Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
GroupUrlLink	28	252	109	0.00%	Show methods
GroupUrlLink.UrlStringTooLongException	30	2	2	0.00%	Show methods

Class GroupUrlLink

Class GroupUrlLink	Line # 28	Total Statements 252	Complexity 109	TOTAL Coverage 0.00%
<clinit>, line 82()   <clinit>, line 82()	8282	2.02	2.02	0.0 0.00%
GroupUrlLink(String)   GroupUrlLink(String)	116116	67.067	23.023	0.0 0.00%
getUrl_suffix() : String   getUrl_suffix() : String	281281	1.01	1.01	0.0 0.00%
getUrl_prefix() : String   getUrl_prefix() : String	289289	1.01	1.01	0.0 0.00%
getTarget() : String   getTarget() : String	297297	1.01	1.01	0.0 0.00%
getLabel() : String   getLabel() : String	305305	1.01	1.01	0.0 0.00%
getIDRegexReplace() : String   getIDRegexReplace() : String	313313	1.01	1.01	0.0 0.00%
_replaceFor(String) : String   _replaceFor(String) : String	318318	4.04	4.04	0.0 0.00%
getSeqRegexReplace() : String   getSeqRegexReplace() : String	333333	1.01	1.01	0.0 0.00%
getInvalidMessage() : String   getInvalidMessage() : String	341341	1.01	1.01	0.0 0.00%
isValid() : boolean   isValid() : boolean	352352	1.01	1.01	0.0 0.00%
makeUrls(String[],String[],String,boolean) : Object[]   makeUrls(String[],String[],String,boolean) : Object[]	373373	2.02	1.01	0.0 0.00%
replacementArgs(String[],String[],String) : Hashtable   replacementArgs(String[],String[],String) : Hashtable	389389	7.07	2.02	0.0 0.00%
makeUrls(Hashtable,boolean) : Object[]   makeUrls(Hashtable,boolean) : Object[]	404404	1.01	1.01	0.0 0.00%
makeUrlStubs(String[],String[],String,boolean) : Object[]   makeUrlStubs(String[],String[],String,boolean) : Object[]	419419	5.05	2.02	0.0 0.00%
constructFrom(Object[]) : String   constructFrom(Object[]) : String	442442	2.02	1.01	0.0 0.00%
makeUrlsIf(boolean,Hashtable,boolean) : Object[]   makeUrlsIf(boolean,Hashtable,boolean) : Object[]	463463	88.088	42.042	0.0 0.00%
getNumberInvolved(Object[]) : int   getNumberInvolved(Object[]) : int	722722	1.01	1.01	0.0 0.00%
getGroupURLType() : int   getGroupURLType() : int	734734	6.06	4.04	0.0 0.00%
toString() : String   toString() : String	750750	16.016	4.04	0.0 0.00%
testUrls(GroupUrlLink,String[][],Object[]) : void   testUrls(GroupUrlLink,String[][],Object[]) : void	784784	13.013	6.06	0.0 0.00%
main(String[]) : void   main(String[]) : void	824824	24.024	5.05	0.0 0.00%
formStrings(SequenceI[]) : String[][]   formStrings(SequenceI[]) : String[][]	900900	5.05	2.02	0.0 0.00%
setLabel(String) : void   setLabel(String) : void	911911	1.01	1.01	0.0 0.00%

 

Class GroupUrlLink.UrlStringTooLongException

Class GroupUrlLink.UrlStringTooLongException	Line # 30	Total Statements 2	Complexity 2	TOTAL Coverage 0.00%
UrlStringTooLongException(int)   UrlStringTooLongException(int)	3232	1.01	1.01	0.0 0.00%
toString() : String   toString() : String	3939	1.01	1.01	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		package jalview.util;
22
23		import jalview.datamodel.Sequence;
24		import jalview.datamodel.SequenceI;
25
26		import java.util.Hashtable;
27
		0% Uncovered Elements: 418 (418) Complexity: 109 Complexity Density: 0.43
28		public class GroupUrlLink
29		{
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
30		public class UrlStringTooLongException extends Exception
31		{
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
32	0	public UrlStringTooLongException(int lng)...
33		{
34	0	urlLength = lng;
35		}
36
37		public int urlLength;
38
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
39	0	@Override...
40		public String toString()
41		{
42	0	return "Generated url is estimated to be too long (" + urlLength
43		+ ")";
44		}
45		}
46
47		/**
48		* Helper class based on the UrlLink class which enables URLs to be
49		* constructed from sequences or IDs associated with a group of sequences. URL
50		* definitions consist of a pipe separated string containing a <label>|<url
51		* construct>|<separator character>[|<sequence separator character>]. The url
52		* construct includes regex qualified tokens which are replaced with seuqence
53		* IDs ($SEQUENCE_IDS$) and/or seuqence regions ($SEQUENCES$) that are
54		* extracted from the group. See <code>UrlLink</code> for more information
55		* about the approach, and the original implementation. Documentation to come.
56		* Note - groupUrls can be very big!
57		*/
58		private String url_prefix, target, label;
59
60		/**
61		* these are all filled in order of the occurence of each token in the url
62		* string template
63		*/
64		private String url_suffix[], separators[], regexReplace[];
65
66		private String invalidMessage = null;
67
68		/**
69		* tokens that can be replaced in the URL.
70		*/
71		private static String[] tokens;
72
73		/**
74		* position of each token (which can appear once only) in the url
75		*/
76		private int[] segs;
77
78		/**
79		* contains tokens in the order they appear in the URL template.
80		*/
81		private String[] mtch;
		0% Uncovered Elements: 4 (4) Complexity: 2 Complexity Density: 1
82	0	static...
83		{
84	0	if (tokens == null)
85		{
86	0	tokens = new String[] { "SEQUENCEIDS", "SEQUENCES", "DATASETID" };
87		}
88		}
89
90		/**
91		* test for GroupURLType bitfield (with default tokens)
92		*/
93		public static final int SEQUENCEIDS = 1;
94
95		/**
96		* test for GroupURLType bitfield (with default tokens)
97		*/
98		public static final int SEQUENCES = 2;
99
100		/**
101		* test for GroupURLType bitfield (with default tokens)
102		*/
103		public static final int DATASETID = 4;
104
105		// private int idseg = -1, seqseg = -1;
106
107		/**
108		* parse the given linkString of the form '<label>|<url>|separator
109		* char[|optional sequence separator char]' into parts. url may contain a
110		* string $SEQUENCEIDS<=optional regex=>$ where <=optional regex=> must be of
111		* the form =/<perl style regex>/=$ or $SEQUENCES<=optional regex=>$ or
112		* $SEQUENCES<=optional regex=>$.
113		*
114		* @param link
115		*/
		0% Uncovered Elements: 105 (105) Complexity: 23 Complexity Density: 0.34
116	0	public GroupUrlLink(String link)...
117		{
118	0	int sep = link.indexOf("|");
119	0	segs = new int[tokens.length];
120	0	int ntoks = 0;
121	0	for (int i = 0; i < segs.length; i++)
122		{
123	0	if ((segs[i] = link.indexOf("$" + tokens[i])) > -1)
124		{
125	0	ntoks++;
126		}
127		}
128		// expect at least one token
129	0	if (ntoks == 0)
130		{
131	0	invalidMessage = "Group URL string must contain at least one of ";
132	0	for (int i = 0; i < segs.length; i++)
133		{
134	0	invalidMessage += " '$" + tokens[i] + "[=/regex=/]$'";
135		}
136	0	return;
137		}
138
139	0	int[] ptok = new int[ntoks + 1];
140	0	String[] tmtch = new String[ntoks + 1];
141	0	mtch = new String[ntoks];
142	0	for (int i = 0, t = 0; i < segs.length; i++)
143		{
144	0	if (segs[i] > -1)
145		{
146	0	ptok[t] = segs[i];
147	0	tmtch[t++] = tokens[i];
148		}
149		}
150	0	ptok[ntoks] = link.length();
151	0	tmtch[ntoks] = "$$$$$$$$$";
152	0	jalview.util.QuickSort.sort(ptok, tmtch);
153	0	for (int i = 0; i < ntoks; i++)
154		{
155	0	mtch[i] = tmtch[i]; // TODO: check order is ascending
156		}
157		/*
158		* replaces the specific code below {}; if (psqids > -1 && pseqs > -1) { if
159		* (psqids > pseqs) { idseg = 1; seqseg = 0;
160		*
161		* ptok = new int[] { pseqs, psqids, link.length() }; mtch = new String[] {
162		* "$SEQUENCES", "$SEQUENCEIDS" }; } else { idseg = 0; seqseg = 1; ptok =
