Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
AlignmentProperties	38	49	16	76	0.00%	Show methods

Class AlignmentProperties

Class AlignmentProperties	Line # 38	Total Statements 49	Complexity 16	Uncovered Elements 76	TOTAL Coverage 0.00%
AlignmentProperties(AlignmentI)   AlignmentProperties(AlignmentI)	4242	1.01	1.01	1.01	0.0 0.00%
writeProperties(PrintWriter,boolean) : void   writeProperties(PrintWriter,boolean) : void	5353	43.043	12.012	65.065	0.0 0.00%
formatAsString() : StringBuffer   formatAsString() : StringBuffer	134134	1.01	1.01	1.01	0.0 0.00%
formatReport(boolean) : StringBuffer   formatReport(boolean) : StringBuffer	139139	3.03	1.01	3.03	0.0 0.00%
formatAsHtml() : StringBuffer   formatAsHtml() : StringBuffer	151151	1.01	1.01	1.01	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.io;
22
23		import jalview.datamodel.Alignment;
24		import jalview.datamodel.AlignmentI;
25
26		import java.io.PrintWriter;
27		import java.io.StringWriter;
28		import java.util.Enumeration;
29		import java.util.Hashtable;
30
31		/**
32		* Render associated attributes of an alignment. The heart of this code was
33		* refactored from jalview.gui.AlignFrame and jalview.appletgui.AlignFrame TODO:
34		* consider extending the html renderer to annotate elements with CSS ids
35		* enabling finer output format control.
36		*
37		*/
		0% Uncovered Elements: 76 (76) Complexity: 16 Complexity Density: 0.33
38		public class AlignmentProperties
39		{
40		AlignmentI alignment;
41
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
42	0	public AlignmentProperties(AlignmentI alignment)...
43		{
44	0	this.alignment = alignment;
45		}
46
47		/**
48		* render the alignment's properties report as text or an HTML fragment
49		*
50		* @param pw
51		* @param html
52		*/
		0% Uncovered Elements: 65 (65) Complexity: 12 Complexity Density: 0.28
53	0	public void writeProperties(PrintWriter pw, boolean html)...
54		{
55	0	final String nl = html ? "<br>" : System.getProperty("line.separator");
56	0	float avg = 0;
57	0	int min = Integer.MAX_VALUE, max = 0;
58	0	for (int i = 0; i < alignment.getHeight(); i++)
59		{
60	0	int size = 1 + alignment.getSequenceAt(i).getEnd()
61		- alignment.getSequenceAt(i).getStart();
62	0	avg += size;
63	0	if (size > max)
64		{
65	0	max = size;
66		}
67	0	if (size < min)
68		{
69	0	min = size;
70		}
71		}
72	0	avg = avg / alignment.getHeight();
73	0	pw.print(nl);
74	0	pw.print("Sequences: " + alignment.getHeight());
75	0	pw.print(nl);
76	0	pw.print("Minimum Sequence Length: " + min);
77	0	pw.print(nl);
78	0	pw.print("Maximum Sequence Length: " + max);
79	0	pw.print(nl);
80	0	pw.print("Average Length: " + (int) avg);
81
82	0	if (((Alignment) alignment).alignmentProperties != null)
83		{
84	0	pw.print(nl);
85	0	pw.print(nl);
86	0	if (html)
87		{
88	0	pw.print("<table border=\"1\">");
89		}
90	0	Hashtable props = ((Alignment) alignment).alignmentProperties;
91	0	Enumeration en = props.keys();
92	0	while (en.hasMoreElements())
93		{
94	0	String key = en.nextElement().toString();
95	0	String vals = props.get(key).toString();
96	0	if (html)
97		{
98		// wrap the text in the table
99	0	StringBuffer val = new StringBuffer();
100	0	int pos = 0, npos;
101	0	do
102		{
103	0	npos = vals.indexOf("\n", pos);
104	0	if (npos == -1)
105		{
106	0	val.append(vals.substring(pos));
107		}
108		else
109		{
110	0	val.append(vals.substring(pos, npos));
111	0	val.append("<br>");
112		}
113	0	pos = npos + 1;
114	0	} while (npos != -1);
115	0	pw.print("<tr><td>" + key + "</td><td>" + val + "</td></tr>");
116		}
117		else
118		{
119	0	pw.print(nl + key + "\t" + vals);
120		}
121		}
122	0	if (html)
123		{
124	0	pw.print("</table>");
125		}
126		}
127		}
128
129		/**
130		* generate a report as plain text
131		*
132		* @return
133		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
134	0	public StringBuffer formatAsString()...
135		{
136	0	return formatReport(false);
137		}
138
		0% Uncovered Elements: 3 (3) Complexity: 1 Complexity Density: 0.33
139	0	protected StringBuffer formatReport(boolean html)...
140		{
141	0	StringWriter content = new StringWriter();
142	0	writeProperties(new PrintWriter(content), html);
143	0	return content.getBuffer();
144		}
145
146		/**
147		* generate a report as a fragment of html
148		*
149		* @return
150		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
151	0	public StringBuffer formatAsHtml()...
152		{
153	0	return formatReport(true);
154		}
155
156		}