import MCview.*;
import jalview.datamodel.*;
+import jalview.datamodel.xdb.embl.*;
+import jalview.analysis.*;
+import java.io.File;
import jalview.io.*;
public class SequenceFetcher
- extends JPanel implements Runnable
+extends JPanel implements Runnable
{
JInternalFrame frame;
AlignFrame alignFrame;
private String getFrameTitle()
{
return ( (alignFrame == null) ? "New " : "Additional ") +
- "Sequence Fetcher";
+ "Sequence Fetcher";
}
private void jbInit()
- throws Exception
+ throws Exception
{
this.setLayout(gridBagLayout1);
database.setPreferredSize(new Dimension(160, 21));
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
jLabel1.setText(
- "Separate multiple accession ids with semi colon \";\"");
+ "Separate multiple accession ids with semi colon \";\"");
ok.setText("OK");
ok.addActionListener(new ActionListener()
{
jPanel1.add(ok);
jPanel1.add(close);
this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
- , GridBagConstraints.WEST,
- GridBagConstraints.NONE,
- new Insets(7, 4, 0, 6), 77, 6));
+ , GridBagConstraints.WEST,
+ GridBagConstraints.NONE,
+ new Insets(7, 4, 0, 6), 77, 6));
this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
- , GridBagConstraints.WEST,
- GridBagConstraints.BOTH,
- new Insets(7, -2, 7, 12), 241, -2));
+ , GridBagConstraints.WEST,
+ GridBagConstraints.BOTH,
+ new Insets(7, -2, 7, 12), 241, -2));
this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0
- , GridBagConstraints.WEST,
- GridBagConstraints.NONE,
- new Insets(0, 4, 0, 0), 1, 0));
+ , GridBagConstraints.WEST,
+ GridBagConstraints.NONE,
+ new Insets(0, 4, 0, 0), 1, 0));
this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
- , GridBagConstraints.CENTER,
- GridBagConstraints.NONE,
- new Insets(0, 0, 0, 6), 211, 1));
+ , GridBagConstraints.CENTER,
+ GridBagConstraints.NONE,
+ new Insets(0, 0, 0, 6), 211, 1));
}
JComboBox database = new JComboBox();
getUniprotFile(textfield.getText());
}
else if (database.getSelectedItem().equals("EMBL")
- || database.getSelectedItem().equals("EMBLCDS"))
+ || database.getSelectedItem().equals("EMBLCDS"))
{
+ String DBRefSource = database.getSelectedItem().equals("EMBLCDS")
+ ? jalview.datamodel.DBRefSource.EMBLCDS
+ : jalview.datamodel.DBRefSource.EMBL;
+
StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
- while (st.hasMoreTokens())
+ SequenceI[] seqs = null;
+ while(st.hasMoreTokens())
{
EBIFetchClient dbFetch = new EBIFetchClient();
- String[] reply = dbFetch.fetchData(
+ File reply = dbFetch.fetchDataAsFile(
database.getSelectedItem().toString().toLowerCase(
) + ":" + st.nextToken(),
- "fasta", "raw");
-//
- if (reply != null)
+ "emblxml",null);
+
+ jalview.datamodel.xdb.embl.EmblFile efile=null;
+ if (reply != null && reply.exists())
{
- for (int i = 0; i < reply.length; i++)
- {
- result.append(reply[i] + "\n");
- }
+ efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
}
- }
-
- if (result != null && result.length() > 1) // arbitrary minimum length for a seuqence file
- {
- System.out.println(result.toString());
+ if (efile!=null) {
+ for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
+ EmblEntry entry = (EmblEntry) i.next();
+ SequenceI[] seqparts = entry.getSequences(false,true, DBRefSource);
+ if (seqparts!=null) {
+ SequenceI[] newseqs = null;
+ int si=0;
+ if (seqs==null) {
+ newseqs = new SequenceI[seqparts.length];
+ } else {
+ newseqs = new SequenceI[seqs.length+seqparts.length];
+
+ for (;si<seqs.length; si++) {
+ newseqs[si] = seqs[si];
+ seqs[si] = null;
+ }
+ }
+ for (int j=0;j<seqparts.length; si++, j++) {
+ newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer
+ }
+ seqs=newseqs;
- parseResult(result.toString(), null);
+ }
+ }
+ } else {
+ result=null;
+ }
}
+ if (seqs!=null && seqs.length>0) {
+ if (parseResult(new Alignment(seqs), null, null)!=null)
+ result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
+ }
}
else if (database.getSelectedItem().equals("PDB"))
{
StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");
String query;
SequenceI[] seqs = null;
- while (qset.hasMoreTokens() && ( (query = qset.nextToken()) != null))
+ while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
{
SequenceI[] seqparts = getPDBFile(query.toUpperCase());
if (seqparts != null)
}
else
{
- SequenceI[] newseqs = new SequenceI[seqs.length + seqparts.length];
- int i = 0;
+ SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];
+ int i=0;
for (; i < seqs.length; i++)
{
newseqs[i] = seqs[i];
seqs[i] = null;
}
- for (int j = 0; j < seqparts.length; i++, j++)
+ for (int j=0;j<seqparts.length; i++, j++)
{
newseqs[i] = seqparts[j];
}
- seqs = newseqs;
+ seqs=newseqs;
}
- result.append("# Success for " + query.toUpperCase() + "\n");
+ result.append("# Success for "+query.toUpperCase()+"\n");
}
}
if (seqs != null && seqs.length > 0)
{
- if (parseResult(new Alignment(seqs), null, null) != null)
+ if (parseResult(new Alignment(seqs), null, null)!=null)