163		* new int[] { psqids, pseqs, link.length() }; mtch = new String[] {
164		* "$SEQUENCEIDS", "$SEQUENCES" }; } } else { if (psqids != -1) { idseg = 0;
165		* ptok = new int[] { psqids, link.length() }; mtch = new String[] {
166		* "$SEQUENCEIDS" }; } else { seqseg = 0; ptok = new int[] { pseqs,
167		* link.length() }; mtch = new String[] { "$SEQUENCES" }; } }
168		*/
169
170	0	int p = sep;
171		// first get the label and target part before the first |
172	0	do
173		{
174	0	sep = p;
175	0	p = link.indexOf("|", sep + 1);
176	0	} while (p > sep && p < ptok[0]);
177		// Assuming that the URL itself does not contain any '|' symbols
178		// sep now contains last pipe symbol position prior to any regex symbols
179	0	label = link.substring(0, sep);
180	0	if (label.indexOf("|") > -1)
181		{
182		// | terminated database name / www target at start of Label
183	0	target = label.substring(0, label.indexOf("|"));
184		}
185	0	else if (label.indexOf(" ") > 2)
186		{
187		// space separated Label - matches database name
188	0	target = label.substring(0, label.indexOf(" "));
189		}
190		else
191		{
192	0	target = label;
193		}
194		// Now Parse URL : Whole URL string first
195	0	url_prefix = link.substring(sep + 1, ptok[0]);
196	0	url_suffix = new String[mtch.length];
197	0	regexReplace = new String[mtch.length];
198		// and loop through tokens
199	0	for (int pass = 0; pass < mtch.length; pass++)
200		{
201	0	int mlength = 3 + mtch[pass].length();
202	0	if (link.indexOf("$" + mtch[pass] + "=/") == ptok[pass] && (p = link
203		.indexOf("/=$", ptok[pass] + mlength)) > ptok[pass] + mlength)
204		{
205		// Extract Regex and suffix
206	0	if (ptok[pass + 1] < p + 3)
207		{
208		// tokens are not allowed inside other tokens - e.g. inserting a
209		// $sequences$ into the regex match for the sequenceid
210	0	invalidMessage = "Token regexes cannot contain other regexes (did you terminate the $"
211		+ mtch[pass] + " regex with a '/=$' ?";
212	0	return;
213		}
214	0	url_suffix[pass] = link.substring(p + 3, ptok[pass + 1]);
215	0	regexReplace[pass] = link.substring(ptok[pass] + mlength, p);
216	0	try
217		{
218	0	com.stevesoft.pat.Regex rg = com.stevesoft.pat.Regex
219		.perlCode("/" + regexReplace[pass] + "/");
220	0	if (rg == null)
221		{
222	0	invalidMessage = "Invalid Regular Expression : '"
223		+ regexReplace[pass] + "'\n";
224		}
225		} catch (Exception e)
226		{
227	0	invalidMessage = "Invalid Regular Expression : '"
228		+ regexReplace[pass] + "'\n";
229		}
230		}
231		else
232		{
233	0	regexReplace[pass] = null;
234		// verify format is really correct.
235	0	if ((p = link.indexOf("$" + mtch[pass] + "$")) == ptok[pass])
236		{
237	0	url_suffix[pass] = link.substring(p + mtch[pass].length() + 2,
238		ptok[pass + 1]);
239		}
240		else
241		{
242	0	invalidMessage = "Warning: invalid regex structure (after '"
243		+ mtch[0] + "') for URL link : " + link;
244		}
245		}
246		}
247	0	int pass = 0;
248	0	separators = new String[url_suffix.length];
249	0	String suffices = url_suffix[url_suffix.length - 1], lastsep = ",";
250		// have a look in the last suffix for any more separators.
251	0	while ((p = suffices.indexOf('|')) > -1)
252		{
253	0	separators[pass] = suffices.substring(p + 1);
254	0	if (pass == 0)
255		{
256		// trim the original suffix string
257	0	url_suffix[url_suffix.length - 1] = suffices.substring(0, p);
258		}
259		else
260		{
261	0	lastsep = (separators[pass - 1] = separators[pass - 1].substring(0,
262		p));
263		}
264	0	suffices = separators[pass];
265	0	pass++;
266		}
267	0	if (pass > 0)
268		{
269	0	lastsep = separators[pass - 1];
270		}
271		// last separator is always used for all the remaining separators
272	0	while (pass < separators.length)
273		{
274	0	separators[pass++] = lastsep;
275		}
276		}
277
278		/**
279		* @return the url_suffix
280		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
281	0	public String getUrl_suffix()...
282		{
283	0	return url_suffix[url_suffix.length - 1];
284		}
285
286		/**
287		* @return the url_prefix
288		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
289	0	public String getUrl_prefix()...
290		{
291	0	return url_prefix;
292		}
293
294		/**
295		* @return the target
296		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
297	0	public String getTarget()...
298		{
299	0	return target;
300		}
301
302		/**
303		* @return the label
304		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
305	0	public String getLabel()...
306		{
307	0	return label;
308		}
309
310		/**
311		* @return the sequence ID regexReplace
312		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
313	0	public String getIDRegexReplace()...
314		{
315	0	return _replaceFor(tokens[0]);
316		}
317
		0% Uncovered Elements: 8 (8) Complexity: 4 Complexity Density: 1
318	0	private String _replaceFor(String token)...
319		{
320	0	for (int i = 0; i < mtch.length; i++)
321		{
322	0	if (segs[i] > -1 && mtch[i].equals(token))
323		{
324	0	return regexReplace[i];
325		}
326		}
327	0	return null;
328		}
329
330		/**
331		* @return the sequence ID regexReplace
332		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
333	0	public String getSeqRegexReplace()...
334		{
335	0	return _replaceFor(tokens[1]);
336		}
337
338		/**
339		* @return the invalidMessage
340		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
341	0	public String getInvalidMessage()...
342		{
343	0	return invalidMessage;
344		}
345
346		/**
347		* Check if URL string was parsed properly.
348		*
349		* @return boolean - if false then <code>getInvalidMessage</code> returns an
350		* error message
351		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
352	0	public boolean isValid()...
353		{
354	0	return invalidMessage == null;
355		}
356
357		/**
358		* return one or more URL strings by applying regex to the given idstring
359		*
360		* @param idstrings
361		* array of id strings to pass to service
362		* @param seqstrings
363		* array of seq strings to pass to service
364		* @param onlyIfMatches
365		* - when true url strings are only made if regex is defined and
366		* matches for all qualified tokens in groupURL - TODO: consider if
367		* onlyIfMatches is really a useful parameter!
368		* @return null or Object[] { int[] { number of seqs substituted},boolean[] {
369		* which seqs were substituted }, StringBuffer[] { substituted lists
370		* for each token }, String[] { url } }
371		* @throws UrlStringTooLongException
372		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
373	0	public Object[] makeUrls(String[] idstrings, String[] seqstrings,...
374		String dsstring, boolean onlyIfMatches)
375		throws UrlStringTooLongException
376		{
377	0	Hashtable rstrings = replacementArgs(idstrings, seqstrings, dsstring);
378	0	return makeUrls(rstrings, onlyIfMatches);
379		}
380
381		/**
382		* gathers input into a hashtable
383		*
384		* @param idstrings
385		* @param seqstrings
386		* @param dsstring
387		* @return
388		*/
		0% Uncovered Elements: 9 (9) Complexity: 2 Complexity Density: 0.29
389	0	private Hashtable replacementArgs(String[] idstrings, String[] seqstrings,...
390		String dsstring)
391		{
392	0	Hashtable rstrings = new Hashtable();
393	0	rstrings.put(tokens[0], idstrings);
394	0	rstrings.put(tokens[1], seqstrings);
395	0	rstrings.put(tokens[2], new String[] { dsstring });
396	0	if (idstrings.length != seqstrings.length)
397		{
398	0	throw new Error(MessageManager.getString(
399		"error.idstring_seqstrings_only_one_per_sequence"));
400		}
401	0	return rstrings;
402		}
403
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
404	0	public Object[] makeUrls(Hashtable repstrings, boolean onlyIfMatches)...
405		throws UrlStringTooLongException
406		{
407	0	return makeUrlsIf(true, repstrings, onlyIfMatches);
408		}
409
410		/**
411		*
412		* @param ids
413		* @param seqstr
414		* @param string
415		* @param b
416		* @return URL stub objects ready to pass to constructFrom
417		* @throws UrlStringTooLongException
418		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
419	0	public Object[] makeUrlStubs(String[] ids, String[] seqstr, String string,...
