Clover icon

Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.io

File NewickFile.java

 

Coverage histogram

../../img/srcFileCovDistChart6.png
33% of files have more coverage

Code metrics

138
270
26
1
997
604
112
0.41
10.38
26
4.31

Classes

Class Line # Actions
NewickFile 77 270 112
0.582949358.3%
 

Contributing tests

This file is covered by 9 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    import com.stevesoft.pat.Regex;
39   
40    /**
41    * Parse a new hanpshire style tree Caveats: NHX files are NOT supported and the
42    * tree distances and topology are unreliable when they are parsed. TODO: on
43    * this: NHX codes are appended in comments beginning with &&NHX. The codes are
44    * given below (from http://www.phylosoft.org/forester/NHX.html): Element Type
45    * Description Corresponding phyloXML element (parent element in parentheses) no
46    * tag string name of this node/clade (MUST BE FIRST, IF ASSIGNED)
47    * <name>(<clade>) : decimal branch length to parent node (MUST BE SECOND, IF
48    * ASSIGNED) <branch_length>(<clade>) :GN= string gene name <name>(<sequence>)
49    * :AC= string sequence accession <accession>(<sequence>) :ND= string node
50    * identifier - if this is being used, it has to be unique within each phylogeny
51    * <node_id>(<clade>) :B= decimal confidence value for parent branch
52    * <confidence>(<clade>) :D= 'T', 'F', or '?' 'T' if this node represents a
53    * duplication event - 'F' if this node represents a speciation event, '?' if
54    * this node represents an unknown event (D= tag should be replaced by Ev= tag)
55    * n/a :Ev=duplications>speciations>gene losses>event type>duplication type int
56    * int int string string event (replaces the =D tag), number of duplication,
57    * speciation, and gene loss events, type of event (transfer, fusion, root,
58    * unknown, other, speciation_duplication_loss, unassigned) <events>(<clade>)
59    * :E= string EC number at this node <annotation>(<sequence>) :Fu= string
60    * function at this node <annotation>(<sequence>)
61    * :DS=protein-length>from>to>support>name>from>... int int int double string
62    * int ... domain structure at this node <domain_architecture>(<sequence>) :S=
63    * string species name of the species/phylum at this node <taxonomy>(<clade>)
64    * :T= integer taxonomy ID of the species/phylum at this node <id>(<taxonomy>)
65    * :W= integer width of parent branch <width>(<clade>) :C=rrr.ggg.bbb
66    * integer.integer.integer color of parent branch <color>(<clade>) :Co= 'Y' or
67    * 'N' collapse this node when drawing the tree (default is not to collapse) n/a
68    * :XB= string custom data associated with a branch <property>(<clade>) :XN=
69    * string custom data associated with a node <property>(<clade>) :O= integer
70    * orthologous to this external node n/a :SN= integer subtree neighbors n/a :SO=
71    * integer super orthologous (no duplications on paths) to this external node
72    * n/a
73    *
74    * @author Jim Procter
75    * @version $Revision$
76    */
 
77    public class NewickFile extends FileParse
78    {
79    SequenceNode root;
80   
81    private boolean HasBootstrap = false;
82   
83    private boolean HasDistances = false;
84   
85    private boolean RootHasDistance = false;
86   
87    // File IO Flags
88    boolean ReplaceUnderscores = false;
89   
90    boolean printRootInfo = true;
91   
92    private Regex[] NodeSafeName = new Regex[] {
93    new Regex().perlCode("m/[\\[,:'()]/"), // test for
94    // requiring
95    // quotes
96    new Regex().perlCode("s/'/''/"), // escaping quote
97    // characters
98    new Regex().perlCode("s/\\/w/_/") // unqoted whitespace
99    // transformation
100    };
101   
102    char QuoteChar = '\'';
103   
104    /**
105    * Creates a new NewickFile object.
106    *
107    * @param inStr
108    * DOCUMENT ME!
109    *
110    * @throws IOException
111    * DOCUMENT ME!
112    */
 
