import jalview.io.*;\r
import java.util.*;\r
\r
-\r
public class SequenceFetcher\r
extends JPanel implements Runnable\r
{\r
database.addItem("EMBL");\r
database.addItem("EMBLCDS");\r
database.addItem("PDB");\r
+ database.addItem("PFAM");\r
\r
try\r
{\r
\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
- if(System.getProperty("os.name").startsWith("Mac"))\r
- Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 400, 140);\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);\r
else\r
- Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 400, 125);\r
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);\r
+ }\r
+\r
+ private String getFrameTitle()\r
+ {\r
+ return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";\r
}\r
\r
private void jbInit()\r
ok_actionPerformed(e);\r
}\r
});\r
- cancel.setText("Cancel");\r
- cancel.addActionListener(new ActionListener()\r
+ close.setText("Close");\r
+ close.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- cancel_actionPerformed(e);\r
+ close_actionPerformed(e);\r
}\r
});\r
textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
}\r
});\r
jPanel1.add(ok);\r
- jPanel1.add(cancel);\r
+ jPanel1.add(close);\r
this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
, GridBagConstraints.WEST,\r
GridBagConstraints.NONE,\r
JComboBox database = new JComboBox();\r
JLabel jLabel1 = new JLabel();\r
JButton ok = new JButton();\r
- JButton cancel = new JButton();\r
+ JButton close = new JButton();\r
JPanel jPanel1 = new JPanel();\r
JTextField textfield = new JTextField();\r
GridBagLayout gridBagLayout1 = new GridBagLayout();\r
- public void cancel_actionPerformed(ActionEvent e)\r
+ public void close_actionPerformed(ActionEvent e)\r
{\r
try\r
{\r
\r
public void ok_actionPerformed(ActionEvent e)\r
{\r
- frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");\r
database.setEnabled(false);\r
textfield.setEnabled(false);\r
ok.setEnabled(false);\r
- cancel.setEnabled(false);\r
+ close.setEnabled(false);\r
\r
Thread worker = new Thread(this);\r
worker.start();\r
}\r
\r
- private void resetDialog() {\r
+ private void resetDialog()\r
+ {\r
database.setEnabled(true);\r
textfield.setEnabled(true);\r
ok.setEnabled(true);\r
- cancel.setEnabled(true);\r
- frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");\r
+ close.setEnabled(true);\r
}\r
\r
public void run()\r
String error = "";\r
if (database.getSelectedItem().equals(noDbSelected))\r
error += "Please select the source database\n";\r
- com.stevesoft.pat.Regex empty=new com.stevesoft.pat.Regex("\\s+","");\r
+ com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");\r
textfield.setText(empty.replaceAll(textfield.getText()));\r
- if (textfield.getText().length()==0)\r
- error+="Please enter a (semi-colon separated list of) database id(s)";\r
- if (error.length()>0) {\r
+ if (textfield.getText().length() == 0)\r
+ error += "Please enter a (semi-colon separated list of) database id(s)";\r
+ if (error.length() > 0)\r
+ {\r
showErrorMessage(error);\r
resetDialog();\r
return;\r
}\r
\r
- result = new StringBuffer();\r
+ result = new StringBuffer();\r
if (database.getSelectedItem().equals("Uniprot"))\r
{\r
getUniprotFile(textfield.getText());\r
}\r
else if (database.getSelectedItem().equals("EMBL")\r
- || database.getSelectedItem().equals("EMBLCDS"))\r
+ || database.getSelectedItem().equals("EMBLCDS"))\r
{\r
EBIFetchClient dbFetch = new EBIFetchClient();\r
String[] reply = dbFetch.fetchData(\r
) + ":" + textfield.getText(),\r
"fasta", "raw");\r
\r
- for (int i = 0; i < reply.length; i++)\r
- result.append(reply[i] + "\n");\r
+ if(reply!=null)\r
+ {\r
+ for (int i = 0; i < reply.length; i++)\r
+ result.append(reply[i] + "\n");\r
\r
- parseResult(result.toString());\r
+ parseResult(result.toString(), null);\r
+ }\r
}\r
else if (database.getSelectedItem().equals("PDB"))\r
{\r
- result = getPDBFile(textfield.getText().toUpperCase());\r
- if (result!=null)\r
- parseResult(result.toString());\r
+ StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");\r
+ String query;\r
+ while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))\r
+ {\r
+ StringBuffer respart = getPDBFile(query.toUpperCase());\r
+ if(respart!=null)\r
+ result.append(respart);\r
+ }\r
+\r
+\r
+ if (result.length()>0)\r
+ parseResult(result.toString(), null);\r
}\r
+ else if( database.getSelectedItem().equals("PFAM"))\r
+ {\r
+ try{\r
+ result.append(new FastaFile(\r
+ "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="\r
+ + textfield.getText().toUpperCase(), "URL").print()\r
+ );\r
\r
+ if(result.length()>0)\r
+ parseResult( result.toString(), textfield.getText().toUpperCase() );\r
+\r
+ }catch(java.io.IOException ex)\r
+ { result = null; }\r
+ }\r
\r
if (result == null || result.length() == 0)\r
