/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.io;\r
\r
-import jalview.datamodel.*;\r
-\r
-import jalview.gui.*;\r
-\r
import java.io.*;\r
-\r
import java.util.*;\r
\r
-import org.exolab.castor.mapping.Mapping;\r
-\r
+import org.exolab.castor.mapping.*;\r
import org.exolab.castor.xml.*;\r
-import jalview.analysis.AlignSeq;\r
-\r
-\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.gui.*;\r
\r
/**\r
* DOCUMENT ME!\r
* @author $author$\r
* @version $Revision$\r
*/\r
-public class DBRefFetcher implements Runnable\r
+public class DBRefFetcher\r
+ implements Runnable\r
{\r
- AlignmentI dataset;\r
+ SequenceI [] dataset;\r
AlignFrame af;\r
CutAndPasteTransfer output = new CutAndPasteTransfer();\r
StringBuffer sbuffer = new StringBuffer();\r
try\r
{\r
// 1. Load the mapping information from the file\r
- Mapping map = new Mapping(uni.getClass().getClassLoader());\r
+ org.exolab.castor.mapping.Mapping map = new org.exolab.castor.mapping.Mapping(uni.getClass().getClassLoader());\r
java.net.URL url = getClass().getResource("/uniprot_mapping.xml");\r
map.loadMapping(url);\r
\r
}\r
catch (Exception e)\r
{\r
- System.out.println("Error getUniprotEntries() "+e);\r
+ System.out.println("Error getUniprotEntries() " + e);\r
}\r
\r
-\r
return uni.getUniprotEntries();\r
}\r
\r
* @param align DOCUMENT ME!\r
* @param ap DOCUMENT ME!\r
*/\r
- public DBRefFetcher(AlignmentI align, AlignFrame af)\r
+ public DBRefFetcher(SequenceI [] seqs, AlignFrame af)\r
{\r
this.af = af;\r
- this.dataset = align.getDataset();\r
+ SequenceI [] ds = new SequenceI[seqs.length];\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ if(seqs[i].getDatasetSequence()!=null)\r
+ ds[i] = seqs[i].getDatasetSequence();\r
+ else\r
+ ds[i] = seqs[i];\r
+ }\r
+ this.dataset = ds;\r
}\r
\r
public boolean fetchDBRefs(boolean waitTillFinished)\r
thread.start();\r
running = true;\r
\r
- if(waitTillFinished)\r
+ if (waitTillFinished)\r
{\r
- while(running)\r
+ while (running)\r
{\r
- try{\r
+ try\r
+ {\r
Thread.sleep(500);\r
- }catch(Exception ex){}\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
}\r
}\r
\r
key = key.toUpperCase();\r
\r
Vector seqs;\r
- if(seqRefs.containsKey(key))\r
+ if (seqRefs.containsKey(key))\r
{\r
- seqs = (Vector)seqRefs.get(key);\r
+ seqs = (Vector) seqRefs.get(key);\r
\r
- if(seqs!=null && !seqs.contains(seq))\r
+ if (seqs != null && !seqs.contains(seq))\r
{\r
seqs.addElement(seq);\r
}\r
- else if(seqs==null)\r
+ else if (seqs == null)\r
{\r
seqs = new Vector();\r
seqs.addElement(seq);\r
seqRefs.put(key, seqs);\r
}\r
\r
-\r
/**\r
* DOCUMENT ME!\r
*/\r
try\r
{\r
int seqIndex = 0;\r
- Vector sequences = dataset.getSequences();\r
\r
- while (seqIndex < sequences.size())\r
+ while (seqIndex < dataset.length)\r
{\r
StringBuffer queryString = new StringBuffer("uniprot:");\r
\r
- for (int i = 0; (seqIndex < sequences.size()) && (i < 50);\r
+ for (int i = 0; (seqIndex < dataset.length) && (i < 50);\r
seqIndex++, i++)\r
{\r
- Sequence sequence = (Sequence) sequences.get(seqIndex);\r
- DBRefEntry [] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {\r
+ SequenceI sequence = dataset[seqIndex];\r
+ DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(sequence.\r
+ getDBRef(), new String[]\r
+ {\r
jalview.datamodel.DBRefSource.UNIPROT});\r
- if (uprefs!=null)\r
+ if (uprefs != null)\r
{\r
- if(uprefs.length+i>50)\r
+ if (uprefs.length + i > 50)\r
+ {\r
break;\r
+ }\r
\r
- for(int j=0; j<uprefs.length; j++)\r
+ for (int j = 0; j < uprefs.length; j++)\r
{\r
addSeqId(sequence, uprefs[j].getAccessionId());\r
- queryString.append(uprefs[i].getAccessionId()+";");\r
+ queryString.append(uprefs[j].getAccessionId() + ";");\r
}\r
}\r
else\r
{\r
StringTokenizer st = new StringTokenizer(sequence.getName(), "|");\r
- if(st.countTokens()+i>50)\r
+ if (st.countTokens() + i > 50)\r
{\r
//Dont send more than 50 id strings to dbFetch!!\r
- seqIndex --;\r
+ seqIndex--;\r
}\r
else\r
{\r
- while(st.hasMoreTokens())\r
- {\r
- String token = st.nextToken();\r
- addSeqId(sequence, token);\r
- queryString.append(token+";");\r
- }\r
+ while (st.hasMoreTokens())\r
+ {\r
+ String token = st.nextToken();\r
+ addSeqId(sequence, token);\r
+ queryString.append(token + ";");\r
+ }\r
}\r
}\r
}\r
}\r
\r
af.setProgressBar("DBRef search completed", startTime);\r
- // promptBeforeBlast();\r
+ // promptBeforeBlast();\r
\r
- running = false;\r
+ running = false;\r
\r
}\r
\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
void ReadUniprotFile(File file)\r
{\r
if (!file.exists())\r
+ {\r
return;\r
+ }\r
\r
SequenceI sequence = null;\r
\r
{\r
sequence = (SequenceI) seqs.elementAt(jj);\r
if (!sequenceMatches.contains(sequence))\r
+ {\r
sequenceMatches.addElement(sequence);\r
+ }\r
}\r
}\r
}\r
{\r
sequence = (SequenceI) seqs.elementAt(jj);\r
if (!sequenceMatches.contains(sequence))\r
+ {\r
sequenceMatches.addElement(sequence);\r
+ }\r
}\r
}\r
}\r
System.out.println("Adding dbref to " + sequence.getName() + " : " +\r
entry.getAccession().elementAt(0).toString());\r
\r
- String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence()).\r
+ String nonGapped = AlignSeq.extractGaps("-. ",\r
+ sequence.getSequenceAsString()).\r
toUpperCase();\r
\r
int absStart = entry.getUniprotSequence().getContent().indexOf(\r
{\r
PDBEntry pdb = (PDBEntry) e.nextElement();\r
if (!pdb.getType().equals(DBRefSource.PDB))\r
+ {\r
continue;\r
+ }\r
\r
sequence.addDBRef(new DBRefEntry(DBRefSource.PDB,\r
"0",\r
}\r
}\r
}\r
-\r
-\r
git://source.jalview.org / jalview.git / blobdiff