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andreasprlicandreasprlic
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refactoring DB search code to be independent of UI
git-svn-id: http://code.open-bio.org/repos/biojava/biojava-live/trunk@10002 7c6358e6-4a41-0410-a743-a5b2a554c398
1 parent ab49b86 commit ea974ad

1 file changed

Lines changed: 35 additions & 198 deletions

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‎biojava3-structure-gui/src/main/java/org/biojava/bio/structure/align/gui/AlignmentCalcDB.java‎

Lines changed: 35 additions & 198 deletions
Original file line numberDiff line numberDiff line change
@@ -27,38 +27,20 @@
2727

2828
import java.io.File;
2929

30-
import java.util.SortedSet;
31-
import java.util.concurrent.ExecutorService;
3230

33-
import java.util.concurrent.ThreadPoolExecutor;
3431
import java.util.concurrent.atomic.AtomicBoolean;
3532
import java.util.logging.Logger;
3633

3734

38-
import org.biojava.bio.structure.Atom;
39-
4035
import org.biojava.bio.structure.Structure;
4136

42-
import org.biojava.bio.structure.StructureTools;
43-
import org.biojava.bio.structure.align.CallableStructureAlignment;
37+
38+
import org.biojava.bio.structure.align.MultiThreadedDBSearch;
4439
import org.biojava.bio.structure.align.StructureAlignment;
45-
import org.biojava.bio.structure.align.ce.CeCPMain;
46-
import org.biojava.bio.structure.align.ce.CeMain;
47-
import org.biojava.bio.structure.align.ce.CeParameters;
48-
import org.biojava.bio.structure.align.ce.CeSideChainMain;
49-
import org.biojava.bio.structure.align.ce.ConfigStrucAligParams;
50-
import org.biojava.bio.structure.align.client.FarmJobParameters;
51-
import org.biojava.bio.structure.align.client.JFatCatClient;
52-
import org.biojava.bio.structure.align.client.PdbPair;
53-
import org.biojava.bio.structure.align.model.AFPChain;
40+
5441
import org.biojava.bio.structure.align.util.AtomCache;
55-
import org.biojava.bio.structure.align.util.SynchronizedOutFile;
56-
import org.biojava.bio.structure.align.util.UserConfiguration;
57-
import org.biojava.bio.structure.domain.DomainProvider;
58-
import org.biojava.bio.structure.domain.DomainProviderFactory;
59-
import org.biojava.bio.structure.domain.RemoteDomainProvider;
6042

61-
import org.biojava3.core.util.ConcurrencyTools;
43+
import org.biojava.bio.structure.align.util.UserConfiguration;
6244

6345
public class AlignmentCalcDB implements AlignmentCalculationRunnable {
6446
public static Logger logger = Logger.getLogger("org.biojava");
@@ -73,15 +55,17 @@ public class AlignmentCalcDB implements AlignmentCalculationRunnable {
7355
AlignmentGui parent;
7456

7557
UserConfiguration config;
76-
SortedSet<String> representatives;
58+
7759

7860
String outFile;
79-
File resultList;
61+
8062
int nrCPUs;
8163
Boolean domainSplit ;
82-
64+
8365
StructureAlignment customAlgorithm;
84-
66+
67+
MultiThreadedDBSearch job = null;
68+
8569
public StructureAlignment getAlgorithm() {
8670
return customAlgorithm;
8771
}
@@ -105,167 +89,33 @@ public AlignmentCalcDB(AlignmentGui parent, Structure s1, String name1, UserCon
10589
this.domainSplit = domainSplit;
10690
}
10791

108-
public static String getLegend(String algorithmName){
109-
110-
if ( algorithmName.equalsIgnoreCase(CeMain.algorithmName) ||
111-
algorithmName.equalsIgnoreCase(CeSideChainMain.algorithmName) ||
112-
algorithmName.equalsIgnoreCase(CeCPMain.algorithmName)) {
113-
return "# name1\tname2\tscore\tz-score\trmsd\tlen1\tlen2\tcov1\tcov2\t%ID\tDescription\t " ;
114-
}
115-
116-
// looks like a FATCAT alignment
117-
118-
return "# name1\tname2\tscore\tprobability\trmsd\tlen1\tlen2\tcov1\tcov2\t%ID\tDescription\t " ;
119-
120-
}
121-
92+
93+
12294
public void run() {
12395

