Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
FastBracket	18	101	43	0.7844311678.4%	Show methods

Class FastBracket

Class FastBracket	Line # 18	Total Statements 101	Complexity 43	TOTAL Coverage 0.7844311678.4%
FastBracket(boolean)   FastBracket(boolean)	2424	1.01	1.01	1.0 1.0100%
process(Bracket,boolean) : Bracket   process(Bracket,boolean) : Bracket	3131	52.052	15.015	0.6666667 0.666666766.7%
newbrack(Vector,boolean) : FastBracket   newbrack(Vector,boolean) : FastBracket	140140	16.016	5.05	0.8333333 0.833333383.3%
neg(Vector) : Vector   neg(Vector) : Vector	171171	17.017	6.06	0.84 0.8484%
mkelem(char,char) : Pattern   mkelem(char,char) : Pattern	206206	1.01	2.02	1.0 1.0100%
min(char,char) : char   min(char,char) : char	212212	1.01	2.02	0.6666667 0.666666766.7%
max(char,char) : char   max(char,char) : char	217217	1.01	2.02	0.6666667 0.666666766.7%
getl(Object) : char   getl(Object) : char	224224	4.04	2.02	1.0 1.0100%
geth(Object) : char   geth(Object) : char	236236	4.04	2.02	1.0 1.0100%
matchInternal(int,Pthings) : int   matchInternal(int,Pthings) : int	247247	4.04	6.06	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.78443116	jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip	1PASS
	0.75449103	jalview.io.StockholmFileTest.pfamFileDataExtractionjalview.io.StockholmFileTest.pfamFileDataExtraction	1PASS
	0.75449103	jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery	1PASS
	0.75449103	jalview.io.StockholmFileTest.curlyWUSSsecondaryStructureForRNASequencejalview.io.StockholmFileTest.curlyWUSSsecondaryStructureForRNASequence	1PASS
	0.75449103	jalview.io.RNAMLfileTest.testRnamlToStockholmIOjalview.io.RNAMLfileTest.testRnamlToStockholmIO	1PASS
	0.75449103	jalview.io.StockholmFileTest.descriptionLineOutputjalview.io.StockholmFileTest.descriptionLineOutput	1PASS
	0.75449103	jalview.io.StockholmFileTest.fullWUSSsecondaryStructureForRNASequencejalview.io.StockholmFileTest.fullWUSSsecondaryStructureForRNASequence	1PASS
	0.75449103	jalview.io.StockholmFileTest.rfamFileIOjalview.io.StockholmFileTest.rfamFileIO	1PASS
	0.75449103	jalview.io.StockholmFileTest.dbrefOutputjalview.io.StockholmFileTest.dbrefOutput	1PASS
	0.75449103	jalview.io.StockholmFileTest.secondaryStructureForRNASequencejalview.io.StockholmFileTest.secondaryStructureForRNASequence	1PASS
	0.75449103	jalview.io.StockholmFileTest.pfamFileIOjalview.io.StockholmFileTest.pfamFileIO	1PASS
	0.75449103	jalview.io.StockholmFileTest.stockholmFileRnaSSAlphaCharsjalview.io.StockholmFileTest.stockholmFileRnaSSAlphaChars	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		import java.util.BitSet;
11		import java.util.Vector;
12
13		/**
14		* Uses table lookup to match [] type constructs, but only if it can use a
15		* lookup table 256 bits in size. It is impractical to make a table if it is too
16		* large.
17		*/
		78.4% Uncovered Elements: 36 (167) Complexity: 43 Complexity Density: 0.43
18		public class FastBracket extends Bracket
19		{
20		int min, max;
21
22		BitSet bs;
23
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
24	513	FastBracket(boolean n)...
25		{
26	513	super(n);
27		}
28
29		// This routine can optimize a bracket, possibly
30		// it will replace it with a FastBracket.
		66.7% Uncovered Elements: 26 (78) Complexity: 15 Complexity Density: 0.29
31	519	static Bracket process(Bracket b, boolean ignc)...
32		{
33	519	Vector v = b.v;
34	519	b.pv = null;
35	519	try
36		{
37
38		// Expand out the vector to make separate
39		// entries for other cases if ignoreCase is
40		// turned on.
41	519	Vector nv = v;
42	519	if (ignc)
43		{
44	0	nv = new Vector();
45	0	for (int i = 0; i < v.size(); i++)
46		{
47	0	Pattern p = (Pattern) v.elementAt(i);
48	0	nv.addElement(p);
49	0	if (p instanceof oneChar)
50		{
51	0	oneChar oc = (oneChar) p;
52	0	nv.addElement(new oneChar(oc.altc));
53		}
54	0	else if (p instanceof Range)
55		{
56	0	Range ra = (Range) p;
57	0	nv.addElement(new Range(ra.altlo, ra.althi));
58		}
59		}
60		}
61	519	v = nv;
62
63		// Bubble sort, make sure elements
64		// are in order. This will allow us
65		// to merge them.
66	1611	for (int i = 0; i < v.size() - 1; i++)
67		{
68	3516	for (int j = 0; j < v.size() - 1; j++)
69		{
70	2424	char c1 = getl(v.elementAt(j));
71	2424	char c2 = getl(v.elementAt(j + 1));
72	2424	if (c2 < c1)
73		{
74	1137	Object o = v.elementAt(j);
75	1137	v.setElementAt(v.elementAt(j + 1), j);
76	1137	v.setElementAt(o, j + 1);
77		}
78		}
79		}
80
81	519	nv = new Vector();
82		// merge -- remove overlaps
83	519	Pattern p = (Pattern) v.elementAt(0);
84	519	nv.addElement(p);
85	1611	for (int i = 1; i < v.size(); i++)
86		{
87	1092	if (geth(p) + 1 >= getl(v.elementAt(i)))
88		{
89	54	Pattern p2 = (Pattern) v.elementAt(i);
90	54	char lo = min(getl(p), getl(p2));
91	54	char hi = max(geth(p), geth(p2));
92	54	nv.setElementAt(p = mkelem(lo, hi), nv.size() - 1);
93		}
94		else
95		{
96	1038	p = (Pattern) v.elementAt(i);
97	1038	nv.addElement(p);
98		}
99		}
100
101	519	b.v = v = nv;
102		} catch (RegSyntax e)
103		{
104	0	e.printStackTrace();
105		}
106
107		// We don't want these things to be empty.
108	519	Vector negv = neg(v);
109	519	if (v.size() == 1)
110		{
111	6	return b;
112		}
113	513	if (negv.size() == 1)
114		{
115	0	b.v = negv;
116	0	b.neg = !b.neg;
117	0	return b;
118		}
119
120		// Now consider if we can make a FastBracket.
121		// Uses a BitSet to do a lookup.
122	513	FastBracket fb = newbrack(v, b.neg);
123	513	if (fb == null)
124		{
125	0	fb = newbrack(negv, !b.neg);
126		}
127	513	if (fb != null)
128		{
129	513	fb.parent = b.parent;
130	513	fb.next = b.next;
131	513	return fb;
132		}
133
134		// return the normal Bracket.
135	0	return b;
136		}
137
138		// Build a FastBracket and set bits. If this can't
139		// be done, return null.
		83.3% Uncovered Elements: 4 (24) Complexity: 5 Complexity Density: 0.31
140	513	final static FastBracket newbrack(Vector v, boolean neg)...
141		{
142	513	FastBracket fb = new FastBracket(neg);
143	513	fb.v = v;
144	513	if (v.size() == 0)
145		{
146	0	return null;
147		}
148	513	fb.min = getl(v.elementAt(0));
149	513	fb.max = geth(v.elementAt(v.size() - 1));
150	513	if (fb.max - fb.min <= 256)
151		{
152	513	fb.bs = new BitSet(fb.max - fb.min + 1);
153	2064	for (int i = 0; i < v.size(); i++)
154		{
155	1551	Object o = v.elementAt(i);
156	1551	int min0 = getl(o) - fb.min;
157	1551	int max0 = geth(o) - fb.min;
158	4296	for (int j = min0; j <= max0; j++)
159		{
160	2745	fb.bs.set(j);
161		}
162		}
163	513	return fb;
164		}
165	0	return null;
166		}
167
168		// Negate a sorted Vector. Applying this
169		// operation twice should yield the same Vector
170		// back.
		84% Uncovered Elements: 4 (25) Complexity: 6 Complexity Density: 0.35
171	519	final static Vector neg(Vector v)...
172		{
173	519	try
174		{
175	519	Vector nv = new Vector();
176	519	if (v.size() == 0)
177		{
178	0	nv.addElement(new Range((char) 0, (char) 65535));
179	0	return nv;
180		}
181	519	int p0 = getl(v.elementAt(0));
182	519	if (p0 != 0)
183		{
184	513	nv.addElement(mkelem((char) 0, (char) (p0 - 1)));
185		}
186	1557	for (int i = 0; i < v.size() - 1; i++)
187		{
188	1038	int hi = getl(v.elementAt(i + 1)) - 1;
189	1038	int lo = geth(v.elementAt(i)) + 1;
190	1038	nv.addElement(mkelem((char) lo, (char) hi));
191		}
192	519	int pN = geth(v.lastElement());
193	519	if (pN != 65535)
194		{
195	513	nv.addElement(mkelem((char) (pN + 1), (char) 65535));
196		}
197	519	return nv;
198		} catch (RegSyntax rs)
199		{
200	0	return null;
201		}
202		}
203
204		// Make either a Range or oneChar Object, depending on which
205		// is appropriate.
		100% Uncovered Elements: 0 (3) Complexity: 2 Complexity Density: 2
206	2118	final static Pattern mkelem(char lo, char hi) throws RegSyntax...
207		{
208	2118	return lo == hi ? (Pattern) (new oneChar(lo))
209		: (Pattern) (new Range(lo, hi));
210		}
211
		66.7% Uncovered Elements: 1 (3) Complexity: 2 Complexity Density: 2
212	54	static final char min(char a, char b)...
213		{
214	54	return a < b ? a : b;
215		}
216
		66.7% Uncovered Elements: 1 (3) Complexity: 2 Complexity Density: 2
217	54	static final char max(char a, char b)...
218		{
219	54	return a > b ? a : b;
220		}
221
222		// getl -- get lower value of Range object,
223		// or get value of oneChar object.
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.5
224	9669	final static char getl(Object o)...
225		{
226	9669	Pattern p = (Pattern) o;
227	9669	if (p instanceof Range)
228		{
229	2541	return ((Range) p).lo;
230		}
231	7128	return ((oneChar) p).c;
232		}
233
234		// geth -- get higher value of Range object,
235		// or get value of oneChar object.
		100% Uncovered Elements: 0 (6) Complexity: 2 Complexity Density: 0.5
236	4821	final static char geth(Object o)...
237		{
238	4821	Pattern p = (Pattern) o;
239	4821	if (p instanceof Range)
240		{
241	1590	return ((Range) p).hi;
242		}
243	3231	return ((oneChar) p).c;
244		}
245
246		// This is the easy part!
		100% Uncovered Elements: 0 (8) Complexity: 6 Complexity Density: 1.5
247	214481	public int matchInternal(int pos, Pthings pt)...
248		{
249	214481	if (pos >= pt.src.length() || Masked(pos, pt))
250		{
251	4959	return -1;
252		}
253	209522	char c = pt.src.charAt(pos);
254	209522	return (neg ^ (c >= min && c <= max && bs.get(c - min)))
255		? nextMatch(pos + 1, pt)
256		: -1;
257		}
258		}