Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
Skip	18	60	37	0.4594594545.9%	Show methods

Class Skip

Class Skip	Line # 18	Total Statements 60	Complexity 37	TOTAL Coverage 0.4594594545.9%
mkmask(int) : int   mkmask(int) : int	2020	2.02	1.01	0.0 0.00%
string(Regex) : String   string(Regex) : String	3939	1.01	2.02	0.0 0.00%
offset(Regex) : int   offset(Regex) : int	4848	1.01	2.02	0.0 0.00%
Skip(String,boolean,int)   Skip(String,boolean,int)	5858	8.08	2.02	0.8 0.880%
find(StringLike) : int   find(StringLike) : int	7676	1.01	1.01	0.0 0.00%
min(int,int) : int   min(int,int) : int	8181	1.01	2.02	0.6666667 0.666666766.7%
find(StringLike,int,int) : int   find(StringLike,int,int) : int	9090	14.014	11.011	0.0 0.00%
findSkip(Regex) : Skip   findSkip(Regex) : Skip	129129	1.01	1.01	1.0 1.0100%
findSkip(Pattern,boolean,boolean) : Skip   findSkip(Pattern,boolean,boolean) : Skip	135135	31.031	15.015	0.7346939 0.734693973.5%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.45945945	jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery	1PASS
	0.45945945	jalview.io.StockholmFileTest.curlyWUSSsecondaryStructureForRNASequencejalview.io.StockholmFileTest.curlyWUSSsecondaryStructureForRNASequence	1PASS
	0.45945945	jalview.io.StockholmFileTest.rfamFileIOjalview.io.StockholmFileTest.rfamFileIO	1PASS
	0.45945945	jalview.io.StockholmFileTest.pfamFileDataExtractionjalview.io.StockholmFileTest.pfamFileDataExtraction	1PASS
	0.45945945	jalview.io.StockholmFileTest.fullWUSSsecondaryStructureForRNASequencejalview.io.StockholmFileTest.fullWUSSsecondaryStructureForRNASequence	1PASS
	0.45945945	jalview.io.StockholmFileTest.dbrefOutputjalview.io.StockholmFileTest.dbrefOutput	1PASS
	0.45945945	jalview.io.StockholmFileTest.descriptionLineOutputjalview.io.StockholmFileTest.descriptionLineOutput	1PASS
	0.45945945	jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip	1PASS
	0.45945945	jalview.io.StockholmFileTest.pfamFileIOjalview.io.StockholmFileTest.pfamFileIO	1PASS
	0.45945945	jalview.io.StockholmFileTest.secondaryStructureForRNASequencejalview.io.StockholmFileTest.secondaryStructureForRNASequence	1PASS
	0.45945945	jalview.io.StockholmFileTest.stockholmFileRnaSSAlphaCharsjalview.io.StockholmFileTest.stockholmFileRnaSSAlphaChars	1PASS
	0.45945945	jalview.io.RNAMLfileTest.testRnamlToStockholmIOjalview.io.RNAMLfileTest.testRnamlToStockholmIO	1PASS

 