124-
AtomCache cache = new AtomCache(config);
125-
12696
StructureAlignment algorithm = null;
97+
12798
if ( parent != null )
12899
algorithm = parent.getStructureAlignment();
129100
else {
130101
algorithm = customAlgorithm;
131102
}
132-
String serverLocation = FarmJobParameters.DEFAULT_SERVER_URL;
133-
if ( representatives == null){
134-
SortedSet<String> repre = JFatCatClient.getRepresentatives(serverLocation,40);
135-
System.out.println("got " + repre.size() + " representatives for comparison");
136-
representatives = repre;
137-
}
138-
139-
String header = "# algorithm:" + algorithm.getAlgorithmName();
140-
141-
String legend = getLegend(algorithm.getAlgorithmName());
142-
143-
144-
145-
File outFileF = new File(outFile);
146-
if ( ! outFileF.isDirectory()){
147-
System.err.println( outFileF.getAbsolutePath() + " is not a directory, can't create result files in there... ");
148-
interrupt();
149-
cleanup();
150-
}
151103

152-
if ( name1 == null)
153-
name1 = "CUSTOM";
154104

155-
SynchronizedOutFile out ;
105+
job = new MultiThreadedDBSearch(name1,structure1, outFile, algorithm, nrCPUs, domainSplit);
156106

157-
resultList = new File(outFileF,"results_" + name1 + ".out");
158-
159-
try {
160-
161-
out = new SynchronizedOutFile(resultList);
162-
163-
out.write(header);
164-
out.write(AFPChain.newline);
165-
out.write(legend);
166-
out.write(AFPChain.newline);
167-
168-
if ( name1.equals("CUSTOM")) {
169-
170-
String config1 = "#param:file1=" + parent.getDBSearch().getPDBUploadPanel().getFilePath1();
171-
out.write(config1);
172-
out.write(AFPChain.newline);
173-
174-
String config2 = "#param:chain1=" + parent.getDBSearch().getPDBUploadPanel().getChain1();
175-
out.write(config2);
176-
out.write(AFPChain.newline);
177-
178-
}
179-
180-
if ( algorithm.getAlgorithmName().startsWith("jCE")){
181-
ConfigStrucAligParams params = algorithm.getParameters();
182-
if ( params instanceof CeParameters){
183-
CeParameters ceParams = (CeParameters) params;
184-
if ( ceParams.getScoringStrategy() != CeParameters.DEFAULT_SCORING_STRATEGY) {
185-
String scoring = "#param:scoring=" + ceParams.getScoringStrategy();
186-
out.write(scoring);
187-
out.write(AFPChain.newline);
188-
}
189-
}
190-
}
191-
192-
} catch (Exception e){
193-
System.err.println("Error while loading representative structure " + name1);
194-
e.printStackTrace();
195-
interrupt();
196-
cleanup();
197-
return;
198-
}
199-
200-
201-
202-
DomainProvider domainProvider = DomainProviderFactory.getDomainProvider();
203-
204-
ConcurrencyTools.setThreadPoolSize(nrCPUs);
205-
206-
Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
207-
208-
int nrJobs = 0;
209-
for (String repre : representatives){
210-
211-
if( domainSplit ) {
212-
SortedSet<String> domainNames = domainProvider.getDomainNames(repre);
213-
//System.out.println(repre +" got domains: " +domainNames);
214-
if( domainNames == null || domainNames.size()==0){
215-
// no domains found, use whole chain.
216-
submit(name1, repre, ca1, algorithm, outFileF, out, cache);
217-
nrJobs++;
218-
continue;
219-
}
220-
//System.out.println("got " + domainNames.size() + " for " + repre);
221-
for( String domain : domainNames){
222-
submit(name1, domain, ca1, algorithm, outFileF, out, cache);
223-
nrJobs++;
224-
}
225-
} else {
226-
submit(name1, repre, ca1, algorithm, outFileF, out, cache);
227-
nrJobs++;
228-
}
229-
230-
}
231-
232-
233-
ThreadPoolExecutor pool = ConcurrencyTools.getThreadPool();
234-
System.out.println(pool.getPoolSize());
235-
236-
long startTime = System.currentTimeMillis();
237-
238-
try {
239-
while ( pool.getCompletedTaskCount() < nrJobs-1 ) {
240-
//long now = System.currentTimeMillis();
241-
//System.out.println( pool.getCompletedTaskCount() + " " + (now-startTime)/1000 + " " + pool.getPoolSize() + " " + pool.getActiveCount() + " " + pool.getTaskCount() );
242-
// if ((now-startTime)/1000 > 60) {
243-
//
244-
// interrupt();
245-
// System.out.println("completed: " + pool.getCompletedTaskCount());
246-
// }
247-
248-
if ( interrupted.get())
249-
break;
250-
251-
Thread.sleep(2000);
107+
AtomCache cache = new AtomCache(config);
108+
System.out.println("using cache: " + cache.getPath());
109+
job.setAtomCache(cache);
252110

