/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
*/
package jalview.gui;
-import javax.swing.*;
+import java.io.*;
+import java.util.*;
+
import java.awt.*;
import java.awt.event.*;
-import jalview.io.EBIFetchClient;
+import javax.swing.*;
+
import MCview.*;
import jalview.datamodel.*;
-import jalview.analysis.AlignSeq;
+import jalview.datamodel.xdb.embl.*;
import java.io.File;
import jalview.io.*;
-import java.util.*;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.EBIFetchClient;
+
+import java.awt.Rectangle;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
public class SequenceFetcher
- extends JPanel implements Runnable
+extends JPanel implements Runnable
{
+ jalview.ws.SequenceFetcher sfetch;
JInternalFrame frame;
AlignFrame alignFrame;
StringBuffer result;
public SequenceFetcher(AlignFrame af)
{
alignFrame = af;
+ sfetch = new jalview.ws.SequenceFetcher();
database.addItem(noDbSelected);
+ /*
+ * Dynamically generated database list
+ * will need a translation function from
+ * internal source to externally distinct names.
+ * UNIPROT and UP_NAME are identical DB sources,
+ * and should be collapsed.
+ *
+
+ String dbs[] = sfetch.getSupportedDb();
+ for (int i=0; i<dbs.length;i++)
+ {
+ if (DBRefSource.isPrimaryDb(dbs[i]))
+ {
+ database.addItem(dbs[i]);
+ // should have some kind of human readable description of each database displayed when
+ * that combo is selected.
+ }
+ }*/
database.addItem("Uniprot");
database.addItem("EMBL");
database.addItem("EMBLCDS");
frame = new JInternalFrame();
frame.setContentPane(this);
- if (System.getProperty("os.name").startsWith("Mac"))
+ if (new jalview.util.Platform().isAMac())
+ {
Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
+ }
else
+ {
Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
+ }
}
private String getFrameTitle()
{
- return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";
+ return ( (alignFrame == null) ? "New " : "Additional ") +
+ "Sequence Fetcher";
}
private void jbInit()
- throws Exception
+ throws Exception
{
- this.setLayout(gridBagLayout1);
+ this.setLayout(borderLayout2);
database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- database.setMinimumSize(new Dimension(160, 21));
- database.setPreferredSize(new Dimension(160, 21));
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
jLabel1.setText(
- "Separate multiple accession ids with semi colon \";\"");
+ "Separate multiple accession ids with semi colon \";\"");
ok.setText("OK");
ok.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
{
- ok_actionPerformed(e);
+ ok_actionPerformed();
}
});
close.setText("Close");
close_actionPerformed(e);
}
});
- textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- textfield.addActionListener(new ActionListener()
+ textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ textArea.setLineWrap(true);
+ textArea.addKeyListener(new KeyAdapter()
{
- public void actionPerformed(ActionEvent e)
+ public void keyPressed(KeyEvent e)
{
- ok_actionPerformed(e);
+ if(e.getKeyCode()==KeyEvent.VK_ENTER)
+ ok_actionPerformed();
}
});
+ jPanel3.setLayout(borderLayout1);
+ borderLayout1.setVgap(5);
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));
- 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));
- 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));
- 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));
+ jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);
+ jPanel2.add(database);
+ jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
+ jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH);
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ this.add(jPanel3, java.awt.BorderLayout.CENTER);
+ jScrollPane1.getViewport().add(textArea);
+
}
JComboBox database = new JComboBox();
JButton ok = new JButton();
JButton close = new JButton();
JPanel jPanel1 = new JPanel();
- JTextField textfield = new JTextField();