420		boolean b) throws UrlStringTooLongException
421		{
422	0	Hashtable rstrings = replacementArgs(ids, seqstr, string);
423	0	Object[] stubs = makeUrlsIf(false, rstrings, b);
424	0	if (stubs != null)
425		{
426	0	return new Object[] { stubs[0], stubs[1], rstrings,
427		new boolean[]
428		{ b } };
429		}
430		// TODO Auto-generated method stub
431	0	return null;
432		}
433
434		/**
435		* generate the URL for the given URL stub object array returned from
436		* makeUrlStubs
437		*
438		* @param stubs
439		* @return URL string.
440		* @throws UrlStringTooLongException
441		*/
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
442	0	public String constructFrom(Object[] stubs)...
443		throws UrlStringTooLongException
444		{
445	0	Object[] results = makeUrlsIf(true, (Hashtable) stubs[2],
446		((boolean[]) stubs[3])[0]);
447	0	return ((String[]) results[3])[0];
448		}
449
450		/**
451		* conditionally generate urls or stubs for a given input.
452		*
453		* @param createFullUrl
454		* set to false if you only want to test if URLs would be generated.
455		* @param repstrings
456		* @param onlyIfMatches
457		* @return null if no url is generated. Object[] { int[] { number of matches
458		* seqs }, boolean[] { which matched }, (if createFullUrl also has
459		* StringBuffer[] { segment generated from inputs that is used in URL
460		* }, String[] { url })}
461		* @throws UrlStringTooLongException
462		*/
		0% Uncovered Elements: 154 (154) Complexity: 42 Complexity Density: 0.48
463	0	protected Object[] makeUrlsIf(boolean createFullUrl, Hashtable repstrings,...
464		boolean onlyIfMatches) throws UrlStringTooLongException
465		{
466	0	int pass = 0;
467
468		// prepare string arrays in correct order to be assembled into URL input
469	0	String[][] idseq = new String[mtch.length][]; // indexed by pass
470	0	int mins = 0, maxs = 0; // allowed two values, 1 or n-sequences.
471	0	for (int i = 0; i < mtch.length; i++)
472		{
473	0	idseq[i] = (String[]) repstrings.get(mtch[i]);
474	0	if (idseq[i].length >= 1)
475		{
476	0	if (mins == 0 && idseq[i].length == 1)
477		{
478	0	mins = 1;
479		}
480	0	if (maxs < 2)
481		{
482	0	maxs = idseq[i].length;
483		}
484		else
485		{
486	0	if (maxs != idseq[i].length)
487		{
488	0	throw new Error(MessageManager.formatMessage(
489		"error.cannot_have_mixed_length_replacement_vectors",
490		new String[]
491		{ (mtch[i]),
492		Integer.valueOf(idseq[i].length).toString(),
493		Integer.valueOf(maxs).toString() }));
494		}
495		}
496		}
497		else
498		{
499	0	throw new Error(MessageManager.getString(
500		"error.cannot_have_zero_length_vector_replacement_strings"));
501		}
502		}
503		// iterate through input, collating segments to be inserted into url
504	0	StringBuffer matched[] = new StringBuffer[idseq.length];
505		// and precompile regexes
506	0	com.stevesoft.pat.Regex[] rgxs = new com.stevesoft.pat.Regex[matched.length];
507	0	for (pass = 0; pass < matched.length; pass++)
508		{
509	0	matched[pass] = new StringBuffer();
510	0	if (regexReplace[pass] != null)
511		{
512	0	rgxs[pass] = com.stevesoft.pat.Regex
513		.perlCode("/" + regexReplace[pass] + "/");
514		}
515		else
516		{
517	0	rgxs[pass] = null;
518		}
519		}
520		// tot up the invariant lengths for this url
521	0	int urllength = url_prefix.length();
522	0	for (pass = 0; pass < matched.length; pass++)
523		{
524	0	urllength += url_suffix[pass].length();
525		}
526
527		// flags to record which of the input sequences were actually used to
528		// generate the
529		// url
530	0	boolean[] thismatched = new boolean[maxs];
531	0	int seqsmatched = 0;
532	0	for (int sq = 0; sq < maxs; sq++)
533		{
534		// initialise flag for match
535	0	thismatched[sq] = false;
536	0	StringBuffer[] thematches = new StringBuffer[rgxs.length];
537	0	for (pass = 0; pass < rgxs.length; pass++)
538		{
539	0	thematches[pass] = new StringBuffer(); // initialise - in case there are
540		// no more
541		// matches.
