo)
893    {
894  0 tf.append(printRootField(root));
895    }
896    else
897    {
898  12 if (root.isDummy())
899    {
900  0 _print(tf, root.right());
901  0 _print(tf, root.left());
902    }
903    else
904    {
905  12 tf.append("(");
906  12 _print(tf, root.right());
907   
908  12 if (root.left() != null)
909    {
910  12 tf.append(",");
911    }
912   
913  12 _print(tf, root.left());
914  12 tf.append(")" + printRootField(root));
915    }
916    }
917    }
918    }
919   
920    // Recursive call for non-root nodes
 
921  346 toggle public void _print(StringBuffer tf, BinaryNode c)
922    {
923  346 if (c != null)
924    {
925  346 if (c.isLeaf())
926    {
927  185 tf.append(printNodeField(c));
928    }
929    else
930    {
931  161 if (c.isDummy())
932    {
933  0 _print(tf, c.left());
934  0 if (c.left() != null)
935    {
936  0 tf.append(",");
937    }
938  0 _print(tf, c.right());
939    }
940    else
941    {
942  161 tf.append("(");
943  161 _print(tf, c.right());
944   
945  161 if (c.left() != null)
946    {
947  161 tf.append(",");
948    }
949   
950  161 _print(tf, c.left());
951  161 tf.append(")" + printNodeField(c));
952    }
953    }
954    }
955    }
956   
957    /**
958    *
959    * @param args
960    * @j2sIgnore
961    */
 
962  0 toggle public static void main(String[] args)
963    {
964  0 try
965    {
966  0 if (args == null || args.length != 1)
967    {
968  0 Jalview.exit(
969    "Takes one argument - file name of a newick tree file.",
970    ExitCode.INVALID_ARGUMENT);
971    }
972   
973  0 File fn = new File(args[0]);
974   
975  0 StringBuffer newickfile = new StringBuffer();
976  0 BufferedReader treefile = new BufferedReader(new FileReader(fn));
977  0 String l;
978   
979  0 while ((l = treefile.readLine()) != null)
980    {
981  0 newickfile.append(l);
982    }
983   
984  0 treefile.close();
985  0 jalview.bin.Console.outPrintln("Read file :\n");
986   
987  0 NewickFile trf = new NewickFile(args[0], DataSourceType.FILE);
988  0 trf.parse();
989  0 jalview.bin.Console.outPrintln("Original file :\n");
990   
991  0 Regex nonl = new Regex("\n+", "");
992  0 jalview.bin.Console
993    .outPrintln(nonl.replaceAll(newickfile.toString()) + "\n");
994   
995  0 jalview.bin.Console.outPrintln("Parsed file.\n");
996  0 jalview.bin.Console
997    .outPrintln("Default output type for original input.\n");
998  0 jalview.bin.Console.outPrintln(trf.print());
999  0 jalview.bin.Console.outPrintln("Without bootstraps.\n");
1000  0 jalview.bin.Console.outPrintln(trf.print(false));
1001  0 jalview.bin.Console.outPrintln("Without distances.\n");
1002  0 jalview.bin.Console.outPrintln(trf.print(true, false));
1003  0 jalview.bin.Console
1004    .outPrintln("Without bootstraps but with distanecs.\n");
1005  0 jalview.bin.Console.outPrintln(trf.print(false, true));
1006  0 jalview.bin.Console.outPrintln("Without bootstraps or distanecs.\n");
1007  0 jalview.bin.Console.outPrintln(trf.print(false, false));
1008  0 jalview.bin.Console
1009    .outPrintln("With bootstraps and with distances.\n");
1010  0 jalview.bin.Console.outPrintln(trf.print(true, true));
1011    } catch (java.io.IOException e)
1012    {
1013  0 jalview.bin.Console.errPrintln("Exception\n" + e);
1014  0 e.printStackTrace();
1015    }
1016    }
1017    }
  • Report generated by OpenClover v 4.4.1 on Wed Sep 17 2025 11:01:30 BST using coverage data from Wed Sep 17 2025 11:01:17 BST.
  • OpenClover is free and open-source software.