/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
database.addItem("EMBL");\r
database.addItem("EMBLCDS");\r
database.addItem("PDB");\r
+ database.addItem("PFAM");\r
\r
try\r
{\r
\r
private String getFrameTitle()\r
{\r
- return ( (alignFrame == null) ? "New " : "Additional ") +\r
- "Sequence Fetcher (WSDBfetch@EBI)";\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
new Insets(0, 4, 0, 0), 1, 0));\r
this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
, GridBagConstraints.CENTER,\r
- GridBagConstraints.HORIZONTAL,\r
- new Insets(0, 0, 0, 6), 200, 1));\r
+ GridBagConstraints.NONE,\r
+ new Insets(0, 0, 0, 6), 211, 1));\r
}\r
\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
database.setEnabled(true);\r
textfield.setEnabled(true);\r
ok.setEnabled(true);\r
- cancel.setEnabled(true);\r
- frame.setTitle(getFrameTitle());\r
+ close.setEnabled(true);\r
}\r
\r
public void run()\r
else if (database.getSelectedItem().equals("EMBL")\r
|| database.getSelectedItem().equals("EMBLCDS"))\r
{\r
- EBIFetchClient dbFetch = new EBIFetchClient();\r
- String[] reply = dbFetch.fetchData(\r
- database.getSelectedItem().toString().toLowerCase(\r
- ) + ":" + textfield.getText(),\r
- "fasta", "raw");\r
+ StringTokenizer st = new StringTokenizer(textfield.getText(), ";");\r
+ while(st.hasMoreTokens())\r
+ {\r
+ EBIFetchClient dbFetch = new EBIFetchClient();\r
+\r
+ String[] reply = dbFetch.fetchData(\r
+ database.getSelectedItem().toString().toLowerCase(\r
+ ) + ":" + st.nextToken(),\r
+ "fasta", "raw");\r
+//\r
+ if (reply != null)\r
+ {\r
+ for (int i = 0; i < reply.length; i++)\r
+ result.append(reply[i] + "\n");\r
+ }\r
+ }\r
\r
- if(reply!=null)\r
+ if(result!=null)\r
{\r
- for (int i = 0; i < reply.length; i++)\r
- result.append(reply[i] + "\n");\r
+ System.out.println(result.toString());\r
\r
- parseResult(result.toString());\r
+ parseResult(result.toString(), null);\r
}\r
}\r
else if (database.getSelectedItem().equals("PDB"))\r
\r
\r
if (result.length()>0)\r
- parseResult(result.toString());\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
- SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
- Vector entries = sff.getUniprotEntries(file);\r
+\r
+ DBRefFetcher dbref = new DBRefFetcher();\r
+ Vector entries = dbref.getUniprotEntries(file);\r
\r
if (entries != null)\r
{\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
{\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
"\n");\r
}\r
\r
//Then read in the features and apply them to the dataset\r
- SequenceI[] sequence = parseResult(result.toString());\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
onlyPdbEntries.addElement(pdb);\r
}\r
\r
- sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
- sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
+ Enumeration en2 = entry.getAccession().elements();\r
+ while (en2.hasMoreElements())\r
+ {\r
+ sequence[i].getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,\r
+ "0",\r
+ en2.nextElement().toString()));\r
+ }\r
+\r
+\r
\r
+\r
+ sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\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
\r
EBIFetchClient ebi = new EBIFetchClient();\r
- String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
- if (reply == null)\r
+ String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();\r
+ if (file == null)\r
return null;\r
try\r
{\r
- PDBfile pdbfile = new PDBfile(reply);\r
+ PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);\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
+\r
result.append("\n>PDB|" + id + "|" +\r
( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
getName() +\r
return result;\r
}\r
\r
- SequenceI[] parseResult(String result)\r
+ SequenceI[] parseResult(String result, String title)\r
{\r
- String format = IdentifyFile.Identify(result, "Paste");\r
+ String format = new IdentifyFile().Identify(result, "Paste");\r
SequenceI[] sequences = null;\r
\r
- if (FormatAdapter.formats.contains(format))\r
+ if (FormatAdapter.isValidFormat(format))\r
{\r
- sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
- format);\r
+ sequences = null;\r
+ try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
+ format);}\r
+ catch(Exception ex){}\r
+\r
if (sequences != null && sequences.length > 0)\r
{\r
if (alignFrame == null)\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences),\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT\r
+);\r
af.currentFileFormat = format;\r
+ if(title==null)\r
+ title = "Retrieved from " + database.getSelectedItem();\r
Desktop.addInternalFrame(af,\r
- "Retrieved from " + database.getSelectedItem(),\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
+ title,\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
af.statusBar.setText("Successfully pasted alignment file");\r
+\r
try\r
{\r
af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
alignFrame.viewport.alignment.addSequence(sequences[i]);\r
\r
////////////////////////////\r
- //Datset needs extension;\r
+ //Dataset needs extension;\r
/////////////////////////////\r
Sequence ds = new Sequence(sequences[i].getName(),\r
AlignSeq.extractGaps("-. ",\r
+ "=" + sequences[i].getStart()\r
+ "-" + sequences[i].getEnd());\r
sequences[i].getDatasetSequence().addPDBId(entry);\r
- // JBPNote - should add a PDB DBRefEntry too since we\r
- // have obtained the PDB file from a verifiable source\r
- DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);\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(jalview.datamodel.DBRefSource.PDB,"0",pdbid);\r
sequences[i].getDatasetSequence().addDBRef(dbentry);\r
}\r
else\r
\r
}\r
\r
- void showErrorMessage(String error)\r
+ void showErrorMessage(final String error)\r
{\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- error, "Error Retrieving Data",\r
+ resetDialog();\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ error, "Error Retrieving Data",\r
JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
}\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff