1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.io.vamsas

File DatastoreRegistry.java

 

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Classes

Class
Line #
Actions
DatastoreRegistry 29 41 21
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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   
27    import jalview.log.JLoggerLog4j;
28   
 
29    public class DatastoreRegistry implements AutoCloseable
30    {
31    protected static JLoggerLog4j log = JLoggerLog4j
32    .getLogger(DatastoreRegistry.class);
33   
34    /**
35    * map between Datastore objects and the objects they are handling- used to
36    * prevent cycles in the synchronization pattern. Keys are both vamsas objects
37    * and jalview objects, values are datastore objects.
38    */
39    IdentityHashMap dsObjReg;
40   
41    /**
42    * all datastore items - value is [jvObject,vObject]
43    */
44    IdentityHashMap dsItemReg;
45   
 
46  0 toggle public DatastoreRegistry()
47    {
48  0 dsObjReg = new IdentityHashMap();
49  0 dsItemReg = new IdentityHashMap();
50    }
51   
52    /**
53    *
54    * @param obj
55    * @return true if obj is in the registry
56    */
 
57  0 toggle public boolean isInvolvedInDsitem(Object obj)
58    {
59  0 return (obj instanceof DatastoreItem) ? dsItemReg.containsKey(obj)
60    : dsObjReg.containsKey(obj);
61    }
62   
63    /**
64    *
65    * @param obj
66    * @return DatastoreItem associated with obj - or null
67    */
 
68  0 toggle public DatastoreItem getDatastoreItemFor(Object obj)
69    {
70  0 if (obj instanceof DatastoreItem)
71    {
72  0 log.debug("Returning DatastoreItem self reference.");// TODO: we could
73    // store the update
74    // hierarchy - so
75    // retrieve parent
76    // for obj.
77  0 return (DatastoreItem) obj;
78    }
79  0 return (DatastoreItem) dsObjReg.get(obj);
80    }
81   
 
82  0 toggle synchronized void registerDsObj(DatastoreItem dsitem)
83    {
84  0 Object[] dsregitem = (Object[]) dsItemReg.get(dsitem);
85  0 if (dsregitem == null)
86    {
87    // create a new item entry
88  0 dsregitem = new Object[] { dsitem.jvobj, dsitem.vobj };
89  0 dsItemReg.put(dsitem, dsregitem);
90  0 dsObjReg.put(dsitem.jvobj, dsitem);
91  0 dsObjReg.put(dsitem.vobj, dsitem);
92    }
93    else
94    {
95    // update registry for any changed references
96    // for the jvobject
97  0 if (dsitem.jvobj != dsregitem[0])
98    {
99    // overwrite existing involved entries.
100  0 if (dsregitem[0] != null)
101    {
102  0 dsObjReg.remove(dsregitem[0]);
103    }
104  0 if ((dsregitem[0] = dsitem.jvobj) != null)
105    {
106  0 dsObjReg.put(dsregitem[0], dsitem);
107    }
108    }
109    // and for the vobject
110  0 if (dsitem.vobj != dsregitem[1])
111    {
112    // overwrite existing involved entries.
113  0 if (dsregitem[1] != null)
114    {
115  0 dsObjReg.remove(dsregitem[1]);
116    }
117  0 if ((dsregitem[1] = dsitem.vobj) != null)
118    {
119  0 dsObjReg.put(dsregitem[1], dsitem);
120    }
121    }
122    }
123    }
124   
125    /**
126    * Remove dsitem from the registry
127    *
128    * @param dsitem
129    * @return null or last known Object[] { jvobject, vobject } references for
130    * this dsitem
131    */
 
132  0 toggle public synchronized Object[] removeDsObj(DatastoreItem dsitem)
133    {
134  0 Object[] dsregitem = null;
135    // synchronized (dsItemReg)
136    {
137    // synchronized (dsObjReg)
138    {
139  0 dsregitem = (Object[]) dsItemReg.remove(dsitem);
140  0 if (dsregitem != null)
141    {
142    // eliminate object refs too
143  0 if (dsregitem[0] != null)
144    {
145  0 dsObjReg.remove(dsregitem[0]);
146    }
147  0 if (dsregitem[1] != null)
148    {
149  0 dsObjReg.remove(dsregitem[1]);
150    }
151    }
152    }
153    }
154  0 return dsregitem;
155    }
156   
 
157  0 toggle @Override
158    public void close()
159    {
160  0 if (dsObjReg != null)
161    {
162  0 Iterator items = dsObjReg.entrySet().iterator();
163    // avoid the nested reference memory leak.
164  0 while (items.hasNext())
165    {
166  0 Object[] vals = (Object[]) ((Map.Entry) items.next()).getValue();
167  0 vals[0] = null;
168  0 vals[1] = null;
169    }
170  0 items = null;
171  0 dsObjReg.clear();
172    }
173  0 if (dsItemReg != null)
174    {
175  0 dsItemReg.clear();
176    }
177    // super.finalize();
178    }
179    }