542		// if a regex is provided, then it must match for all sequences in all
543		// tokens for it to be considered.
544	0	if (idseq[pass].length <= sq)
545		{
546		// no more replacement strings to try for this token
547	0	continue;
548		}
549	0	if (rgxs[pass] != null)
550		{
551	0	com.stevesoft.pat.Regex rg = rgxs[pass];
552	0	int rematchat = 0;
553		// concatenate all matches of re in the given string!
554	0	while (rg.searchFrom(idseq[pass][sq], rematchat))
555		{
556	0	rematchat = rg.matchedTo();
557	0	thismatched[sq] |= true;
558	0	urllength += rg.charsMatched(); // count length
559	0	if ((urllength + 32) > Platform.getMaxCommandLineLength())
560		{
561	0	throw new UrlStringTooLongException(urllength);
562		}
563
564	0	if (!createFullUrl)
565		{
566	0	continue; // don't bother making the URL replacement text.
567		}
568		// do we take the cartesian products of the substituents ?
569	0	int ns = rg.numSubs();
570	0	if (ns == 0)
571		{
572	0	thematches[pass].append(rg.stringMatched());// take whole regex
573		}
574		/*
575		* else if (ns==1) { // take only subgroup match return new String[]
576		* { rg.stringMatched(1), url_prefix+rg.stringMatched(1)+url_suffix
577		* }; }
578		*/
579		// deal with multiple submatch case - for moment we do the simplest
580		// - concatenate the matched regions, instead of creating a complete
581		// list for each alternate match over all sequences.
582		// TODO: specify a 'replace pattern' - next refinement
583		else
584		{
585		// debug
586		/*
587		* for (int s = 0; s <= rg.numSubs(); s++) {
588		* System.err.println("Sub " + s + " : " + rg.matchedFrom(s) +
589		* " : " + rg.matchedTo(s) + " : '" + rg.stringMatched(s) + "'");
590		* }
591		*/
592		// try to collate subgroup matches
593	0	StringBuffer subs = new StringBuffer();
594		// have to loop through submatches, collating them at top level
595		// match
596	0	int s = 0; // 1;
597	0	while (s <= ns)
598		{
599	0	if (s + 1 <= ns && rg.matchedTo(s) > -1
600		&& rg.matchedTo(s + 1) > -1
601		&& rg.matchedTo(s + 1) < rg.matchedTo(s))
602		{
603		// s is top level submatch. search for submatches enclosed by
604		// this one
605	0	int r = s + 1;
606	0	StringBuffer rmtch = new StringBuffer();
607	0	while (r <= ns && rg.matchedTo(r) <= rg.matchedTo(s))
608		{
609	0	if (rg.matchedFrom(r) > -1)
610		{
611	0	rmtch.append(rg.stringMatched(r));
612		}
613	0	r++;
614		}
615	0	if (rmtch.length() > 0)
616		{
617	0	subs.append(rmtch); // simply concatenate
618		}
619	0	s = r;
620		}
621		else
622		{
623	0	if (rg.matchedFrom(s) > -1)
624		{
625	0	subs.append(rg.stringMatched(s)); // concatenate
626		}
627	0	s++;
628		}
629		}
630	0	thematches[pass].append(subs);
631		}
632		}
633		}
634		else
635		{
636		// are we only supposed to take regex matches ?
637	0	if (!onlyIfMatches)
638		{
639	0	thismatched[sq] |= true;
640	0	urllength += idseq[pass][sq].length(); // tot up length
641	0	if (createFullUrl)
642		{
643	0	thematches[pass] = new StringBuffer(idseq[pass][sq]); // take
644		// whole
645		// string -
646		// regardless - probably not a
647		// good idea!
648		/*
649		* TODO: do some boilerplate trimming of the fields to make them
650		* sensible e.g. trim off any 'prefix' in the id string (see
651		* UrlLink for the below) - pre 2.4 Jalview behaviour if
652		* (idstring.indexOf("|") > -1) { idstring =
653		* idstring.substring(idstring.lastIndexOf("|") + 1); }
654		*/
655		}
656
657		}
658		}
659		}
660
661		// check if we are going to add this sequence's results ? all token
662		// replacements must be valid for this to happen!