{
result.append(
- "# Successfully parsed the PDB File Queries into an Alignment");
+ "# Successfully parsed the PDB File Queries into an Alignment");
}
}
}
- else if (database.getSelectedItem().equals("PFAM"))
+ else if( database.getSelectedItem().equals("PFAM"))
{
try
{
result.append(new FastaFile(
"http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
- + textfield.getText().toUpperCase(), "URL").print()
- );
+ + textfield.getText().toUpperCase(), "URL").print()
+ );
- if (result.length() > 0)
+ if(result.length()>0)
{
- parseResult(result.toString(), textfield.getText().toUpperCase());
+ parseResult( result.toString(), textfield.getText().toUpperCase() );
}
}
if (result == null || result.length() == 0)
{
showErrorMessage("Error retrieving " + textfield.getText()
- + " from " + database.getSelectedItem());
+ + " from " + database.getSelectedItem());
}
resetDialog();
}
result.append(name + "\n" + entry.getUniprotSequence().getContent() +
- "\n");
+ "\n");
}
en2.nextElement().toString()));
}
+
+
+
al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
{
{
SequenceFeature sf = (SequenceFeature) e.nextElement();
sf.setFeatureGroup("Uniprot");
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
}
}
}
EBIFetchClient ebi = new EBIFetchClient();
String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").
- getAbsolutePath();
+ getAbsolutePath();
if (file == null)
{
return null;
// Get the Chain's Sequence - who's dataset includes any special features added from the PDB file
SequenceI sq = pdbchain.sequence;
// Specially formatted name for the PDB chain sequences retrieved from the PDB
- sq.setName("PDB|" + id + "|" + sq.getName());
+ sq.setName("PDB|"+id+"|"+sq.getName());
// Might need to add more metadata to the PDBEntry object
// like below
/*
* PDBEntry entry = new PDBEntry();
- // Construct the PDBEntry
- entry.setId(id);
- if (entry.getProperty() == null)
- entry.setProperty(new Hashtable());
- entry.getProperty().put("chains",
- pdbchain.id
- + "=" + sq.getStart()
- + "-" + sq.getEnd());
- sq.getDatasetSequence().addPDBId(entry);
+ // Construct the PDBEntry
+ entry.setId(id);
+ if (entry.getProperty() == null)
+ entry.setProperty(new Hashtable());
+ entry.getProperty().put("chains",
+ pdbchain.id
+ + "=" + sq.getStart()
+ + "-" + sq.getEnd());
+ sq.getDatasetSequence().addPDBId(entry);
*/
// Add PDB DB Refs
// We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
// JBPNote - PDB DBRefEntry should also carry the chain and mapping information
DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,
- "0", id + pdbchain.id);
+ "0", id + pdbchain.id);
sq.addDBRef(dbentry);
// and add seuqence to the retrieved set
result.addElement(sq.deriveSequence());
catch (Exception ex) // Problem parsing PDB file
{
jalview.bin.Cache.log.warn("Exception when retrieving " +
- textfield.getText() + " from " +
- database.getSelectedItem(), ex);
+ textfield.getText() + " from " +
+ database.getSelectedItem(), ex);
return null;
}
SequenceI[] results = new SequenceI[result.size()];
for (int i = 0, j = result.size(); i < j; i++)
{
results[i] = (SequenceI) result.elementAt(i);
- result.setElementAt(null, i);
+ result.setElementAt(null,i);
}
return results;
}
-
Alignment parseResult(String result, String title)
{
String format = new IdentifyFile().Identify(result, "Paste");
try
{
sequences = new FormatAdapter().readFile(result.toString(), "Paste",
- format);
+ format);
}
catch (Exception ex)
{}
- if (sequences != null)
+ if (sequences!=null)
{
return parseResult(sequences, title, format);
}
else
{
showErrorMessage("Error retrieving " + textfield.getText()
- + " from " + database.getSelectedItem());
+ + " from " + database.getSelectedItem());
}
return null;
if (alignFrame == null)
{
AlignFrame af = new AlignFrame(al,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- if (currentFileFormat != null)
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (currentFileFormat!=null)
{
af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
}
- if (title == null)
+ if(title==null)
{
title = "Retrieved from " + database.getSelectedItem();
}
Desktop.addInternalFrame(af,
- title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
af.statusBar.setText("Successfully pasted alignment file");
alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries
}
alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
- getHeight());
+ getHeight());
alignFrame.viewport.alignment.getWidth();
alignFrame.viewport.firePropertyChange("alignment", null,
- alignFrame.viewport.
- getAlignment().getSequences());
+ alignFrame.viewport.
+ getAlignment().getSequences());
}
}
return al;
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- error, "Error Retrieving Data",
- JOptionPane.WARNING_MESSAGE);
+ error, "Error Retrieving Data",
+ JOptionPane.WARNING_MESSAGE);
}
});
}
}
+
git://source.jalview.org / jalview.git / commitdiff