Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
ParseProperties	29	46	16	0.00%	Show methods

Class ParseProperties

Class ParseProperties	Line # 29	Total Statements 46	Complexity 16	TOTAL Coverage 0.00%
ParseProperties(AlignmentI)   ParseProperties(AlignmentI)	5252	1.01	1.01	0.0 0.00%
getScoresFromDescription(String,String,String,boolean) : int   getScoresFromDescription(String,String,String,boolean) : int	5757	1.01	1.01	0.0 0.00%
getScoresFromDescription(String[],String[],String,boolean) : int   getScoresFromDescription(String[],String[],String,boolean) : int	6565	1.01	1.01	0.0 0.00%
getScoresFromDescription(SequenceI[],String[],String[],String,boolean) : int   getScoresFromDescription(SequenceI[],String[],String[],String,boolean) : int	8989	43.043	13.013	0.0 0.00%

 

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