Classes

Class	Line #	Total Statements	Complexity	Uncovered Elements	TOTAL Coverage	Actions
DatastoreRegistry	27	42	21	78	0.00%	Show methods

Class DatastoreRegistry

Class DatastoreRegistry	Line # 27	Total Statements 42	Complexity 21	Uncovered Elements 78	TOTAL Coverage 0.00%
DatastoreRegistry()   DatastoreRegistry()	4444	2.02	1.01	2.02	0.0 0.00%
isInvolvedInDsitem(Object) : boolean   isInvolvedInDsitem(Object) : boolean	5555	1.01	2.02	3.03	0.0 0.00%
getDatastoreItemFor(Object) : DatastoreItem   getDatastoreItemFor(Object) : DatastoreItem	6666	4.04	2.02	6.06	0.0 0.00%
registerDsObj(DatastoreItem) : void   registerDsObj(DatastoreItem) : void	8080	16.016	8.08	30.030	0.0 0.00%
removeDsObj(DatastoreItem) : Object[]   removeDsObj(DatastoreItem) : Object[]	130130	8.08	4.04	14.014	0.0 0.00%
finalize() : void   finalize() : void	155155	11.011	4.04	17.017	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.vamsas;
22
23		import java.util.IdentityHashMap;
24		import java.util.Iterator;
25		import java.util.Map;
26
		0% Uncovered Elements: 78 (78) Complexity: 21 Complexity Density: 0.5
27		public class DatastoreRegistry
28		{
29		protected static org.apache.log4j.Logger log = org.apache.log4j.Logger
30		.getLogger(DatastoreRegistry.class);
31
32		/**
33		* map between Datastore objects and the objects they are handling- used to
34		* prevent cycles in the synchronization pattern. Keys are both vamsas objects
35		* and jalview objects, values are datastore objects.
36		*/
37		IdentityHashMap dsObjReg;
38
39		/**
40		* all datastore items - value is [jvObject,vObject]
41		*/
42		IdentityHashMap dsItemReg;
43
		0% Uncovered Elements: 2 (2) Complexity: 1 Complexity Density: 0.5
44	0	public DatastoreRegistry()...
45		{
46	0	dsObjReg = new IdentityHashMap();
47	0	dsItemReg = new IdentityHashMap();
48		}
49
50		/**
51		*
52		* @param obj
53		* @return true if obj is in the registry
54		*/
		0% Uncovered Elements: 3 (3) Complexity: 2 Complexity Density: 2
55	0	public boolean isInvolvedInDsitem(Object obj)...
56		{
57	0	return (obj instanceof DatastoreItem) ? dsItemReg.containsKey(obj)
58		: dsObjReg.containsKey(obj);
59		}
60
61		/**
62		*
63		* @param obj
64		* @return DatastoreItem associated with obj - or null
65		*/
		0% Uncovered Elements: 6 (6) Complexity: 2 Complexity Density: 0.5
66	0	public DatastoreItem getDatastoreItemFor(Object obj)...
67		{
68	0	if (obj instanceof DatastoreItem)
69		{
70	0	log.debug("Returning DatastoreItem self reference.");// TODO: we could
71		// store the update
72		// hierarchy - so
73		// retrieve parent
74		// for obj.
75	0	return (DatastoreItem) obj;
76		}
77	0	return (DatastoreItem) dsObjReg.get(obj);
78		}
79
		0% Uncovered Elements: 30 (30) Complexity: 8 Complexity Density: 0.5
80	0	synchronized void registerDsObj(DatastoreItem dsitem)...
81		{
82	0	Object[] dsregitem = (Object[]) dsItemReg.get(dsitem);
83	0	if (dsregitem == null)
84		{
85		// create a new item entry
86	0	dsregitem = new Object[] { dsitem.jvobj, dsitem.vobj };
87	0	dsItemReg.put(dsitem, dsregitem);
88	0	dsObjReg.put(dsitem.jvobj, dsitem);
89	0	dsObjReg.put(dsitem.vobj, dsitem);
90		}
91		else
92		{
93		// update registry for any changed references
94		// for the jvobject
95	0	if (dsitem.jvobj != dsregitem[0])
96		{
97		// overwrite existing involved entries.
98	0	if (dsregitem[0] != null)
99		{
100	0	dsObjReg.remove(dsregitem[0]);
101		}
102	0	if ((dsregitem[0] = dsitem.jvobj) != null)
103		{
104	0	dsObjReg.put(dsregitem[0], dsitem);
105		}
106		}
107		// and for the vobject
108	0	if (dsitem.vobj != dsregitem[1])
109		{
110		// overwrite existing involved entries.
111	0	if (dsregitem[1] != null)
112		{
113	0	dsObjReg.remove(dsregitem[1]);
114		}
115	0	if ((dsregitem[1] = dsitem.vobj) != null)
116		{
117	0	dsObjReg.put(dsregitem[1], dsitem);
118		}
119		}
120		}
121		}
122
123		/**
124		* Remove dsitem from the registry
125		*
126		* @param dsitem
127		* @return null or last known Object[] { jvobject, vobject } references for
128		* this dsitem
129		*/
		0% Uncovered Elements: 14 (14) Complexity: 4 Complexity Density: 0.5
130	0	public synchronized Object[] removeDsObj(DatastoreItem dsitem)...
131		{
132	0	Object[] dsregitem = null;
133		// synchronized (dsItemReg)
134		{
135		// synchronized (dsObjReg)
136		{
137	0	dsregitem = (Object[]) dsItemReg.remove(dsitem);
138	0	if (dsregitem != null)
139		{
140		// eliminate object refs too
141	0	if (dsregitem[0] != null)
142		{
143	0	dsObjReg.remove(dsregitem[0]);
144		}
145	0	if (dsregitem[1] != null)
146		{
147	0	dsObjReg.remove(dsregitem[1]);
148		}
149		}
150		}
151		}
152	0	return dsregitem;
153		}
154
		0% Uncovered Elements: 17 (17) Complexity: 4 Complexity Density: 0.36
155	0	@Override...
156		protected void finalize() throws Throwable
157		{
158	0	if (dsObjReg != null)
159		{
160	0	Iterator items = dsObjReg.entrySet().iterator();
161		// avoid the nested reference memory leak.
162	0	while (items.hasNext())
163		{
164	0	Object[] vals = (Object[]) ((Map.Entry) items.next()).getValue();
165	0	vals[0] = null;
166	0	vals[1] = null;
167		}
168	0	items = null;
169	0	dsObjReg.clear();
170		}
171	0	if (dsItemReg != null)
172		{
173	0	dsItemReg.clear();
174		}
175	0	super.finalize();
176		}
177		}