Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ParseProperties	30	46	16	0.941176594.1%	Show methods

Class ParseProperties

Class ParseProperties	Line # 30	Total Statements 46	Complexity 16	TOTAL Coverage 0.941176594.1%
ParseProperties(AlignmentI)   ParseProperties(AlignmentI)	5353	1.01	1.01	1.0 1.0100%
getScoresFromDescription(String,String,String,boolean) : int   getScoresFromDescription(String,String,String,boolean) : int	5858	1.01	1.01	1.0 1.0100%
getScoresFromDescription(String[],String[],String,boolean) : int   getScoresFromDescription(String[],String[],String,boolean) : int	6666	1.01	1.01	1.0 1.0100%
getScoresFromDescription(SequenceI[],String[],String[],String,boolean) : int   getScoresFromDescription(SequenceI[],String[],String[],String,boolean) : int	9090	43.043	13.013	0.93442625 0.9344262593.4%

 

Contributing tests

Contributing tests

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	Test contribution	Test	Result	Actions
	0.86764705	jalview.analysis.ParsePropertiesTest.testGetScoresFromDescription_twoScoresjalview.analysis.ParsePropertiesTest.testGetScoresFromDescription_twoScores	1PASS
	0.6617647	jalview.analysis.ParsePropertiesTest.testGetScoresFromDescription_wordBoundariesjalview.analysis.ParsePropertiesTest.testGetScoresFromDescription_wordBoundaries	1PASS
	0.61764705	jalview.analysis.ParsePropertiesTest.testGetScoresFromDescriptionjalview.analysis.ParsePropertiesTest.testGetScoresFromDescription	1PASS

 

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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.analysis;
22
23		import jalview.datamodel.AlignmentAnnotation;
24		import jalview.datamodel.AlignmentI;
25		import jalview.datamodel.SequenceI;
26		import jalview.util.Platform;
27
28		import com.stevesoft.pat.Regex;
29
		94.1% Uncovered Elements: 4 (68) Complexity: 16 Complexity Density: 0.35
30		public class ParseProperties
31		{
32		/**
33		* Methods for parsing free text properties on alignments and sequences. There
34		* are a number of ways we might want to do this: arbitrary regex. and an
35		* associated score name for the number that's extracted. Regex that provides
36		* both score and name.
37		*
38		* We may also want to : - modify description to remove parsed numbers (this
39		* behaviour is dangerous since exporting the alignment would lose the
40		* original form then) -
41		*
42		*/
43		/**
44		* The alignment being operated on
45		*/
46		private AlignmentI al = null;
47
48		/**
49		* initialise a new property parser
50		*
51		* @param al
52		*/
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
53	3	public ParseProperties(AlignmentI al)...
54		{
55	3	this.al = al;
56		}
57
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
58	3	public int getScoresFromDescription(String ScoreName,...
59		String ScoreDescriptions, String regex, boolean repeat)
60		{
61	3	return getScoresFromDescription(new String[] { ScoreName },
62		new String[]
63		{ ScoreDescriptions }, regex, repeat);
64		}
65
		100% Uncovered Elements: 0 (1) Complexity: 1 Complexity Density: 1
66	3	public int getScoresFromDescription(String[] ScoreNames,...
67		String[] ScoreDescriptions, String regex, boolean repeat)
68		{
69	3	return getScoresFromDescription(al.getSequencesArray(), ScoreNames,
70		ScoreDescriptions, regex, repeat);
71		}
72
73		/**
74		* Extract scores for sequences by applying regex to description string.
75		*
76		* @param seqs
77		* seuqences to extract annotation from.
78		* @param ScoreNames
79		* labels for each numeric field in regex match
80		* @param ScoreDescriptions
81		* description for each numeric field in regex match
82		* @param regex
83		* Regular Expression string for passing to
84		* <code>new com.stevesoft.patt.Regex(regex)</code>
85		* @param repeat
86		* true means the regex will be applied multiple times along the
87		* description string of each sequence
88		* @return total number of sequences that matched the regex
89		*/
		93.4% Uncovered Elements: 4 (61) Complexity: 13 Complexity Density: 0.3
90	3	public int getScoresFromDescription(SequenceI[] seqs, String[] ScoreNames,...
91		String[] ScoreDescriptions, String regex, boolean repeat)
92		{
93	3	int count = 0;
94	3	Regex pattern = Platform.newRegex(regex);
95	3	if (pattern.numSubs() > ScoreNames.length)
96		{
97		// Check that we have enough labels and descriptions for any parsed
98		// scores.
99	1	int onamelen = ScoreNames.length;
100	1	String[] tnames = new String[pattern.numSubs() + 1];
101	1	System.arraycopy(ScoreNames, 0, tnames, 0, ScoreNames.length);
102	1	String base = tnames[ScoreNames.length - 1];
103	1	ScoreNames = tnames;
104	1	String descrbase = ScoreDescriptions[onamelen - 1];
105	1	if (descrbase == null)
106		{
107	0	descrbase = "Score parsed from (" + regex + ")";
108		}
109	1	tnames = new String[pattern.numSubs() + 1];
110	1	System.arraycopy(ScoreDescriptions, 0, tnames, 0,
111		ScoreDescriptions.length);
112	1	ScoreDescriptions = tnames;
113	3	for (int i = onamelen; i < ScoreNames.length; i++)
114		{
115	2	ScoreNames[i] = base + "_" + i;
116	2	ScoreDescriptions[i] = descrbase + " (column " + i + ")";
117		}
118		}
119	15	for (int i = 0; i < seqs.length; i++)
120		{
121	12	String descr = seqs[i].getDescription();
122	12	if (descr == null)
123		{
124	0	continue;
125		}
126	12	int pos = 0;
127	12	boolean added = false;
128	12	int reps = 0;
129	31	while ((repeat || pos == 0) && pattern.searchFrom(descr, pos))
130		{
131	19	pos = pattern.matchedTo();
132	41	for (int cols = 0; cols < pattern.numSubs(); cols++)
133		{
134	22	String sstring = pattern.stringMatched(cols + 1);
135	22	double score = Double.NaN;
136	22	try
137		{
138	22	score = Double.valueOf(sstring).doubleValue();
139		} catch (Exception e)
140		{
141		// don't try very hard to parse if regex was wrong.
142	5	continue;
143		}
144		// add score to sequence annotation.
145	17	AlignmentAnnotation an = new AlignmentAnnotation(
146	17	ScoreNames[cols] + ((reps > 0) ? "_" + reps : ""),
147		ScoreDescriptions[cols], null);
148	17	an.setScore(score);
149	17	jalview.bin.Console.outPrintln(seqs[i].getName() + " score: '"
150		+ ScoreNames[cols] + "' = " + score); // DEBUG
151	17	an.setSequenceRef(seqs[i]);
152	17	seqs[i].addAlignmentAnnotation(an);
153	17	al.addAnnotation(an);
154	17	added = true;
155		}
156	19	reps++; // repeated matches
157		}
158	12	if (added)
159		{
160	10	count++;
161		}
162		}
163	3	return count;
164		}
165		}