113  8 toggle public NewickFile(String inStr) throws IOException
114    {
115  8 super(inStr, DataSourceType.PASTE);
116    }
117   
118    /**
119    * Creates a new NewickFile object.
120    *
121    * @param inFile
122    * DOCUMENT ME!
123    * @param protocol
124    * DOCUMENT ME!
125    *
126    * @throws IOException
127    * DOCUMENT ME!
128    */
 
129  7 toggle public NewickFile(String inFile, DataSourceType protocol)
130    throws IOException
131    {
132  7 super(inFile, protocol);
133    }
134   
 
135  0 toggle public NewickFile(FileParse source) throws IOException
136    {
137  0 super(source);
138    }
139   
140    /**
141    * Creates a new NewickFile object.
142    *
143    * @param newtree
144    * DOCUMENT ME!
145    */
 
146  5 toggle public NewickFile(SequenceNode newtree)
147    {
148  5 root = newtree;
149    }
150   
151    /**
152    * Creates a new NewickFile object.
153    *
154    * @param newtree
155    * DOCUMENT ME!
156    * @param bootstrap
157    * DOCUMENT ME!
158    */
 
159  0 toggle public NewickFile(SequenceNode newtree, boolean bootstrap)
160    {
161  0 HasBootstrap = bootstrap;
162  0 root = newtree;
163    }
164   
165    /**
166    * Creates a new NewickFile object.
167    *
168    * @param newtree
169    * DOCUMENT ME!
170    * @param bootstrap
171    * DOCUMENT ME!
172    * @param distances
173    * DOCUMENT ME!
174    */
 
175  0 toggle public NewickFile(SequenceNode newtree, boolean bootstrap,
176    boolean distances)
177    {
178  0 root = newtree;
179  0 HasBootstrap = bootstrap;
180  0 HasDistances = distances;
181    }
182   
183    /**
184    * Creates a new NewickFile object.
185    *
186    * @param newtree
187    * DOCUMENT ME!
188    * @param bootstrap
189    * DOCUMENT ME!
190    * @param distances
191    * DOCUMENT ME!
192    * @param rootdistance
193    * DOCUMENT ME!
194    */
 
195  0 toggle public NewickFile(SequenceNode newtree, boolean bootstrap,
196    boolean distances, boolean rootdistance)
197    {
198  0 root = newtree;
199  0 HasBootstrap = bootstrap;
200  0 HasDistances = distances;
201  0 RootHasDistance = rootdistance;
202    }
203   
204    /**
205    * DOCUMENT ME!
206    *
207    * @param Error
208    * DOCUMENT ME!
209    * @param Er
210    * DOCUMENT ME!
211    * @param r
212    * DOCUMENT ME!
213    * @param p
214    * DOCUMENT ME!
215    * @param s
216    * DOCUMENT ME!
217    *
218    * @return DOCUMENT ME!
219    */
 
220  0 toggle private String ErrorStringrange(String Error, String Er, int r, int p,
221    String s)
222    {
223  0 return ((Error == null) ? "" : Error) + Er + " at position " + p + " ( "
224  0 + s.substring(((p - r) < 0) ? 0 : (p - r),
225  0 ((p + r) > s.length()) ? s.length() : (p + r))
226    + " )\n";
227    }
228   
229    // @tree annotations
230    // These are set automatically by the reader
 
231  27 toggle public boolean HasBootstrap()
232    {
233  27 return HasBootstrap;
234    }
235   
236    /**
237    * DOCUMENT ME!
238    *
239    * @return DOCUMENT ME!
240    */
 
241  27 toggle public boolean HasDistances()
242    {
243  27 return HasDistances;
244    }
245   
 