- GridBagLayout gridBagLayout1 = new GridBagLayout();
+ JTextArea textArea = new JTextArea();
+ JScrollPane jScrollPane1 = new JScrollPane();
+ JPanel jPanel2 = new JPanel();
+ JPanel jPanel3 = new JPanel();
+ BorderLayout borderLayout1 = new BorderLayout();
+ BorderLayout borderLayout2 = new BorderLayout();
public void close_actionPerformed(ActionEvent e)
{
try
{}
}
- public void ok_actionPerformed(ActionEvent e)
+ public void ok_actionPerformed()
{
database.setEnabled(false);
- textfield.setEnabled(false);
+ textArea.setEnabled(false);
ok.setEnabled(false);
close.setEnabled(false);
private void resetDialog()
{
database.setEnabled(true);
- textfield.setEnabled(true);
+ textArea.setEnabled(true);
ok.setEnabled(true);
close.setEnabled(true);
}
{
String error = "";
if (database.getSelectedItem().equals(noDbSelected))
+ {
error += "Please select the source database\n";
+ }
com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
- textfield.setText(empty.replaceAll(textfield.getText()));
- if (textfield.getText().length() == 0)
+ textArea.setText(empty.replaceAll(textArea.getText()));
+ if (textArea.getText().length() == 0)
+ {
error += "Please enter a (semi-colon separated list of) database id(s)";
+ }
if (error.length() > 0)
{
showErrorMessage(error);
result = new StringBuffer();
if (database.getSelectedItem().equals("Uniprot"))
{
- getUniprotFile(textfield.getText());
+ getUniprotFile(textArea.getText());
}
else if (database.getSelectedItem().equals("EMBL")
- || database.getSelectedItem().equals("EMBLCDS"))
+ || database.getSelectedItem().equals("EMBLCDS"))
{
- StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
+ String DBRefSource = database.getSelectedItem().equals("EMBLCDS")
+ ? jalview.datamodel.DBRefSource.EMBLCDS
+ : jalview.datamodel.DBRefSource.EMBL;
+
+ StringTokenizer st = new StringTokenizer(textArea.getText(), ";");
+ SequenceI[] seqs = null;
while(st.hasMoreTokens())
{
EBIFetchClient dbFetch = new EBIFetchClient();
-
- String[] reply = dbFetch.fetchData(
- database.getSelectedItem().toString().toLowerCase(
- ) + ":" + st.nextToken(),
- "fasta", "raw");
-//
- if (reply != null)
+ String qry = database.getSelectedItem().toString().toLowerCase(
+ ) + ":" + st.nextToken();
+ File reply = dbFetch.fetchDataAsFile(
+ qry,
+ "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.append("# no response for "+qry);
+ }
+ }
+ 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(), ";");
+ StringTokenizer qset = new StringTokenizer(textArea.getText(), ";");
String query;
+ SequenceI[] seqs = null;
while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
{
- StringBuffer respart = getPDBFile(query.toUpperCase());
- if(respart!=null)
- result.append(respart);
+ SequenceI[] seqparts = getPDBFile(query.toUpperCase());
+ if (seqparts != null)
+ {
+ if (seqs == null)
+ {
+ seqs = seqparts;
+ }
+ else
+ {
+ 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++)
+ {
+ newseqs[i] = seqparts[j];
+ }
+ seqs=newseqs;
+ }
+ result.append("# Success for "+query.toUpperCase()+"\n");
+ }
+ }
+ if (seqs != null && seqs.length > 0)
+ {
+ if (parseResult(new Alignment(seqs), null, null)!=null)
+ {
+ result.append(
+ "# Successfully parsed the PDB File Queries into an Alignment");
+ }
}
-
-
- if (result.length()>0)
- parseResult(result.toString(), null);
}
else if( database.getSelectedItem().equals("PFAM"))
{
- try{
+ try
+ {
result.append(new FastaFile(
- "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
- + textfield.getText().toUpperCase(), "URL").print()
- );
+ "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
+ + textArea.getText().toUpperCase(), "URL").print()
+ );
- if(result.length()>0)
- parseResult( result.toString(), textfield.getText().toUpperCase() );
+ if(result.length()>0)
+ {
+ parseResult( result.toString(), textArea.getText().toUpperCase() );
+ }
- }catch(java.io.IOException ex)
- { result = null; }
+ }
+ catch (java.io.IOException ex)
