X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=45d944df495781e0f1eb80e5de296c98085f5e56;hb=2f8f4850cd8437b7c2a2450df2391426aaa3e1b8;hp=a66ec2fca2f1a808076c35220629e860f4449d0e;hpb=2de36153a84ca246643cd28b2ce05e9f4159dd89;p=jalview.git
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index a66ec2f..3b93059 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,730 +1,942 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * as published by the Free Software Foundation; either version 2
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.io.*;
-import java.util.*;
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingConstants;
+
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.core.GFTSPanel;
+import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel;
+import jalview.fts.service.uniprot.UniprotFTSPanel;
+import jalview.io.FileFormatI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.seqfetcher.DbSourceProxy;
-import java.awt.*;
-import java.awt.event.*;
+/**
+ * A panel where the use may choose a database source, and enter one or more
+ * accessions, to retrieve entries from the database.
+ *
+ * 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;
-import javax.swing.*;
+ private String display;
-import MCview.*;
-import jalview.datamodel.*;
-import jalview.datamodel.xdb.embl.*;
-import java.io.File;
-import jalview.io.*;
-import jalview.ws.DBRefFetcher;
-import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.ASequenceFetcher;
-import jalview.ws.seqfetcher.DbSourceProxy;
+ public StringPair(String s1, String s2)
+ {
+ key = s1;
+ display = s2;
+ }
-import java.awt.Rectangle;
-import java.awt.BorderLayout;
-import java.awt.Dimension;
+ 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 database;
+
+ JCheckBox replacePunctuation;
+
+ JButton okBtn;
+
+ JButton exampleBtn;
+
+ JButton closeBtn;
+
+ JButton backBtn;
+
+ JTextArea textArea;
-public class SequenceFetcher
-extends JPanel implements Runnable
-{
- // ASequenceFetcher sfetch;
JInternalFrame frame;
+
IProgressIndicator guiWindow;
+
AlignFrame alignFrame;
- StringBuffer result;
- final String noDbSelected = "-- Select Database --";
- Hashtable sources = new Hashtable();
- private static jalview.ws.SequenceFetcher sfetch=null;
- public SequenceFetcher(IProgressIndicator guiIndic)
- {
- final IProgressIndicator guiWindow = guiIndic;
- final SequenceFetcher us = this;
- // launch initialiser thread
- Thread sf = new Thread(new Runnable() {
- public void run()
- {
- if (sfetch==null)
- {
- /**
- * give a visual indication that sequence fetcher construction is occuring
- */
- if ( guiWindow!=null )
- {
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers", this.hashCode());
- }
- jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
- if ( guiWindow!=null )
- {
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers", this.hashCode());
- }
- sfetch = sf;
-
- }
- us.initGui(guiWindow);
- }
- });
- sf.start();
- }
+ GFTSPanel parentSearchPanel;
+
+ IProgressIndicator progressIndicator;
+
+ volatile boolean _isConstructing = false;
+
/**
- * called by thread spawned by constructor
- * @param guiWindow
+ * Returns the shared instance of the SequenceFetcher client
+ *
+ * @return
*/
- private void initGui(IProgressIndicator guiWindow) {
- this.guiWindow = guiWindow;
- if (guiWindow instanceof AlignFrame)
- {
- alignFrame = (AlignFrame) guiWindow;
- }
-
- 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.getOrderedSupportedSources();
- for (int i=0; i();
+ database.setFont(JvSwingUtils.getLabelFont());
+ StringPair instructionItem = new StringPair(
+ MessageManager.getString("action.select_ddbb"));
+ database.setPrototypeDisplayValue(instructionItem);
+ String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb();
+ Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
+ database.addItem(instructionItem);
+ for (String source : sources)
+ {
+ List slist = sfetch.getSourceProxy(source);