663		// (including single value replacements - eg. dataset name)
664	0	if (thismatched[sq])
665		{
666	0	if (createFullUrl)
667		{
668	0	for (pass = 0; pass < matched.length; pass++)
669		{
670	0	if (idseq[pass].length > 1 && matched[pass].length() > 0)
671		{
672	0	matched[pass].append(separators[pass]);
673		}
674	0	matched[pass].append(thematches[pass]);
675		}
676		}
677	0	seqsmatched++;
678		}
679		}
680		// finally, if any sequences matched, then form the URL and return
681	0	if (seqsmatched == 0 || (createFullUrl && matched[0].length() == 0))
682		{
683		// no matches - no url generated
684	0	return null;
685		}
686		// check if we are beyond the feasible command line string limit for this
687		// platform
688	0	if ((urllength + 32) > Platform.getMaxCommandLineLength())
689		{
690	0	throw new UrlStringTooLongException(urllength);
691		}
692	0	if (!createFullUrl)
693		{
694		// just return the essential info about what the URL would be generated
695		// from
696	0	return new Object[] { new int[] { seqsmatched }, thismatched };
697		}
698		// otherwise, create the URL completely.
699
700	0	StringBuffer submiturl = new StringBuffer();
701	0	submiturl.append(url_prefix);
702	0	for (pass = 0; pass < matched.length; pass++)
703		{
704	0	submiturl.append(matched[pass]);
705	0	if (url_suffix[pass] != null)
706		{
707	0	submiturl.append(url_suffix[pass]);
708		}
709		}
710
711	0	return new Object[] { new int[] { seqsmatched }, thismatched, matched,
712		new String[]
713		{ submiturl.toString() } };
714		}
715
716		/**
717		*
718		* @param urlstub
719		* @return number of distinct sequence (id or seuqence) replacements predicted
720		* for this stub
721		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
722	0	public int getNumberInvolved(Object[] urlstub)...
723		{
724	0	return ((int[]) urlstub[0])[0]; // returns seqsmatched from
725		// makeUrlsIf(false,...)
726		}
727
728		/**
729		* get token types present in this url as a bitfield indicating presence of
730		* each token from tokens (LSB->MSB).
731		*
732		* @return groupURL class as integer
733		*/
		0% Uncovered Elements: 12 (12) Complexity: 4 Complexity Density: 0.67
734	0	public int getGroupURLType()...
735		{
736	0	int r = 0;
737	0	for (int pass = 0; pass < tokens.length; pass++)
738		{
739	0	for (int i = 0; i < mtch.length; i++)
740		{
741	0	if (mtch[i].equals(tokens[pass]))
742		{
743	0	r += 1 << pass;
744		}
745		}
746		}
747	0	return r;
748		}
749
		0% Uncovered Elements: 22 (22) Complexity: 4 Complexity Density: 0.25
750	0	@Override...
751		public String toString()
752		{
753	0	StringBuffer result = new StringBuffer();
754	0	result.append(label + "|" + url_prefix);
755	0	int r;
756	0	for (r = 0; r < url_suffix.length; r++)
757		{
758	0	result.append("$");
759	0	result.append(mtch[r]);
760	0	if (regexReplace[r] != null)
761		{
762	0	result.append("=/");
763	0	result.append(regexReplace[r]);
764	0	result.append("/=");
765		}
766	0	result.append("$");
767	0	result.append(url_suffix[r]);
768		}
769	0	for (r = 0; r < separators.length; r++)
770		{
771	0	result.append("|");
772	0	result.append(separators[r]);
773		}
774	0	return result.toString();
775		}
776
777		/**
778		* report stats about the generated url string given an input set
779		*
780		* @param ul
781		* @param idstring
782		* @param url
783		*/
		0% Uncovered Elements: 23 (23) Complexity: 6 Complexity Density: 0.46
784	0	private static void testUrls(GroupUrlLink ul, String[][] idstring,...