+ {
+ result = null;
+ }
}
if (result == null || result.length() == 0)
- showErrorMessage("Error retrieving " + textfield.getText()
- + " from " + database.getSelectedItem());
+ {
+ showErrorMessage("Error retrieving " + textArea.getText()
+ + " from " + database.getSelectedItem());
+ }
resetDialog();
return;
if (entry.getProtein() != null)
{
- name.append(" " + entry.getProtein().getName().elementAt(0));
+ name.append(" " + entry.getProtein().getName().elementAt(0));
}
result.append(name + "\n" + entry.getUniprotSequence().getContent() +
- "\n");
+ "\n");
}
//Then read in the features and apply them to the dataset
- SequenceI[] sequence = parseResult(result.toString(), null);
+ Alignment al = parseResult(result.toString(), null);
for (int i = 0; i < entries.size(); i++)
{
UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
{
PDBEntry pdb = (PDBEntry) e.nextElement();
if (!pdb.getType().equals("PDB"))
+ {
continue;
+ }
onlyPdbEntries.addElement(pdb);
}
Enumeration en2 = entry.getAccession().elements();
while (en2.hasMoreElements())
{
- sequence[i].getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
- "0",
- en2.nextElement().toString()));
+ al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
+ DBRefSource.UNIPROT,
+ "0",
+ en2.nextElement().toString()));
}
- sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
+ al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
if (entry.getFeature() != null)
{
e = entry.getFeature().elements();
{
SequenceFeature sf = (SequenceFeature) e.nextElement();
sf.setFeatureGroup("Uniprot");
- sequence[i].getDatasetSequence().addSequenceFeature( sf );
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
}
}
}
}
}
- StringBuffer getPDBFile(String id)
+ SequenceI[] getPDBFile(String id)
{
- StringBuffer result = new StringBuffer();
+ Vector result = new Vector();
String chain = null;
if (id.indexOf(":") > -1)
{
}
EBIFetchClient ebi = new EBIFetchClient();
- String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+ String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").
+ getAbsolutePath();
if (file == null)
+ {
return null;
+ }
try
{
PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
if (chain == null ||
( (PDBChain) pdbfile.chains.elementAt(i)).id.
toUpperCase().equals(chain))
+ {
+ PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
+ // 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());
+ // 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);
+ */
+ // 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);
+ sq.addDBRef(dbentry);
+ // and add seuqence to the retrieved set
+ result.addElement(sq.deriveSequence());
+ }
+ }
- result.append("\n>PDB|" + id + "|" +
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
- getName() +
- "\n"
- +
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
- getSequenceAsString());
+ if (result.size() < 1)
+ {
+ throw new Exception("WsDBFetch for PDB id resulted in zero result size");
}
}
catch (Exception ex) // Problem parsing PDB file
{
jalview.bin.Cache.log.warn("Exception when retrieving " +
- textfield.getText() + " from " +
- database.getSelectedItem(), ex);
+ textArea.getText() + " from " +
+ database.getSelectedItem(), ex);
return null;
}
- return result;
- }
- SequenceI[] parseResult(String result, String title)
+ 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);
+ }
+ return results;
+ }
+ Alignment parseResult(String result, String title)
{
String format = new IdentifyFile().Identify(result, "Paste");
- SequenceI[] sequences = null;
-
+ Alignment sequences = null;
if (FormatAdapter.isValidFormat(format))
{
sequences = null;
- try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
- format);}
- catch(Exception ex){}
+ try
+ {
+ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
+ format);
+ }
+ catch (Exception ex)
+ {}
+
+ if (sequences!=null)
+ {
+ return parseResult(sequences, title, format);
+ }
+ }
+ else