246  15 toggle public boolean HasRootDistance()
247    {
248  15 return RootHasDistance;
249    }
250   
251    /**
252    * parse the filesource as a newick file (new hampshire and/or extended)
253    *
254    * @throws IOException
255    * with a line number and character position for badly formatted NH
256    * strings
257    */
 
258  15 toggle public void parse() throws IOException
259    {
260  15 String nf;
261   
262    { // fill nf with complete tree file
263   
264  15 StringBuffer file = new StringBuffer();
265   
266  ? while ((nf = nextLine()) != null)
267    {
268  15 file.append(nf);
269    }
270   
271  15 nf = file.toString();
272    }
273   
274  15 root = new SequenceNode();
275   
276  15 SequenceNode realroot = null;
277  15 SequenceNode c = root;
278   
279  15 int d = -1;
280  15 int cp = 0;
281    // int flen = nf.length();
282   
283  15 String Error = null;
284  15 String nodename = null;
285  15 String commentString2 = null; // comments after simple node props
286   
287  15 float DefDistance = (float) 0.001; // @param Default distance for a node -
288    // very very small
289  15 int DefBootstrap = -1; // @param Default bootstrap for a node
290   
291  15 float distance = DefDistance;
292  15 int bootstrap = DefBootstrap;
293   
294  15 boolean ascending = false; // flag indicating that we are leaving the
295    // current node
296   
297  15 Regex majorsyms = new Regex(
298    "[(\\['),;]");
299   
300  15 int nextcp = 0;
301  15 int ncp = cp;
302  15 boolean parsednodename = false;
303  392 while (majorsyms.searchFrom(nf, cp) && (Error == null))
304    {
305  377 int fcp = majorsyms.matchedFrom();
306  377 char schar;
307  377 switch (schar = nf.charAt(fcp))
308    {
309  118 case '(':
310   
311    // ascending should not be set
312    // New Internal node
313  118 if (ascending)
314    {
315  0 Error = ErrorStringrange(Error, "Unexpected '('", 7, fcp, nf);
316   
317  0 continue;
318    }
319  118 d++;
320   
321  118 if (c.right() == null)
322    {
323  59 c.setRight(new SequenceNode(null, c, null, DefDistance,
324    DefBootstrap, false));
325  59 c = (SequenceNode) c.right();
326    }
327    else
328    {
329  59 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  59 c.setLeft(new SequenceNode(null, c, null, DefDistance,
338    DefBootstrap, false));
339  59 c = (SequenceNode) c.left();
340    }
341   
342  118 if (realroot == null)
343    {
344  15 realroot = c;
345    }
346   
347  118 nodename = null;
348  118 distance = DefDistance;
349  118 bootstrap = DefBootstrap;
350  118 cp = fcp + 1;
351   
352  118 break;
353   
354    // Deal with quoted fields
355  8 case '\'':
356   
357  8 Regex qnodename = new 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 Regex xpandquotes = 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  251 default:
383  251 if (schar == ';')
384    {
385  15 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  251 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 Regex comment = new 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    // Parse simpler field strings
420  251 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  251 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  251 Regex uqnodename = new Regex(
434    "\\b([^' :;\\](),]+)");
435  251 Regex nbootstrap = new Regex(
436    "\\s*([0-9+]+)\\s*:");
437  251 Regex ndist = new Regex(
438    ":([-0-9Ee.+]+)");
439   
440  251 if (!parsednodename && uqnodename.search(fstring)
441    && ((uqnodename.matchedFrom(1) == 0) || (fstring
442    .charAt(uqnodename.matchedFrom(1) - 1) != ':'))) // JBPNote
443    // HACK!
444    {
445  125 if (nodename == null)
446    {
447  125 if (ReplaceUnderscores)
448    {
449  0 nodename = uqnodename.stringMatched(1).replace('_', ' ');
450    }
451    else
452    {
453  125 nodename = uqnodename.stringMatched(1);
454    }
455    }
456    else
457    {
458  0 Error = ErrorStringrange(Error,
459    "File has broken algorithm - overwritten nodename", 10,
460    fcp, nf);
461    }
462    }
463    // get comment bootstraps
464   
465  251 if (nbootstrap.search(fstring))
466    {
467  0 if (nbootstrap.stringMatched(1)
468    .equals(uqnodename.stringMatched(1)))
469    {
470  0 nodename = null; // no nodename here.
471    }
472  0 if (nodename == null || nodename.length() == 0
473    || nbootstrap.matchedFrom(1) > (uqnodename.matchedFrom(1)
