Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
ChimeraListener	51	11	7	19	0.00%	Show methods

Class ChimeraListener

Class ChimeraListener	Line # 51	Total Statements 11	Complexity 7	Uncovered Elements 19	TOTAL Coverage 0.00%
ChimeraListener(JalviewChimeraBinding)   ChimeraListener(JalviewChimeraBinding)	100100	4.04	1.01	4.04	0.0 0.00%
processRequest(HttpServletRequest,HttpServletResponse) : void   processRequest(HttpServletRequest,HttpServletResponse) : void	111111	6.06	4.04	10.010	0.0 0.00%
processModelChanged(String) : void   processModelChanged(String) : void	136136	0.00	1.01	0.00	-1.0 -1.0 -
getName() : String   getName() : String	144144	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.ext.rbvi.chimera;
22
23		import jalview.httpserver.AbstractRequestHandler;
24		import jalview.structure.SelectionSource;
25
26		import java.net.BindException;
27
28		import javax.servlet.http.HttpServletRequest;
29		import javax.servlet.http.HttpServletResponse;
30
31		/**
32		* This is a simple Http handler that can listen for selections in Chimera.
33		* <p/>
34		* Lifecycle:
35		* <ul>
36		* <li>Start the Chimera process</li>
37		* <li>Start the REST service on Chimera, get the port number it is listening on
38		* </li>
39		* <li>Start the ChimeraListener, get the URL it is listening on</li>
40		* <li>The first listener started will start the singleton HttpServer</li>
41		* <li>Send a 'listen' command to Chimera with the URL of the listener</li>
42		* <li>When Jalview's Chimera window is closed, shut down the
43		* ChimeraListener</li>
44		* <li>Multiple linked Chimera instances will each have a separate listener (but
45		* share one Http server)</li>
46		* </ul>
47		*
48		* @author gmcarstairs
49		*
50		*/
		0% Uncovered Elements: 19 (19) Complexity: 7 Complexity Density: 0.64
51		public class ChimeraListener extends AbstractRequestHandler
52		implements SelectionSource
53		{
54		/*
55		* Chimera notification parameter name
56		*/
57		private static final String CHIMERA_NOTIFICATION = "chimeraNotification";
58
59		/*
60		* Chimera model changed notifications start with this
61		*/
62		private static final String MODEL_CHANGED = "ModelChanged: ";
63
64		/*
65		* Chimera selection changed notification message
66		*/
67		private static final String SELECTION_CHANGED = "SelectionChanged: selection changed\n";
68
69		/*
70		* A static counter so each listener can be associated with a distinct context
71		* root (/chimera0,1,2,3...). This is needed so we can fetch selections from
72		* multiple Chimera instances without confusion.
73		*/
74		private static int chimeraId = 0;
75
76		/*
77		* Prefix for path below context root (myChimeraId is appended)
78		*/
79		private static final String PATH_PREFIX = "chimera";
80
81		/*
82		* Value of chimeraId (0, 1, 2...) for this instance
83		*/
84		private int myChimeraId = 0;
85
86		/*
87		* A reference to the object by which we can talk to Chimera
88		*/
89		private JalviewChimeraBinding chimeraBinding;
90
91		/**
92		* Constructor that registers this as an Http request handler on path
93		* /chimeraN, where N is incremented for each instance. Call getUri to get the
94		* resulting URI for this handler.
95		*
96		* @param chimeraBinding
97		* @throws BindException
98		* if no free port can be assigned
99		*/
		0% Uncovered Elements: 4 (4) Complexity: 1 Complexity Density: 0.25
100	0	public ChimeraListener(JalviewChimeraBinding binding) throws BindException...
101		{
102	0	myChimeraId = chimeraId++;
103	0	this.chimeraBinding = binding;
104	0	setPath(PATH_PREFIX + myChimeraId);
105	0	registerHandler();
106		}
107
108		/**
109		* Process a message from Chimera
110		*/
		0% Uncovered Elements: 10 (10) Complexity: 4 Complexity Density: 0.67
111	0	@Override...
112		protected void processRequest(HttpServletRequest request,
113		HttpServletResponse response)
114		{
115		// dumpRequest(request);
116	0	String message = request.getParameter(CHIMERA_NOTIFICATION);
117	0	if (SELECTION_CHANGED.equals(message))
118		{
119	0	this.chimeraBinding.highlightChimeraSelection();
120		}
121	0	else if (message != null && message.startsWith(MODEL_CHANGED))
122		{
123	0	processModelChanged(message.substring(MODEL_CHANGED.length()));
124		}
125		else
126		{
127	0	System.err.println("Unexpected chimeraNotification: " + message);
128		}
129		}
130
131		/**
132		* Handle a ModelChanged notification from Chimera
133		*
134		* @param substring
135		*/
		- Uncovered Elements: 0 (0) Complexity: 1 Complexity Density: -
136	0	protected void processModelChanged(String message)...
137		{
138		// System.out.println(message + " (not implemented in Jalview)");
139		}
140
141		/**
142		* Returns a display name for this service
143		*/
		0% Uncovered Elements: 1 (1) Complexity: 1 Complexity Density: 1
144	0	@Override...
145		public String getName()
146		{
147	0	return "ChimeraListener";
148		}
149		}