X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=77bac76a32f9c4c0f891c74206c4ba84afb6fc5b;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=99c1d5e545b5c2ecc0e2c5bde1ea4fd3e8822bc6;hpb=6f595029738e21743279f9f1e350ec8870700c6d;p=jalview.git
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 99c1d5e..77bac76 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,489 +1,1001 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import javax.swing.*;
-import java.awt.*;
-import java.awt.event.*;
-import jalview.io.EBIFetchClient;
-import MCview.*;
-import jalview.datamodel.*;
-import jalview.analysis.AlignSeq;
-import java.io.File;
-import jalview.io.*;
-import java.util.*;
-
-public class SequenceFetcher
- extends JPanel implements Runnable
-{
- JInternalFrame frame;
- AlignFrame alignFrame;
- StringBuffer result;
- final String noDbSelected = "-- Select Database --";
- public SequenceFetcher(AlignFrame af)
- {
- alignFrame = af;
- database.addItem(noDbSelected);
- database.addItem("Uniprot");
- database.addItem("EMBL");
- database.addItem("EMBLCDS");
- database.addItem("PDB");
- database.addItem("PFAM");
-
- try
- {
- jbInit();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- frame = new JInternalFrame();
- frame.setContentPane(this);
- if (System.getProperty("os.name").startsWith("Mac"))
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
- else
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
- }
-
- private String getFrameTitle()
- {
- return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";
- }
-
- private void jbInit()
- throws Exception
- {
- this.setLayout(gridBagLayout1);
-
- 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.setText(
- "Separate multiple accession ids with semi colon \";\"");
- ok.setText("OK");
- ok.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
- close.setText("Close");
- close.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- close_actionPerformed(e);
- }
- });
- textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- textfield.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
- 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));
- }
-
- JComboBox database = new JComboBox();
- JLabel jLabel1 = new JLabel();
- JButton ok = new JButton();
- JButton close = new JButton();
- JPanel jPanel1 = new JPanel();
- JTextField textfield = new JTextField();
- GridBagLayout gridBagLayout1 = new GridBagLayout();
- public void close_actionPerformed(ActionEvent e)
- {
- try
- {
- frame.setClosed(true);
- }
- catch (Exception ex)
- {}
- }
-
- public void ok_actionPerformed(ActionEvent e)
- {
- database.setEnabled(false);
- textfield.setEnabled(false);
- ok.setEnabled(false);
- close.setEnabled(false);
-
- Thread worker = new Thread(this);
- worker.start();
- }
-
- private void resetDialog()
- {
- database.setEnabled(true);
- textfield.setEnabled(true);
- ok.setEnabled(true);
- close.setEnabled(true);
- }
-
- public void run()
- {
- 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)
- error += "Please enter a (semi-colon separated list of) database id(s)";
- if (error.length() > 0)
- {
- showErrorMessage(error);
- resetDialog();
- return;
- }
-
- result = new StringBuffer();
- if (database.getSelectedItem().equals("Uniprot"))
- {
- getUniprotFile(textfield.getText());
- }
- else if (database.getSelectedItem().equals("EMBL")
- || database.getSelectedItem().equals("EMBLCDS"))
- {
- StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
- while(st.hasMoreTokens())
- {
- EBIFetchClient dbFetch = new EBIFetchClient();
-
- String[] reply = dbFetch.fetchData(
- database.getSelectedItem().toString().toLowerCase(
- ) + ":" + st.nextToken(),
- "fasta", "raw");
-//
- if (reply != null)
- {
- for (int i = 0; i < reply.length; i++)
- result.append(reply[i] + "\n");
- }
- }
-
- if(result!=null)
- {
- System.out.println(result.toString());
-
- parseResult(result.toString(), null);
- }
- }
- else if (database.getSelectedItem().equals("PDB"))
- {
- StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");
- String query;
- while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
- {
- StringBuffer respart = getPDBFile(query.toUpperCase());
- if(respart!=null)
- result.append(respart);
- }
-
-
- if (result.length()>0)
- parseResult(result.toString(), null);
- }
- 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()
- );
-
- if(result.length()>0)
- parseResult( result.toString(), textfield.getText().toUpperCase() );
-
- }catch(java.io.IOException ex)
- { result = null; }
- }
-
- if (result == null || result.length() == 0)
- showErrorMessage("Error retrieving " + textfield.getText()
- + " from " + database.getSelectedItem());
-
- resetDialog();
- return;
- }
-
- void getUniprotFile(String id)
- {
- EBIFetchClient ebi = new EBIFetchClient();
- File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
-
- DBRefFetcher dbref = new DBRefFetcher();