474    + uqnodename.stringMatched().length()))
475    {
476  0 try
477    {
478  0 bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
479    .intValue();
480  0 HasBootstrap = true;
481    } catch (Exception e)
482    {
483  0 Error = ErrorStringrange(Error, "Can't parse bootstrap value",
484    4, ncp + nbootstrap.matchedFrom(), nf);
485    }
486    }
487    }
488   
489  251 boolean nodehasdistance = false;
490   
491  251 if (ndist.search(fstring))
492    {
493  236 try
494    {
495  236 distance = (Float.valueOf(ndist.stringMatched(1))).floatValue();
496  236 HasDistances = true;
497  236 nodehasdistance = true;
498    } catch (Exception e)
499    {
500  0 Error = ErrorStringrange(Error,
501    "Can't parse node distance value", 7,
502    ncp + ndist.matchedFrom(), nf);
503    }
504    }
505   
506  251 if (ascending)
507    {
508    // Write node info here
509  118 c.setName(nodename);
510    // Trees without distances still need a render distance
511  118 c.dist = (HasDistances) ? distance : DefDistance;
512    // be consistent for internal bootstrap defaults too
513  118 c.setBootstrap((HasBootstrap) ? bootstrap : DefBootstrap);
514  118 if (c == realroot)
515    {
516  15 RootHasDistance = nodehasdistance; // JBPNote This is really
517    // UGLY!!! Ensure root node gets
518    // its given distance
519    }
520  118 parseNHXNodeProps(c, commentString2);
521  118 commentString2 = null;
522    }
523    else
524    {
525    // Find a place to put the leaf
526  133 SequenceNode newnode = new SequenceNode(null, c, nodename,
527  133 (HasDistances) ? distance : DefDistance,
528  133 (HasBootstrap) ? bootstrap : DefBootstrap, false);
529  133 parseNHXNodeProps(c, commentString2);
530  133 commentString2 = null;
531   
532  133 if (c.right() == null)
533    {
534  74 c.setRight(newnode);
535    }
536    else
537    {
538  59 if (c.left() == null)
539    {
540  59 c.setLeft(newnode);
541    }
542    else
543    {
544    // Insert a dummy node for polytomy
545    // dummy nodes have distances
546  0 SequenceNode newdummy = new SequenceNode(null, c, null,
547  0 (HasDistances ? 0 : DefDistance), 0, true);
548  0 newdummy.SetChildren(c.left(), newnode);
549  0 c.setLeft(newdummy);
550    }
551    }
552    }
553   
554  251 if (ascending)
555    {
556    // move back up the tree from preceding closure
557  118 c = c.AscendTree();
558   
559  118 if ((d > -1) && (c == null))
560    {
561  0 Error = ErrorStringrange(Error,
562    "File broke algorithm: Lost place in tree (is there an extra ')' ?)",
563    7, fcp, nf);
564    }
565    }
566   
567  251 if (nf.charAt(fcp) == ')')
568    {
569  118 d--;
570  118 ascending = true;
571    }
572    else
573    {
574  133 if (nf.charAt(fcp) == ',')
575    {
576  118 if (ascending)
577    {
578  44 ascending = false;
579    }
580    else
581    {
582    // Just advance focus, if we need to
583  74 if ((c.left() != null) && (!c.left().isLeaf()))
584    {
585  0 c = (SequenceNode) c.left();
586    }
587    }
588    }
589    }
590   
591    // Reset new node properties to obvious fakes
592  251 nodename = null;
593  251 distance = DefDistance;
594  251 bootstrap = DefBootstrap;
595  251 commentString2 = null;
596  251 parsednodename = false;
597    }
598  377 if (nextcp == 0)
599    {
600  369 ncp = cp = fcp + 1;
601    }
602    else
603    {
604  8 cp = nextcp;
605  8 nextcp = 0;
606    }
607    }
608   
609  15 if (Error != null)
610    {
611  0 throw (new IOException(
612    MessageManager.formatMessage("exception.newfile", new String[]
613    { Error.toString() })));
614    }
615  15 if (root == null)
616    {
617  0 throw (new IOException(
618    MessageManager.formatMessage("exception.newfile", new String[]
619    { MessageManager.getString("label.no_tree_read_in") })));
620    }
621    // THe next line is failing for topali trees - not sure why yet. if
622    // (root.right()!=null && root.isDummy())
623  15 root = (SequenceNode) root.right().detach(); // remove the imaginary root.
624   
625  15 if (!RootHasDistance)
626    {
627  15 root.dist = (HasDistances) ? 0 : DefDistance;
628    }
629    }
630   
631    /**
632    * parse NHX codes in comment strings and update NewickFile state flags for
633    * distances and bootstraps, and add any additional properties onto the node.
634    *
635    * @param c
636    * @param commentString
637    * @param commentString2
638    */
 
639  251 toggle private void parseNHXNodeProps(SequenceNode c, String commentString)
640    {
641    // TODO: store raw comment on the sequenceNode so it can be recovered when
642    // tree is output
643  251 if (commentString != null && commentString.startsWith("&&NHX"))
644    {
645  0 StringTokenizer st = new StringTokenizer(commentString.substring(5),
646    ":");
647  0 while (st.hasMoreTokens())
648    {
649  0 String tok = st.nextToken();
650  0 int colpos = tok.indexOf("=");
651   
652  0 if (colpos > -1)
653    {
654  0 String code = tok.substring(0, colpos);
655  0 String value = tok.substring(colpos + 1);
656  0 try
657    {
658    // parse out code/value pairs
659  0 if (code.toLowerCase().equals("b"))
660    {
661  0 int v = -1;
662  0 Float iv = Float.valueOf(value);
663  0 v = iv.intValue(); // jalview only does integer bootstraps
664    // currently
665  0 c.setBootstrap(v);
666  0 HasBootstrap = true;
667    }
668    // more codes here.
669    } catch (Exception e)
670    {
671  0 System.err.println(
672    "Couldn't parse code '" + code + "' = '" + value + "'");
673  0 e.printStackTrace(System.err);
674    }
675    }
676    }
677    }
678   
679    }
680   
681    /**
682    * DOCUMENT ME!
683    *
684    * @return DOCUMENT ME!
685    */
 
686  36 toggle public SequenceNode getTree()
687    {
688  36 return root;
689    }
690   
691    /**
692    * Generate a newick format tree according to internal flags for bootstraps,
693    * distances and root distances.
694    *
695    * @return new hampshire tree in a single line
696    */
 
697  5 toggle public String print()
698    {
699  5 synchronized (this)
700    {
701  5 StringBuffer tf = new StringBuffer();
702  5 print(tf, root);
703   
704  5 return (tf.append(";").toString());
705    }
706    }
707   
708    /**
709    *
710    *
711    * Generate a newick format tree according to internal flags for distances and
712    * root distances and user specificied writing of bootstraps.
713    *
714    * @param withbootstraps
715    * controls if bootstrap values are explicitly written.
716    *
717    * @return new hampshire tree in a single line
718    */
 