showErrorMessage("Error retrieving " + textfield.getText()\r
+ " from " + database.getSelectedItem());\r
- else\r
- textfield.setText("");\r
+\r
resetDialog();\r
+ return;\r
}\r
\r
void getUniprotFile(String id)\r
{\r
EBIFetchClient ebi = new EBIFetchClient();\r
- File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);\r
+ File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
+ // File file = new File("H:/jalview/classes/fer1.xml");\r
SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
Vector entries = sff.getUniprotEntries(file);\r
\r
- if(entries!=null)\r
+ if (entries != null)\r
{\r
//First, make the new sequences\r
Enumeration en = entries.elements();\r
while (en.hasMoreElements())\r
{\r
UniprotEntry entry = (UniprotEntry) en.nextElement();\r
- StringBuffer name = new StringBuffer( ">Uniprot/Swiss-Prot" );\r
+\r
+ StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
Enumeration en2 = entry.getAccession().elements();\r
- while(en2.hasMoreElements())\r
+ while (en2.hasMoreElements())\r
{\r
name.append("|");\r
name.append(en2.nextElement());\r
}\r
en2 = entry.getName().elements();\r
- while(en2.hasMoreElements())\r
+ while (en2.hasMoreElements())\r
{\r
name.append("|");\r
name.append(en2.nextElement());\r
}\r
\r
- if(entry.getProteinName()!=null)\r
- name.append(" "+entry.getProteinName().elementAt(0));\r
+ if (entry.getProtein() != null)\r
+ {\r
+ name.append(" " + entry.getProtein().getName().elementAt(0));\r
+ }\r
\r
- result.append(name +"\n"+entry.getUniprotSequence().getContent());\r
+ result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
+ "\n");\r
\r
}\r
\r
//Then read in the features and apply them to the dataset\r
- SequenceI [] sequence = parseResult(result.toString());\r
- for(int i=0; i<entries.size(); i++)\r
+ SequenceI[] sequence = parseResult(result.toString(), null);\r
+ for (int i = 0; i < entries.size(); i++)\r
{\r
UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
Enumeration e = entry.getDbReference().elements();\r
}\r
\r
sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
- sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
-\r
+ if (entry.getFeature() != null)\r
+ {\r
+ e = entry.getFeature().elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ sf.setFeatureGroup("Uniprot");\r
+ sequence[i].getDatasetSequence().addSequenceFeature( sf );\r
+ }\r
+ }\r
}\r
}\r
}\r
\r
- StringBuffer getPDBFile(String id)\r
+ StringBuffer getPDBFile(String id)\r
+ {\r
+ StringBuffer result = new StringBuffer();\r
+ String chain = null;\r
+ if (id.indexOf(":") > -1)\r
{\r
- StringBuffer result = new StringBuffer();\r
- String chain = null;\r
- if (id.indexOf(":") > -1)\r
- {\r
- chain = id.substring(id.indexOf(":") + 1);\r
- id = id.substring(0, id.indexOf(":"));\r
- }\r
+ chain = id.substring(id.indexOf(":") + 1);\r
+ id = id.substring(0, id.indexOf(":"));\r
+ }\r
\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
- if (reply==null)\r
- return null;\r
- try\r
- {\r
- PDBfile pdbfile = new PDBfile(reply);\r
- for (int i = 0; i < pdbfile.chains.size(); i++)\r
- {\r
- if (chain == null ||\r
- ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
- toUpperCase().equals(chain))\r
- result.append("\n>PDB|" + id + "|" +\r
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
- getName() +\r
- "\n"\r
- +\r
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
- getSequence());\r
- }\r
- }\r
- catch (Exception ex) // Problem parsing PDB file\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
+ if (reply == null)\r
+ return null;\r
+ try\r
+ {\r
+ PDBfile pdbfile = new PDBfile(reply);\r
+ for (int i = 0; i < pdbfile.chains.size(); i++)\r
{\r
- jalview.bin.Cache.log.warn("Exception when retrieving " + textfield.getText() + " from " +\r
- database.getSelectedItem(), ex);\r
- return null;\r
+ if (chain == null ||\r
+ ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
+ toUpperCase().equals(chain))\r
+ result.append("\n>PDB|" + id + "|" +\r
+ ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
+ getName() +\r
+ "\n"\r
+ +\r
+ ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
+ getSequence());\r
}\r
-\r
- return result;\r
}\r
+ catch (Exception ex) // Problem parsing PDB file\r
+ {\r
+ jalview.bin.Cache.log.warn("Exception when retrieving " +\r
+ textfield.getText() + " from " +\r
+ database.getSelectedItem(), ex);\r
+ return null;\r
+ }\r
+\r
+ return result;\r
+ }\r
\r
- SequenceI[] parseResult(String result)\r
+ SequenceI[] parseResult(String result, String title)\r
+ {\r
+ String format = new IdentifyFile().Identify(result, "Paste");\r
+ SequenceI[] sequences = null;\r
+\r
+ if (FormatAdapter.formats.contains(format))\r
{\r
- String format = IdentifyFile.Identify(result, "Paste");\r
- SequenceI[] sequences = null;\r
+ sequences = null;\r
