+++ /dev/null
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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.xml.*;\r
-import jalview.analysis.AlignSeq;\r
-\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class SequenceFeatureFetcher implements Runnable\r
-{\r
-\r
- AlignmentI align;\r
- AlignmentI dataset;\r
- AlignmentPanel ap;\r
- ArrayList unknownSequences;\r
- CutAndPasteTransfer output = new CutAndPasteTransfer();\r
- StringBuffer sbuffer = new StringBuffer();\r
- boolean uniprotFlag = false;\r
-\r
- public SequenceFeatureFetcher()\r
- {}\r
-\r
- public Vector getUniprotEntries(File file)\r
- {\r
-\r
- UniprotFile uni = new UniprotFile();\r
- try\r
- {\r
- // 1. Load the mapping information from the file\r
- Mapping map = new Mapping(uni.getClass().getClassLoader());\r
- java.net.URL url = getClass().getResource("/uniprot_mapping.xml");\r
- map.loadMapping(url);\r
-\r
- // 2. Unmarshal the data\r
- Unmarshaller unmar = new Unmarshaller(uni);\r
- unmar.setIgnoreExtraElements(true);\r
- unmar.setMapping(map);\r
- // unmar.setDebug(true);\r
-\r
- uni = (UniprotFile) unmar.unmarshal(new FileReader(file));\r
- }\r
- catch (Exception e)\r
- {\r
- System.out.println("Error getUniprotEntries() "+e);\r
- }\r
-\r
-\r
- return uni.getUniprotEntries();\r
- }\r
-\r
- /**\r
- * Creates a new SequenceFeatureFetcher object.\r
- *\r
- * @param align DOCUMENT ME!\r
- * @param ap DOCUMENT ME!\r
- */\r
- public SequenceFeatureFetcher(AlignmentI align, AlignmentPanel ap)\r
- {\r
- unknownSequences = new ArrayList();\r
- this.align = align;\r
- this.dataset = align.getDataset();\r
- this.ap = ap;\r
-\r
- Thread thread = new Thread(this);\r
- thread.start();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
- {\r
- try\r
- {\r
- int seqIndex = 0;\r
- Vector sequences = dataset.getSequences();\r
-\r
- while (seqIndex < sequences.size())\r
- {\r
- Vector ids = new Vector();\r
-\r
- for (int i = 0; (seqIndex < sequences.size()) && (i < 50);\r
- seqIndex++, i++)\r
- {\r
- Sequence sequence = (Sequence) sequences.get(seqIndex);\r
- Vector uprefs = jalview.util.DBRefUtils.selectRefs(sequence.getDBRef(), new String[] {\r
- jalview.datamodel.DBRefSource.UNIPROT});\r
- if (uprefs!=null)\r
- {\r
- // we know the id for this entry, so don't note its ID in the unknownSequences list\r
- for (int j=0,k=uprefs.size(); j<k; j++)\r
- ids.add(((DBRefEntry) uprefs.get(j)).getAccessionId());\r
- unknownSequences.add(sequence);\r
- } else {\r
- if (!ids.contains(sequence.getName()))\r
- {\r
- ids.add(sequence.getName());\r
- unknownSequences.add(sequence);\r
- }\r
- }\r
- }\r
-\r
- ///////////////////////////////////\r
- ///READ FROM EBI\r
- if (ids.size() > 0)\r
- {\r
- StringBuffer remainingIds = new StringBuffer("uniprot:");\r
- for (int i = 0; i < ids.size(); i++)\r
- {\r
- if(ids.get(i).toString().indexOf("|")>-1)\r
- {\r
- remainingIds.append(ids.get(i).toString().substring(\r
- ids.get(i).toString().lastIndexOf("|") + 1));\r
- uniprotFlag = true;\r
- }\r
- remainingIds.append(ids.get(i) + ";");\r
- }\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- File file = ebi.fetchDataAsFile(remainingIds.toString(),\r
- "xml", "raw");\r
-\r
-\r
-\r
- if (file != null)\r
- {\r
- ReadUniprotFile(file, ids);\r
- }\r
- }\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- if (sbuffer.length() > 0)\r
- {\r
- output.setText(\r
- "Your sequences have been matched to Uniprot. Some of the ids have been\n" +\r
- "altered, most likely the start/end residue will have been updated.\n" +\r
- "Save your alignment to maintain the updated id.\n\n" +\r
- sbuffer.toString());\r
- Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);\r
- // The above is the dataset, we must now find out the index\r
- // of the viewed sequence\r
-\r
- }\r
-\r
- promptBeforeBlast();\r
-\r
- }\r
-\r
-\r
- void promptBeforeBlast()\r
- {\r
- // This must be outside the run() body as java 1.5\r
- // will not return any value from the OptionPane to the expired thread.\r
- if (unknownSequences.size() > 0)\r
- {\r
- // int reply = javax.swing.JOptionPane.showConfirmDialog(\r
- // Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences."\r
- // +"\nPerform blast for unknown sequences?",\r
- // "Blast for Unidentified Sequences",\r
- // javax.swing.JOptionPane.YES_NO_OPTION, javax.swing.JOptionPane.QUESTION_MESSAGE);\r