719  5 toggle public String print(boolean withbootstraps)
720    {
721  5 synchronized (this)
722    {
723  5 boolean boots = this.HasBootstrap;
724  5 this.HasBootstrap = withbootstraps;
725   
726  5 String rv = print();
727  5 this.HasBootstrap = boots;
728   
729  5 return rv;
730    }
731    }
732   
733    /**
734    *
735    * Generate newick format tree according to internal flags for writing root
736    * node distances.
737    *
738    * @param withbootstraps
739    * explicitly write bootstrap values
740    * @param withdists
741    * explicitly write distances
742    *
743    * @return new hampshire tree in a single line
744    */
 
745  5 toggle public String print(boolean withbootstraps, boolean withdists)
746    {
747  5 synchronized (this)
748    {
749  5 boolean dists = this.HasDistances;
750  5 this.HasDistances = withdists;
751   
752  5 String rv = print(withbootstraps);
753  5 this.HasDistances = dists;
754   
755  5 return rv;
756    }
757    }
758   
759    /**
760    * Generate newick format tree according to user specified flags
761    *
762    * @param withbootstraps
763    * explicitly write bootstrap values
764    * @param withdists
765    * explicitly write distances
766    * @param printRootInfo
767    * explicitly write root distance
768    *
769    * @return new hampshire tree in a single line
770    */
 
771  2 toggle public String print(boolean withbootstraps, boolean withdists,
772    boolean printRootInfo)
773    {
774  2 synchronized (this)
775    {
776  2 boolean rootinfo = printRootInfo;
777  2 this.printRootInfo = printRootInfo;
778   
779  2 String rv = print(withbootstraps, withdists);
780  2 this.printRootInfo = rootinfo;
781   
782  2 return rv;
783    }
784    }
785   
786    /**
787    * DOCUMENT ME!
788    *
789    * @return DOCUMENT ME!
790    */
 
791  0 toggle char getQuoteChar()
792    {
793  0 return QuoteChar;
794    }
795   
796    /**
797    * DOCUMENT ME!
798    *
799    * @param c
800    * DOCUMENT ME!
801    *
802    * @return DOCUMENT ME!
803    */
 
804  0 toggle char setQuoteChar(char c)
805    {
806  0 char old = QuoteChar;
807  0 QuoteChar = c;
808   
809  0 return old;
810    }
811   
812    /**
813    * DOCUMENT ME!
814    *
815    * @param name
816    * DOCUMENT ME!
817    *
818    * @return DOCUMENT ME!
819    */
 
820  39 toggle private String nodeName(String name)
821    {
822  39 if (NodeSafeName[0].search(name))
823    {
824  4 return QuoteChar + NodeSafeName[1].replaceAll(name) + QuoteChar;
825    }
826    else
827    {
828  35 return NodeSafeName[2].replaceAll(name);
829    }
830    }
831   
832    /**
833    * DOCUMENT ME!
834    *
835    * @param c
836    * DOCUMENT ME!
837    *
838    * @return DOCUMENT ME!
839    */
 
840  68 toggle private String printNodeField(SequenceNode c)
841    {
842  68 return ((c.getName() == null) ? "" : nodeName(c.getName()))
843  68 + ((HasBootstrap) ? ((c.getBootstrap() > -1)
844  0 ? ((c.getName() != null ? " " : "") + c.getBootstrap())
845    : "") : "")
846  68 + ((HasDistances) ? (":" + c.dist) : "");
847    }
848   
849    /**
850    * DOCUMENT ME!
851    *
852    * @param root
853    * DOCUMENT ME!
854    *
855    * @return DOCUMENT ME!
856    */
 
857  5 toggle private String printRootField(SequenceNode root)
858    {
859  5 return (printRootInfo)
860  3 ? (((root.getName() == null) ? "" : nodeName(root.getName()))
861  3 + ((HasBootstrap)
862  0 ? ((root.getBootstrap() > -1)
863  0 ? ((root.getName() != null ? " " : "")
864    + +root.getBootstrap())
865    : "")
866    : "")
867  3 + ((RootHasDistance) ? (":" + root.dist) : ""))
868    : "";
869    }
870   
871    // Non recursive call deals with root node properties
 
