001/* 002 * BioJava development code 003 * 004 * This code may be freely distributed and modified under the 005 * terms of the GNU Lesser General Public Licence. This should 006 * be distributed with the code. If you do not have a copy, 007 * see: 008 * 009 * http://www.gnu.org/copyleft/lesser.html 010 * 011 * Copyright for this code is held jointly by the individual 012 * authors. These should be listed in @author doc comments. 013 * 014 * For more information on the BioJava project and its aims, 015 * or to join the biojava-l mailing list, visit the home page 016 * at: 017 * 018 * http://www.biojava.org/ 019 * 020 * Created on Nov 5, 2009 021 * Author: Andreas Prlic 022 * 023 */ 024 025package org.biojava.nbio.structure.align.gui; 026 027 028import org.biojava.nbio.structure.Structure; 029import org.biojava.nbio.structure.align.MultiThreadedDBSearch; 030import org.biojava.nbio.structure.align.StructureAlignment; 031import org.biojava.nbio.structure.align.util.AtomCache; 032import org.biojava.nbio.structure.align.util.UserConfiguration; 033import org.biojava.nbio.structure.scop.ScopFactory; 034 035import java.io.File; 036import java.util.concurrent.atomic.AtomicBoolean; 037//import org.slf4j.Logger; 038//import org.slf4j.LoggerFactory; 039 040public class AlignmentCalcDB implements AlignmentCalculationRunnable { 041 042 043 public static String SCOP_VERSION = "1.75"; 044 045 //private static final Logger logger = LoggerFactory.getLogger(AlignmentCalcDB.class); 046 047 AtomicBoolean interrupted ; 048 049 050 String name1; 051 052 Structure structure1; 053 054 AlignmentGui parent; 055 056 UserConfiguration config; 057 058 059 String outFile; 060 061 int nrCPUs; 062 Boolean domainSplit ; 063 064 StructureAlignment customAlgorithm; 065 066 MultiThreadedDBSearch job = null; 067 068 public StructureAlignment getAlgorithm() { 069 return customAlgorithm; 070 } 071 072 public void setAlgorithm(StructureAlignment algo) { 073 this.customAlgorithm = algo; 074 } 075 076 public AlignmentCalcDB(AlignmentGui parent, Structure s1, String name1, UserConfiguration config,String outFile, Boolean domainSplit) { 077 078 this.parent= parent; 079 080 structure1 = s1; 081 082 this.name1 = name1; 083 084 this.config = config; 085 //this.representatives = representatives; 086 interrupted = new AtomicBoolean(false); 087 this.outFile = outFile; 088 this.domainSplit = domainSplit; 089 090 System.out.println("AlignmentCalcDB: Using SCOP version " + SCOP_VERSION); 091 ScopFactory.setScopDatabase(SCOP_VERSION); 092 093 } 094 095 096 097 @Override 098 public void run() { 099 100 StructureAlignment algorithm = null; 101 102 if ( parent != null ) 103 algorithm = parent.getStructureAlignment(); 104 else { 105 algorithm = customAlgorithm; 106 } 107 108 109 if ( name1.startsWith("file:/")) 110 name1= "CUSTOM"; 111 112 job = new MultiThreadedDBSearch(name1,structure1, outFile, algorithm, nrCPUs, domainSplit); 113 114 AtomCache cache = new AtomCache(config); 115 System.out.println("using cache: " + cache.getPath()); 116 System.out.println("name1: " + name1); 117 System.out.println("structure:" + structure1.getName()); 118 job.setAtomCache(cache); 119 120 if ( name1.equals("CUSTOM")) { 121 job.setCustomFile1(parent.getDBSearch().getPDBUploadPanel().getFilePath1()); 122 job.setCustomChain1(parent.getDBSearch().getPDBUploadPanel().getChain1()); 123 } 124 125 job.run(); 126 127 File resultList = job.getResultFile(); 128 // if ((now-startTime)/1000 > 30) { 129 130 131 // try { 132 // out.flush(); 133 // out.close(); 134 // } catch (Exception e) { 135 // e.printStackTrace(); 136 // } 137 if ( parent != null ) { 138 parent.notifyCalcFinished(); 139 if ( resultList != null) { 140 DBResultTable table = new DBResultTable(); 141 table.show(resultList,config); 142 } 143 } 144 145 } 146 147 148 149 150 151 /** stops what is currently happening and does not continue 152 * 153 * 154 */ 155 @Override 156 public void interrupt() { 157 interrupted.set(true); 158 if ( job != null) 159 job.interrupt(); 160 161 162 163 } 164 165 @Override 166 public void cleanup() 167 { 168 parent.notifyCalcFinished(); 169 170 parent=null; 171 // cleanup... 172 173 structure1 = null; 174 config = null; 175 176 if ( job != null) 177 job.cleanup(); 178 179 } 180 181 @Override 182 public void setNrCPUs(int useNrCPUs) { 183 nrCPUs = useNrCPUs; 184 185 } 186 187 public synchronized boolean isInterrupted() { 188 return interrupted.get(); 189 } 190 191 192 193 194 195}