- javax.swing.JOptionPane.showMessageDialog(\r
- Desktop.desktop, "Couldn't find a match for "+unknownSequences.size()+" sequences.",\r
- "Unidentified Sequences",\r
- javax.swing.JOptionPane.WARNING_MESSAGE);\r
-\r
-\r
- // if(reply == javax.swing.JOptionPane.YES_OPTION)\r
- // new WSWUBlastClient(ap, align, unknownSequences);\r
- }\r
-\r
-\r
- ap.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param result DOCUMENT ME!\r
- * @param out DOCUMENT ME!\r
- * @param align DOCUMENT ME!\r
- */\r
- void ReadUniprotFile(File file, Vector ids)\r
- {\r
- if(!file.exists())\r
- return;\r
-\r
- SequenceI sequence = null;\r
-\r
- Vector entries = getUniprotEntries(file);\r
-\r
- int i, iSize = entries==null?0:entries.size();\r
- UniprotEntry entry;\r
- for (i = 0; i < iSize; i++)\r
- {\r
- entry = (UniprotEntry) entries.elementAt(i);\r
- String idmatch = entry.getAccession().elementAt(0).toString();\r
- sequence = dataset.findName(idmatch);\r
-\r
- if (sequence == null)\r
- {\r
- //Sequence maybe Name, not Accession\r
- idmatch = entry.getName().elementAt(0).toString();\r
- sequence = dataset.findName(idmatch);\r
- }\r
-\r
- if(sequence!=null)\r
- ids.remove(sequence.getName());\r
-\r
- else if (sequence == null && uniprotFlag)\r
- {\r
- sequence = dataset.findName("UniProt/Swiss-Prot|"+entry.getAccession().elementAt(0)+"|"+idmatch);\r
- ids.remove(idmatch);\r
- }\r
-\r
- if(sequence ==null)\r
- {\r
- System.out.println(idmatch+" not found");\r
- continue;\r
- }\r
-\r
-\r
- String nonGapped = AlignSeq.extractGaps("-. ", sequence.getSequence());\r
-\r
- int absStart = entry.getUniprotSequence().getContent().indexOf(\r
- nonGapped.toString());\r
-\r
- if (absStart == -1)\r
- {\r
- // Is UniprotSequence contained in dataset sequence?\r
- absStart = nonGapped.toString().indexOf(entry.getUniprotSequence().getContent());\r
- if(absStart == -1)\r
- {\r
- sbuffer.append(sequence.getName() +\r
- " SEQUENCE NOT %100 MATCH \n");\r
-\r
- continue;\r
- }\r
- else\r
- {\r
-\r
- if(entry.getFeature()!=null)\r
- {\r
- Enumeration e = entry.getFeature().elements();\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- sf.setBegin(sf.getBegin() + absStart + 1);\r
- sf.setEnd(sf.getEnd() + absStart + 1);\r
- }\r
- }\r
-\r
- sbuffer.append(sequence.getName() +\r
- " HAS "+absStart+" PREFIXED RESIDUES COMPARED TO UNIPROT - ANY SEQUENCE FEATURES"\r
- +" HAVE BEEN ADJUSTED ACCORDINGLY \n");\r
- absStart = 0;\r
- }\r
-\r
- }\r
-\r
- unknownSequences.remove(sequence);\r
-\r
- int absEnd = absStart + nonGapped.toString().length();\r
- absStart += 1;\r
-\r
- Enumeration e = entry.getDbReference().elements();\r
- Vector onlyPdbEntries = new Vector();\r
- while(e.hasMoreElements())\r
- {\r
- PDBEntry pdb = (PDBEntry)e.nextElement();\r
- if(!pdb.getType().equals("PDB"))\r
- continue;\r
-\r
- onlyPdbEntries.addElement(pdb);\r
- }\r
-\r
- sequence.setPDBId(onlyPdbEntries);\r
- if (entry.getFeature()!=null) {\r
- e = entry.getFeature().elements();\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- sf.setFeatureGroup("Uniprot");\r
- sequence.addSequenceFeature( sf );\r
- }\r
- }\r
- sequence.setStart(absStart);\r
- sequence.setEnd(absEnd);\r
-\r
-\r
- int n = 0;\r
- SequenceI seq2;\r
- while (n < align.getHeight())\r
- {\r
- //This loop enables multiple sequences with the same\r
- //id to have features added and seq limits updated\r
- seq2 = align.getSequenceAt(n);\r
- if (seq2.getName().equals(idmatch))\r
- {\r
-\r
- nonGapped = AlignSeq.extractGaps("-. ", seq2.getSequence());\r
-\r
- absStart = sequence.getSequence().indexOf(nonGapped);\r
- absEnd = absStart + nonGapped.toString().length() - 1;\r
-\r
- // This is the Viewd alignment sequences\r
- // No need to tell the user of the dataset updates\r
- if ( (seq2.getStart() != absStart+sequence.getStart())\r
- || (seq2.getEnd() != absEnd+sequence.getStart()))\r
- {\r
- sbuffer.append("Updated: " + seq2.getName() + " " +\r
- seq2.getStart() + "/" + seq2.getEnd() +\r
- " to " + (absStart + sequence.getStart()) + "/" +\r
- (absEnd + sequence.getStart()) + "\n");\r
-\r
- seq2.setStart(absStart + sequence.getStart());\r
- seq2.setEnd(absEnd + sequence.getStart());\r
- }\r
- }\r
-\r
- n++;\r
- }\r
- }\r
- }\r
-}\r
-\r
-\r
git://source.jalview.org / jalview.git / commitdiff