+ try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
+ format);}\r
+ catch(Exception ex){}\r
\r
- if (FormatAdapter.formats.contains(format))\r
+ if (sequences != null && sequences.length > 0)\r
{\r
- sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);\r
- if (sequences != null && sequences.length>0)\r
+ if (alignFrame == null)\r
{\r
- if(alignFrame==null)\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+ af.currentFileFormat = format;\r
+ if(title==null)\r
+ title = "Retrieved from " + database.getSelectedItem();\r
+ Desktop.addInternalFrame(af,\r
+ title,\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.statusBar.setText("Successfully pasted alignment file");\r
+ try\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- af.currentFileFormat = format;\r
- Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
- try\r
- {\r
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
- }\r
- catch (Exception ex)\r
- {}\r
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
}\r
- else\r
+ catch (Exception ex)\r
+ {}\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0; i < sequences.length; i++)\r
{\r
- for (int i = 0; i < sequences.length; i++)\r
- {\r
- alignFrame.viewport.alignment.addSequence(sequences[i]);\r
-\r
- ////////////////////////////\r
- //Datset needs extension;\r
- /////////////////////////////\r
- Sequence ds = new Sequence(sequences[i].getName(),\r
- AlignSeq.extractGaps("-. ",\r
- sequences[i].getSequence()),\r
- sequences[i].getStart(),\r
- sequences[i].getEnd());\r
- sequences[i].setDatasetSequence(ds);\r
- alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
- }\r
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
- getHeight());\r
- alignFrame.viewport.alignment.getWidth();\r
- alignFrame.viewport.firePropertyChange("alignment", null,\r
- alignFrame.viewport.getAlignment().getSequences());\r
-\r
+ alignFrame.viewport.alignment.addSequence(sequences[i]);\r
+\r
+ ////////////////////////////\r
+ //Dataset needs extension;\r
+ /////////////////////////////\r
+ Sequence ds = new Sequence(sequences[i].getName(),\r
+ AlignSeq.extractGaps("-. ",\r
+ sequences[i].getSequence()),\r
+ sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ sequences[i].setDatasetSequence(ds);\r
+ alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
}\r
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
+ getHeight());\r
+ alignFrame.viewport.alignment.getWidth();\r
+ alignFrame.viewport.firePropertyChange("alignment", null,\r
+ alignFrame.viewport.\r
+ getAlignment().getSequences());\r
+\r
+ }\r
\r
- if (database.getSelectedItem().equals("PDB"))\r
+ if (database.getSelectedItem().equals("PDB"))\r
+ {\r
+ // Parse out the ids from the structured names\r
+ boolean errors = false;\r
+ for (int i = 0; i < sequences.length; i++)\r
{\r
- for (int i = 0; i < sequences.length; i++)\r
+ PDBEntry entry = new PDBEntry();\r
+ com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(\r
+ "PDB\\|([0-9A-z]{4})\\|(.)");\r
+ if (idbits.search(sequences[i].getName()))\r
{\r
- PDBEntry entry = new PDBEntry();\r
- entry.setId(textfield.getText());\r
+ String pdbid = idbits.substring(1);\r
+ String pdbccode = idbits.substring(2);\r
+ // Construct the PDBEntry\r
+ entry.setId(pdbid);\r
+ if (entry.getProperty() == null)\r
+ entry.setProperty(new Hashtable());\r
+ entry.getProperty().put("chains",\r
+ pdbccode\r
+ + "=" + sequences[i].getStart()\r
+ + "-" + sequences[i].getEnd());\r
sequences[i].getDatasetSequence().addPDBId(entry);\r
+\r
+ // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source\r
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping information\r
+ DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);\r
+ sequences[i].getDatasetSequence().addDBRef(dbentry);\r
+ }\r
+ else\r
+ {\r
+ // don't add an entry for this chain, but this is probably a bug\r
+ // that the user should know about.\r
+ jalview.bin.Cache.log.warn(\r
+ "No PDBEntry constructed for sequence " + i + " : " +\r
+ sequences[i].getName());\r
+ errors = true;\r
}\r
}\r
-\r
+ if (errors)\r
+ jalview.bin.Cache.log.warn(\r
+ "Query string that resulted in PDBEntry construction failure was :\n" +\r
+ textfield.getText());\r
}\r
- else\r
- showErrorMessage( "Error retrieving "+textfield.getText()\r
- +" from "+database.getSelectedItem());\r
+\r
}\r
+ else\r
+ showErrorMessage("Error retrieving " + textfield.getText()\r
+ + " from " + database.getSelectedItem());\r
+ }\r
\r
- return sequences;\r
+ return sequences;\r
\r
}\r
\r
void showErrorMessage(String error)\r
{\r
+ resetDialog();\r
JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);\r
+ error, "Error Retrieving Data",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ return;\r
}\r
}\r
\r
-\r
-\r
-\r
git://source.jalview.org / jalview.git / blobdiff