Source view

1		//
2		// This software is now distributed according to
3		// the Lesser Gnu Public License. Please see
4		// http://www.gnu.org/copyleft/lesser.txt for
5		// the details.
6		// -- Happy Computing!
7		//
8		package com.stevesoft.pat;
9
10		/**
11		* This class is used internally to search ahead for some optimized Regex
12		* objects. It searches within a String for occrences of a given String -- like
13		* a more flexible version of String.indexOf.
14		*
15		* @see com.stevesoft.pat.Skip2
16		* @see com.stevesoft.pat.SkipBMH
17		*/
		45.9% Uncovered Elements: 60 (111) Complexity: 37 Complexity Density: 0.62
18		public class Skip
19		{
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
20	0	static int mkmask(int c)...
21		{
22	0	char x = (char) c;
23	0	return ~(CaseMgr.toUpperCase(x) | CaseMgr.toLowerCase(x)
24		| CaseMgr.toTitleCase(x));
25		}
26
27		String src;
28
29		int c, mask;
30
31		int offset;
32
33		boolean ign, m1;
34
35		/**
36		* Examine a Regex to determine what String it will attempt to skip to when
37		* searching for patterns. Return -1 if we aren't doing this.
38		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
39	0	public static String string(Regex r)...
40		{
41	0	return r.skipper == null ? null : r.skipper.src;
42		}
43
44		/**
45		* Determine the offset of the String within the pattern that we are skipping
46		* to. Return -1 if we aren't doing this.
47		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
48	0	public static int offset(Regex r)...
49		{
50	0	return r.skipper == null ? -1 : r.skipper.offset;
51		}
52
53		/**
54		* Initialize, give it a String to search for, tell it whether or not to
55		* ignoreCase, and what the offset is of the String within the String to be
56		* searched.
57		*/
		80% Uncovered Elements: 2 (10) Complexity: 2 Complexity Density: 0.25
58	45	public Skip(String s, boolean ign, int o)...
59		{
60	45	src = s;
61	45	c = s.charAt(0);
62	45	if (ign)
63		{
64	0	mask = mkmask(c);
65		}
66		else
67		{
68	45	mask = 0;
69		}
70	45	offset = o;
71	45	this.ign = ign;
72	45	m1 = (s.length() == 1);
73		}
74
75		/** The same as find(s,0,s.length()) */
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
76	0	public final int find(StringLike s)...
77		{
78	0	return find(s, 0, s.length());
79		}
80
		66.7% Uncovered Elements: 1 (3) Complexity: 2 Complexity Density: 2
81	127535	static final int min(int a, int b)...
82		{
83	127535	return a < b ? a : b;
84		}
85
86		/**
87		* Searches a given region of text beginning at position start and ending at
88		* position end for the skip object.
89		*/
		0% Uncovered Elements: 30 (30) Complexity: 11 Complexity Density: 0.79
90	0	public int find(StringLike s, int start, int end)...
91		{
92	0	if (start > end)
93		{
94	0	return -1;
95		}
96	0	start += offset;
97	0	int vend = min(s.length() - 1, end + offset);
98	0	if (mask != c)
99		{
100	0	for (int i = start; i <= vend; i++)
101		{
102	0	if (0 == (s.charAt(i) & mask))
103		{
104		// if(m1||s.regionMatches(ign,i,src,0,src.length()) )
105	0	if (m1 || CaseMgr.regionMatches(s, ign, i, src, 0, src.length()))
106		{
107	0	return i - offset;
108		}
109		}
110		}
111		}
112		else
113		{
114	0	for (int i = start; i <= vend; i++)
115		{
116	0	if (c == s.charAt(i))
117		{
118		// if(m1||s.regionMatches(ign,i,src,0,src.length()) )
119	0	if (m1 || CaseMgr.regionMatches(s, ign, i, src, 0, src.length()))
120		{
121	0	return i - offset;
122		}
123		}
124		}
125		}
126	0	return -1;
127		}
128
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
129	318	static Skip findSkip(Regex r)...
130		{
131	318	return findSkip(r.thePattern, r.ignoreCase, !r.dontMatchInQuotes);
132		}
133
134		// look for things that can be skipped
		73.5% Uncovered Elements: 13 (49) Complexity: 15 Complexity Density: 0.48
135	543	static Skip findSkip(Pattern p, boolean ignoreCase, boolean trnc)...
136		{
137	543	StringBuffer sb = new StringBuffer();
138	543	Skip subsk = null;
139	543	int offset = 0;
140	543	int skipc = -1, skipoff = 0;
141	588	for (; p != null; p = p.next)
142		{
143	588	if (p instanceof oneChar)
144		{
145	45	skipc = ((oneChar) p).c;
146	45	skipoff = offset;
147		}
148	588	if (p instanceof oneChar && p.next instanceof oneChar)
149		{
150	45	Pattern psav = p;
151	45	sb.append(((oneChar) p).c);
152	90	while (p.next instanceof oneChar)
153		{
154	45	sb.append(((oneChar) p.next).c);
155	45	p = p.next;
156		}
157	45	String st = sb.toString();
158	45	Skip sk = null;
159	45	if (st.length() > 2)
160		{
161	0	sk = new SkipBMH(st, ignoreCase, offset);
162		}
163		else
164		{
165	45	sk = new Skip2(st, ignoreCase, offset);
166		}
167	45	if (trnc && st.length() > 2)
168		{ // chop out a whole string...
169	0	psav.next = new Skipped(st.substring(1));
170	0	psav.next.next = p.next;
171	0	psav.next.parent = p.parent;
172		}
173	45	return sk;
174		}
175	?	else if (p instanceof Or && ((Or) p).v.size() == 1
176		&& !((Or) p).leftForm().equals("(?!")
177		&& null != (subsk = findSkip(
178		(Pattern) ((Or) p).v.elementAt(0), ignoreCase, trnc)))
179		{
180	0	subsk.offset += offset;
181	0	return subsk;
182		}
183	543	else if (p.minChars().equals(p.maxChars()))
184		{
185	45	offset += p.minChars().intValue();
186		}
187		else
188		{
189	498	return skipc < 0 ? null
190		: new Skip("" + (char) skipc, ignoreCase, skipoff);
191		}
192		}
193	0	return null;
194		}
195		}