+ {
+ showErrorMessage("Error retrieving " + textArea.getText()
+ + " from " + database.getSelectedItem());
+ }
+
+ return null;
+ }
+
+ Alignment parseResult(Alignment al, String title, String currentFileFormat)
+ {
- if (sequences != null && sequences.length > 0)
+ if (al != null && al.getHeight() > 0)
+ {
+ if (alignFrame == null)
{
- if (alignFrame == null)
+ AlignFrame af = new AlignFrame(al,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (currentFileFormat!=null)
{
- AlignFrame af = new AlignFrame(new Alignment(sequences),
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT
-);
- af.currentFileFormat = format;
- if(title==null)
- title = "Retrieved from " + database.getSelectedItem();
- Desktop.addInternalFrame(af,
- title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText("Successfully pasted alignment file");
-
- try
- {
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
- }
- catch (Exception ex)
- {}
+ af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
}
- else
- {
- for (int i = 0; i < sequences.length; i++)
- {
- alignFrame.viewport.alignment.addSequence(sequences[i]);
-
- ////////////////////////////
- //Dataset needs extension;
- /////////////////////////////
- Sequence ds = new Sequence(sequences[i].getName(),
- AlignSeq.extractGaps("-. ",
- sequences[i].getSequenceAsString()),
- sequences[i].getStart(),
- sequences[i].getEnd());
- sequences[i].setDatasetSequence(ds);
- alignFrame.viewport.alignment.getDataset().addSequence(ds);
- }
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
- getHeight());
- alignFrame.viewport.alignment.getWidth();
- alignFrame.viewport.firePropertyChange("alignment", null,
- alignFrame.viewport.
- getAlignment().getSequences());
+ if(title==null)
+ {
+ title = "Retrieved from " + database.getSelectedItem();
}
- if (database.getSelectedItem().equals("PDB"))
+ Desktop.addInternalFrame(af,
+ title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ af.statusBar.setText("Successfully pasted alignment file");
+
+ try
{
- // Parse out the ids from the structured names
- boolean errors = false;
- for (int i = 0; i < sequences.length; i++)
- {
- PDBEntry entry = new PDBEntry();
- com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(
- "PDB\\|([0-9A-z]{4})\\|(.)");
- if (idbits.search(sequences[i].getName()))
- {
- String pdbid = idbits.substring(1);
- String pdbccode = idbits.substring(2);
- // Construct the PDBEntry
- entry.setId(pdbid);
- if (entry.getProperty() == null)
- entry.setProperty(new Hashtable());
- entry.getProperty().put("chains",
- pdbccode
- + "=" + sequences[i].getStart()
- + "-" + sequences[i].getEnd());
- sequences[i].getDatasetSequence().addPDBId(entry);
-
- // 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",pdbid);
- sequences[i].getDatasetSequence().addDBRef(dbentry);
- }
- else
- {
- // don't add an entry for this chain, but this is probably a bug
- // that the user should know about.
- jalview.bin.Cache.log.warn(
- "No PDBEntry constructed for sequence " + i + " : " +
- sequences[i].getName());
- errors = true;
- }
- }
- if (errors)
- jalview.bin.Cache.log.warn(
- "Query string that resulted in PDBEntry construction failure was :\n" +
- textfield.getText());
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
}
-
+ catch (Exception ex)
+ {}
}
else
- showErrorMessage("Error retrieving " + textfield.getText()
- + " from " + database.getSelectedItem());
+ {
+ for (int i = 0; i < al.getHeight(); i++)
+ {
+ alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries
+ }
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
+ getHeight());
+ alignFrame.viewport.alignment.getWidth();
+ alignFrame.viewport.firePropertyChange("alignment", null,
+ alignFrame.viewport.
+ getAlignment().getSequences());
+ }
}
-
- return sequences;
-
+ return al;
}
void showErrorMessage(final String error)
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 / blobdiff