- Vector entries = dbref.getUniprotEntries(file);
-
- if (entries != null)
- {
- //First, make the new sequences
- Enumeration en = entries.elements();
- while (en.hasMoreElements())
- {
- UniprotEntry entry = (UniprotEntry) en.nextElement();
-
- StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
- Enumeration en2 = entry.getAccession().elements();
- while (en2.hasMoreElements())
- {
- name.append("|");
- name.append(en2.nextElement());
- }
- en2 = entry.getName().elements();
- while (en2.hasMoreElements())
- {
- name.append("|");
- name.append(en2.nextElement());
- }
-
- if (entry.getProtein() != null)
- {
- name.append(" " + entry.getProtein().getName().elementAt(0));
- }
-
- result.append(name + "\n" + entry.getUniprotSequence().getContent() +
- "\n");
-
- }
-
- //Then read in the features and apply them to the dataset
- SequenceI[] sequence = parseResult(result.toString(), null);
- for (int i = 0; i < entries.size(); i++)
- {
- UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
- Enumeration e = entry.getDbReference().elements();
- Vector onlyPdbEntries = new Vector();
- while (e.hasMoreElements())
- {
- PDBEntry pdb = (PDBEntry) e.nextElement();
- if (!pdb.getType().equals("PDB"))
- continue;
-
- onlyPdbEntries.addElement(pdb);
- }
-
- sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
- if (entry.getFeature() != null)
- {
- e = entry.getFeature().elements();
- while (e.hasMoreElements())
- {
- SequenceFeature sf = (SequenceFeature) e.nextElement();
- sf.setFeatureGroup("Uniprot");
- sequence[i].getDatasetSequence().addSequenceFeature( sf );
- }
- }
- }
- }
- }
-
- StringBuffer getPDBFile(String id)
- {
- StringBuffer result = new StringBuffer();
- String chain = null;
- if (id.indexOf(":") > -1)
- {
- chain = id.substring(id.indexOf(":") + 1);
- id = id.substring(0, id.indexOf(":"));
- }
-
- EBIFetchClient ebi = new EBIFetchClient();
- String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
- if (file == null)
- return null;
- try
- {
- PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
- for (int i = 0; i < pdbfile.chains.size(); i++)
- {
- if (chain == null ||
- ( (PDBChain) pdbfile.chains.elementAt(i)).id.
- toUpperCase().equals(chain))
-
- result.append("\n>PDB|" + id + "|" +
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
- getName() +
- "\n"
- +
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
- getSequence());
- }
- }
- catch (Exception ex) // Problem parsing PDB file
- {
- jalview.bin.Cache.log.warn("Exception when retrieving " +
- textfield.getText() + " from " +
- database.getSelectedItem(), ex);
- return null;
- }
-
- return result;
- }
-
- SequenceI[] parseResult(String result, String title)
- {
- String format = new IdentifyFile().Identify(result, "Paste");
- SequenceI[] sequences = null;
-
- if (FormatAdapter.formats.contains(format))
- {
- sequences = null;
- try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
- format);}
- catch(Exception ex){}
-
- if (sequences != null && sequences.length > 0)
- {
- if (alignFrame == null)
- {
- AlignFrame af = new AlignFrame(new Alignment(sequences));
- af.currentFileFormat = format;
- if(title==null)
- title = "Retrieved from " + database.getSelectedItem();
- Desktop.addInternalFrame(af,
- title,
- AlignFrame.NEW_WINDOW_WIDTH,
- AlignFrame.NEW_WINDOW_HEIGHT);
- af.statusBar.setText("Successfully pasted alignment file");
-
- try
- {
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
- }
- catch (Exception ex)
- {}
- }
- 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].getSequence()),
- 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 (database.getSelectedItem().equals("PDB"))
- {
- // 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());
- }
-
- }
- else
- showErrorMessage("Error retrieving " + textfield.getText()
- + " from " + database.getSelectedItem());
- }
-
- return sequences;
-
- }
-
- void showErrorMessage(final String error)
- {
- resetDialog();
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- error, "Error Retrieving Data",
- JOptionPane.WARNING_MESSAGE);
- }
- });
- }
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see
+ * If the selected source is Uniprot or PDB, a free text search panel is opened
+ * instead to perform the search and selection.
+ */
+public class SequenceFetcher extends JPanel implements Runnable
+{
+ private class StringPair
+ {
+ private String key;
+
+ private String display;
+
+ public StringPair(String s1, String s2)
+ {
+ key = s1;
+ display = s2;
+ }
+
+ public StringPair(String s)
+ {
+ this(s, s);
+ }
+
+ public String getKey()
+ {
+ return key;
+ }
+
+ public String getDisplay()
+ {
+ return display;
+ }
+
+ @Override
+ public String toString()
+ {
+ return display;
+ }
+
+ public boolean equals(StringPair other)
+ {
+ return other.key == this.key;
+ }
+ }
+
+ private static jalview.ws.SequenceFetcher sfetch = null;
+
+ JLabel exampleAccession;
+
+ JComboBox