Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
VarnaCommands	40	47	21	0.00%	Show methods

Class VarnaCommands

Class VarnaCommands	Line # 40	Total Statements 47	Complexity 21	TOTAL Coverage 0.00%
getColourBySequenceCommand(StructureSelectionManager,String[],SequenceI[][],SequenceRenderer,FeatureColourFinder,AlignmentI) : String[]   getColourBySequenceCommand(StructureSelectionManager,String[],SequenceI[][],SequenceRenderer,FeatureColourFinder,AlignmentI) : String[]	4848	33.033	16.016	0.0 0.00%
condenseCommand(StringBuffer,int) : StringBuffer   condenseCommand(StringBuffer,int) : StringBuffer	131131	14.014	5.05	0.0 0.00%

 

Contributing tests

Source view

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.ext.varna;
22
23		import jalview.api.SequenceRenderer;
24		import jalview.datamodel.AlignmentI;
25		import jalview.datamodel.SequenceI;
26		import jalview.renderer.seqfeatures.FeatureColourFinder;
27		import jalview.structure.StructureMapping;
28		import jalview.structure.StructureSelectionManager;
29
30		import java.awt.Color;
31		import java.util.ArrayList;
32
33		/**
34		* Routines for generating Jmol commands for Jalview/Jmol binding another
35		* cruisecontrol test.
36		*
37		* @author JimP
38		*
39		*/
		0% Uncovered Elements: 77 (77) Complexity: 21 Complexity Density: 0.45
40		public class VarnaCommands
41		{
42
43		/**
44		* Jmol utility which constructs the commands to colour chains by the given
45		* alignment
46		*
47		*/
		0% Uncovered Elements: 55 (55) Complexity: 16 Complexity Density: 0.48
48	0	public static String[] getColourBySequenceCommand(...
49		StructureSelectionManager ssm, String[] files,
50		SequenceI[][] sequence, SequenceRenderer sr,
51		FeatureColourFinder finder, AlignmentI alignment)
52		{
53	0	ArrayList<String> str = new ArrayList<String>();
54	0	StringBuffer command = new StringBuffer();
55
56	0	for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
57		{
58	0	StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
59
60	0	if (mapping == null || mapping.length < 1)
61		{
62	0	continue;
63		}
64
65	0	int lastPos = -1;
66	0	for (int s = 0; s < sequence[pdbfnum].length; s++)
67		{
68	0	for (int sp, m = 0; m < mapping.length; m++)
69		{
70	0	if (mapping[m].getSequence() == sequence[pdbfnum][s]
71		&& (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
72		{
73	0	SequenceI asp = alignment.getSequenceAt(sp);
74	0	for (int r = 0; r < asp.getLength(); r++)
75		{
76		// no mapping to gaps in sequence
77	0	if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
78		{
79	0	continue;
80		}
81	0	int pos = mapping[m].getPDBResNum(asp.findPosition(r));
82
83	0	if (pos < 1 || pos == lastPos)
84		{
85	0	continue;
86		}
87
88	0	lastPos = pos;
89
90	0	Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
91		finder);
92
93	0	String newSelcom = (mapping[m].getChain() != " "
94		? ":" + mapping[m].getChain()
95		: "") + "/" + (pdbfnum + 1) + ".1" + ";color["
96		+ col.getRed() + "," + col.getGreen() + ","
97		+ col.getBlue() + "]";
98	0	if (command.length() > newSelcom.length() && command
99		.substring(command.length() - newSelcom.length())
100		.equals(newSelcom))
101		{
102	0	command = VarnaCommands.condenseCommand(command, pos);
103	0	continue;
104		}
105		// TODO: deal with case when buffer is too large for Jmol to parse
106		// - execute command and flush
107
108	0	command.append(";");
109	0	if (command.length() > 51200)
110		{
111		// add another chunk
112	0	str.add(command.toString());
113	0	command.setLength(0);
114		}
115	0	command.append("select " + pos);
116	0	command.append(newSelcom);
117		}
118	0	break;
119		}
120		}
121		}
122		}
123		{
124		// add final chunk
125	0	str.add(command.toString());
126	0	command.setLength(0);
127		}
128	0	return str.toArray(new String[str.size()]);
129		}
130
		0% Uncovered Elements: 20 (20) Complexity: 5 Complexity Density: 0.36
131	0	public static StringBuffer condenseCommand(StringBuffer command, int pos)...
132		{
133
134		// work back to last 'select'
135	0	int p = command.length(), q = p;
136	0	do
137		{
138	0	p -= 6;
139	0	if (p < 1)
140		{
141	0	p = 0;
142		}
143	0	;
144	?	} while ((q = command.indexOf("select", p)) == -1 && p > 0);
145
146	0	StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
147
148	0	command = command.delete(0, q + 7);
149
150	0	String start;
151
152	0	if (command.indexOf("-") > -1)
153		{
154	0	start = command.substring(0, command.indexOf("-"));
155		}
156		else
157		{
158	0	start = command.substring(0, command.indexOf(":"));
159		}
160
161	0	sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
162
163	0	return sb;
164		}
165
166		}