253-
}
254-
out.close();
255-
}
256-
catch (Exception e){
257-
e.printStackTrace();
258-
interrupt();
259-
cleanup();
111+
if ( name1.equals("CUSTOM")) {
112+
job.setCustomFile1(parent.getDBSearch().getPDBUploadPanel().getFilePath1());
113+
job.setCustomChain1(parent.getDBSearch().getPDBUploadPanel().getChain1());
260114
}
261115

262-
if (domainProvider instanceof RemoteDomainProvider){
263-
RemoteDomainProvider remote = (RemoteDomainProvider) domainProvider;
264-
remote.flushCache();
265-
}
266-
long now = System.currentTimeMillis();
267-
System.out.println("Calculation took : " + (now-startTime)/1000 + " sec.");
268-
System.out.println( pool.getCompletedTaskCount() + " " + pool.getPoolSize() + " " + pool.getActiveCount() + " " + pool.getTaskCount() );
116+
job.run();
117+
118+
File resultList = job.getResultFile();
269119
// if ((now-startTime)/1000 > 30) {
270120

271121

@@ -277,44 +127,28 @@ public void run() {
277127
// }
278128
if ( parent != null ) {
279129
parent.notifyCalcFinished();
280-
DBResultTable table = new DBResultTable();
281-
table.show(resultList,config);
130+
if ( resultList != null) {
131+
DBResultTable table = new DBResultTable();
132+
table.show(resultList,config);
133+
}
282134
}
283-
284-
}
285-
286135

136+
}
287137

288-
private void submit(String name12, String repre, Atom[] ca1, StructureAlignment algorithm , File outFileF , SynchronizedOutFile out , AtomCache cache ) {
289-
CallableStructureAlignment ali = new CallableStructureAlignment();
290138

291-
PdbPair pair = new PdbPair(name1, repre);
292-
try {
293-
ali.setCa1(ca1);
294-
} catch (Exception e){
295-
e.printStackTrace();
296-
ConcurrencyTools.shutdown();
297-
return;
298-
}
299-
ali.setAlgorithmName(algorithm.getAlgorithmName());
300-
ali.setParameters(algorithm.getParameters());
301-
ali.setPair(pair);
302-
ali.setOutFile(out);
303-
ali.setOutputDir(outFileF);
304-
ali.setCache(cache);
305139

306-
ConcurrencyTools.submit(ali);
307140

308-
}
309141

310142
/** stops what is currently happening and does not continue
311143
*
312144
*
313145
*/
314146
public void interrupt() {
315147
interrupted.set(true);
316-
ExecutorService pool = ConcurrencyTools.getThreadPool();
317-
pool.shutdownNow();
148+
if ( job != null)
149+
job.interrupt();
150+
151+
318152

319153
}
320154

@@ -328,6 +162,9 @@ public void cleanup()
328162
structure1 = null;
329163
config = null;
330164

165+
if ( job != null)
166+
job.cleanup();
167+
331168
}
332169

333170
public void setNrCPUs(int useNrCPUs) {

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