Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AMSAFile	29	31	14	0.00%	Show methods

Class AMSAFile

Class AMSAFile	Line # 29	Total Statements 31	Complexity 14	TOTAL Coverage 0.00%
AMSAFile(AlignmentI)   AMSAFile(AlignmentI)	3737	1.01	1.01	0.0 0.00%
AMSAFile(String,DataSourceType)   AMSAFile(String,DataSourceType)	4242	1.01	1.01	0.0 0.00%
AMSAFile(FileParse)   AMSAFile(FileParse)	4848	1.01	1.01	0.0 0.00%
print(SequenceI[],boolean) : String   print(SequenceI[],boolean) : String	5858	28.028	11.011	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.AlignmentAnnotation;
24		import jalview.datamodel.AlignmentI;
25		import jalview.datamodel.SequenceI;
26
27		import java.io.IOException;
28
		0% Uncovered Elements: 53 (53) Complexity: 14 Complexity Density: 0.45
29		public class AMSAFile extends jalview.io.FastaFile
30		{
31
32		AlignmentI al;
33
34		/**
35		* Creates a new AMSAFile object for output.
36		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
37	0	public AMSAFile(AlignmentI al)...
38		{
39	0	this.al = al;
40		}
41
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
42	0	public AMSAFile(String inFile, DataSourceType sourceType)...
43		throws IOException
44		{
45	0	super(inFile, sourceType);
46		}
47
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
48	0	public AMSAFile(FileParse source) throws IOException...
49		{
50	0	super(source);
51		}
52
53		/**
54		* DOCUMENT ME!
55		*
56		* @return DOCUMENT ME!
57		*/
		0% Uncovered Elements: 46 (46) Complexity: 11 Complexity Density: 0.39
58	0	@Override...
59		public String print(SequenceI[] sqs, boolean jvsuffix)
60		{
61	0	super.print(sqs, jvsuffix);
62
63	0	AlignmentAnnotation aa;
64	0	if (al.getAlignmentAnnotation() != null)
65		{
66
67	0	for (int i = 0; i < al.getAlignmentAnnotation().length; i++)
68		{
69	0	aa = al.getAlignmentAnnotation()[i];
70
71	0	if (aa.autoCalculated || !aa.visible)
72		{
73	0	continue;
74		}
75
76	0	out.append(">#_" + aa.label);
77	0	if (aa.description != null)
78		{
79	0	out.append(" " + aa.description);
80		}
81
82	0	out.append(newline);
83
84	0	int nochunks = Math.min(aa.annotations.length, al.getWidth()) / len
85		+ 1;
86
87	0	for (int j = 0; j < nochunks; j++)
88		{
89	0	int start = j * len;
90	0	int end = start + len;
91	0	if (end > aa.annotations.length)
92		{
93	0	end = aa.annotations.length;
94		}
95
96	0	String ch;
97	0	for (int k = start; k < end; k++)
98		{
99	0	if (aa.annotations[k] == null)
100		{
101	0	ch = " ";
102		}
103		else
104		{
105	0	ch = aa.annotations[k].displayCharacter;
106		}
107	0	if (ch.length() > 1)
108		{
109	0	this.warningMessage = "Truncated column annotation to first letter.";
110	0	ch = ch.substring(0, 1);
111		}
112	0	out.append(ch);
113
114		}
115	0	out.append(newline);
116		}
117		}
118		}
119	0	return out.toString();
120		}
121		}