785		Object[] url)
786		{
787
788	0	if (url == null)
789		{
790	0	System.out.println("Created NO urls.");
791		}
792		else
793		{
794	0	System.out.println("Created a url from " + ((int[]) url[0])[0]
795		+ "out of " + idstring[0].length + " sequences.");
796	0	System.out.println("Sequences that did not match:");
797	0	for (int sq = 0; sq < idstring[0].length; sq++)
798		{
799	0	if (!((boolean[]) url[1])[sq])
800		{
801	0	System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "
802		+ idstring[1][sq]);
803		}
804		}
805	0	System.out.println("Sequences that DID match:");
806	0	for (int sq = 0; sq < idstring[0].length; sq++)
807		{
808	0	if (((boolean[]) url[1])[sq])
809		{
810	0	System.out.println("Seq " + sq + ": " + idstring[0][sq] + "\t: "
811		+ idstring[1][sq]);
812		}
813		}
814	0	System.out.println("The generated URL:");
815	0	System.out.println(((String[]) url[3])[0]);
816		}
817		}
818
819		/**
820		*
821		* @param argv
822		* @j2sIgnore
823		*/
		0% Uncovered Elements: 28 (28) Complexity: 5 Complexity Density: 0.21
824	0	public static void main(String argv[])...
825		{
826		// note - JAL-1383 - these services are all dead
827	0	String[] links = new String[] {
828		"EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
829		"EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=linkInDatasetFromJalview&input=$SEQUENCES$&inputType=1|,",
830		"EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,",
831		"EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Enfin%20Default%20Workflow&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",
832		"EnVision2|IDS|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=linkInDatasetFromJalview&input=$SEQUENCEIDS$&inputType=0|,",
833		"EnVision2|Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=$SEQUENCEIDS$&datasetName=$DATASETID$&input=$SEQUENCES$&inputType=1|,",
834		"EnVision2 Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([a-zA-Z]+)/=$&inputType=1|,",
835		"EnVision2 Seqs|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/[A-Za-z]+/=$&inputType=1|,"
836		/*
837		* http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?input=P38389,P38398
838		* &inputType=0&workflow=Enfin%20Default%20Workflow&datasetName=
839		* linkInDatasetFromPRIDE
840		*/
841		};
842
843	0	SequenceI[] seqs = new SequenceI[] {
844		new Sequence("StupidLabel:gi|9234|pdb|102L|A",
845		"asdiasdpasdpadpwpadasdpaspdw"), };
846	0	String[][] seqsandids = formStrings(seqs);
847	0	for (int i = 0; i < links.length; i++)
848		{
849	0	GroupUrlLink ul = new GroupUrlLink(links[i]);
850	0	if (ul.isValid())
851		{
852	0	System.out.println("\n\n\n");
853	0	System.out.println(
854		"Link " + i + " " + links[i] + " : " + ul.toString());
855	0	System.out.println(" pref : " + ul.getUrl_prefix());
856	0	System.out.println(" IdReplace : " + ul.getIDRegexReplace());
857	0	System.out.println(" SeqReplace : " + ul.getSeqRegexReplace());
858	0	System.out.println(" Suffixes : " + ul.getUrl_suffix());
859
860	0	System.out.println(
861		"<insert input id and sequence strings here> Without onlyIfMatches:");
862	0	Object[] urls;
863	0	try
864		{
865	0	urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
866		false);
867	0	testUrls(ul, seqsandids, urls);
868		} catch (UrlStringTooLongException ex)
869		{
870	0	System.out.println("too long exception " + ex);
871		}
872	0	System.out.println(
873		"<insert input id and sequence strings here> With onlyIfMatches set:");
874	0	try
875		{
876	0	urls = ul.makeUrls(seqsandids[0], seqsandids[1], "mydataset",
877		true);
878	0	testUrls(ul, seqsandids, urls);
879		} catch (UrlStringTooLongException ex)
880		{
881	0	System.out.println("too long exception " + ex);
882		}
883		}
884		else
885		{
886	0	System.err.println("Invalid URLLink : " + links[i] + " : "
887		+ ul.getInvalidMessage());
888		}
889		}
890		}
891
892		/**
893		* covenience method to generate the id and sequence string vector from a set
894		* of seuqences using each sequence's getName() and getSequenceAsString()
895		* method
896		*
897		* @param seqs
898		* @return String[][] {{sequence ids},{sequence strings}}
899		*/
		0% Uncovered Elements: 7 (7) Complexity: 2 Complexity Density: 0.4
900	0	public static String[][] formStrings(SequenceI[] seqs)...
901		{
902	0	String[][] idset = new String[2][seqs.length];
903	0	for (int i = 0; i < seqs.length; i++)
904		{
905	0	idset[0][i] = seqs[i].getName();
906	0	idset[1][i] = seqs[i].getSequenceAsString();
907		}
908	0	return idset;
909		}
910
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
911	0	public void setLabel(String newlabel)...
912		{
913	0	this.label = newlabel;
914		}
915
916		}