872  5 toggle public void print(StringBuffer tf, SequenceNode root)
873    {
874  5 if (root != null)
875    {
876  5 if (root.isLeaf() && printRootInfo)
877    {
878  0 tf.append(printRootField(root));
879    }
880    else
881    {
882  5 if (root.isDummy())
883    {
884  0 _print(tf, (SequenceNode) root.right());
885  0 _print(tf, (SequenceNode) root.left());
886    }
887    else
888    {
889  5 tf.append("(");
890  5 _print(tf, (SequenceNode) root.right());
891   
892  5 if (root.left() != null)
893    {
894  5 tf.append(",");
895    }
896   
897  5 _print(tf, (SequenceNode) root.left());
898  5 tf.append(")" + printRootField(root));
899    }
900    }
901    }
902    }
903   
904    // Recursive call for non-root nodes
 
905  68 toggle public void _print(StringBuffer tf, SequenceNode c)
906    {
907  68 if (c != null)
908    {
909  68 if (c.isLeaf())
910    {
911  39 tf.append(printNodeField(c));
912    }
913    else
914    {
915  29 if (c.isDummy())
916    {
917  0 _print(tf, (SequenceNode) c.left());
918  0 if (c.left() != null)
919    {
920  0 tf.append(",");
921    }
922  0 _print(tf, (SequenceNode) c.right());
923    }
924    else
925    {
926  29 tf.append("(");
927  29 _print(tf, (SequenceNode) c.right());
928   
929  29 if (c.left() != null)
930    {
931  29 tf.append(",");
932    }
933   
934  29 _print(tf, (SequenceNode) c.left());
935  29 tf.append(")" + printNodeField(c));
936    }
937    }
938    }
939    }
940   
941    /**
942    *
943    * @param args
944    * @j2sIgnore
945    */
 
946  0 toggle public static void main(String[] args)
947    {
948  0 try
949    {
950  0 if (args == null || args.length != 1)
951    {
952  0 System.err.println(
953    "Takes one argument - file name of a newick tree file.");
954  0 System.exit(0);
955    }
956   
957  0 File fn = new File(args[0]);
958   
959  0 StringBuffer newickfile = new StringBuffer();
960  0 BufferedReader treefile = new BufferedReader(new FileReader(fn));
961  0 String l;
962   
963  0 while ((l = treefile.readLine()) != null)
964    {
965  0 newickfile.append(l);
966    }
967   
968  0 treefile.close();
969  0 System.out.println("Read file :\n");
970   
971  0 NewickFile trf = new NewickFile(args[0], DataSourceType.FILE);
972  0 trf.parse();
973  0 System.out.println("Original file :\n");
974   
975  0 Regex nonl = new Regex("\n+", "");
976  0 System.out.println(nonl.replaceAll(newickfile.toString()) + "\n");
977   
978  0 System.out.println("Parsed file.\n");
979  0 System.out.println("Default output type for original input.\n");
980  0 System.out.println(trf.print());
981  0 System.out.println("Without bootstraps.\n");
982  0 System.out.println(trf.print(false));
983  0 System.out.println("Without distances.\n");
984  0 System.out.println(trf.print(true, false));
985  0 System.out.println("Without bootstraps but with distanecs.\n");
986  0 System.out.println(trf.print(false, true));
987  0 System.out.println("Without bootstraps or distanecs.\n");
988  0 System.out.println(trf.print(false, false));
989  0 System.out.println("With bootstraps and with distances.\n");
990  0 System.out.println(trf.print(true, true));
991    } catch (java.io.IOException e)
992    {
993  0 System.err.println("Exception\n" + e);
994  0 e.printStackTrace();
995    }
996    }
997    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.