+ if (slist.size() == 1 && slist.get(0) != null)
+ {
+ database.addItem(new StringPair(source, slist.get(0).getDbName()));
+ }
+ else
+ {
+ database.addItem(new StringPair(source));
+ }
+ }
+ setDatabaseSelectedItem(selectedDb);
+ if (database.getSelectedIndex() == -1)
+ {
+ database.setSelectedIndex(0);
+ }
+ database.setMaximumRowCount(database.getItemCount());
+ database.addActionListener(new ActionListener()
{
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ String currentSelection = ((StringPair) database.getSelectedItem())
+ .getKey();
+ updateExampleQuery(currentSelection);
+
+ if ("pdb".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new PDBFTSPanel(SequenceFetcher.this);
+ }
+ else if ("uniprot".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new UniprotFTSPanel(SequenceFetcher.this);
+ }
+ else if ("3d-beacons".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new TDBeaconsFTSPanel(SequenceFetcher.this);
+ }
+ else
+ {
+ otherSourceAction();
+ }
+ }
+ });
+
+ exampleAccession = new JLabel("");
+ exampleAccession.setFont(new Font("Verdana", Font.BOLD, 11));
+ JLabel jLabel1 = new JLabel(MessageManager
+ .getString("label.separate_multiple_accession_ids"));
+ jLabel1.setFont(new Font("Verdana", Font.ITALIC, 11));
+ jLabel1.setHorizontalAlignment(SwingConstants.LEFT);
+
+ replacePunctuation = new JCheckBox(
+ MessageManager.getString("label.replace_commas_semicolons"));
+ replacePunctuation.setHorizontalAlignment(SwingConstants.LEFT);
+ replacePunctuation.setFont(new Font("Verdana", Font.ITALIC, 11));
+ okBtn = new JButton(MessageManager.getString("action.ok"));
+ okBtn.addActionListener(new ActionListener()
+ {
+ @Override
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed();
}
});
- clear.setText("Clear");
+ JButton clear = new JButton(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clear_actionPerformed();
}
});
- example.setText("Example");
- example.addActionListener(new ActionListener()
+ exampleBtn = new JButton(MessageManager.getString("label.example"));
+ exampleBtn.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
example_actionPerformed();
}
});
- close.setText("Close");
- close.addActionListener(new ActionListener()
+ closeBtn = new JButton(MessageManager.getString("action.cancel"));
+ closeBtn.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
close_actionPerformed(e);
}
});
- textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- textArea.setLineWrap(true);
- textArea.addKeyListener(new KeyAdapter()
+ backBtn = new JButton(MessageManager.getString("action.back"));
+ backBtn.addActionListener(new ActionListener()
{
- public void keyPressed(KeyEvent e)
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- if(e.getKeyCode()==KeyEvent.VK_ENTER)
- ok_actionPerformed();
+ parentSearchPanel.btn_back_ActionPerformed();
}
});
- jPanel3.setLayout(borderLayout1);
- borderLayout1.setVgap(5);
- jPanel1.add(ok);
- jPanel1.add(example);
- jPanel1.add(clear);
- jPanel1.add(close);
- jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
- jPanel2.setLayout(borderLayout3);
-
- database.addActionListener(new ActionListener() {
+ // back not visible unless embedded
+ backBtn.setVisible(false);
- public void actionPerformed(ActionEvent e)
+ textArea = new JTextArea();
+ textArea.setFont(JvSwingUtils.getLabelFont());
+ textArea.setLineWrap(true);
+ textArea.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent e)
{
- DbSourceProxy db=null;
- try {
- db = sfetch.getSourceProxy((String)sources.get(database.getSelectedItem()));
- dbeg.setText("Example query: "+db.getTestQuery());
- } catch (Exception ex)
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
{
- dbeg.setText("");
+ ok_actionPerformed();
}
- jPanel2.repaint();
}
});
- dbeg.setText("");
- jPanel2.add(database, java.awt.BorderLayout.NORTH);
- jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
- jPanel2.add(jLabel1, java.awt.BorderLayout.SOUTH);
- // jPanel2.setPreferredSize(new Dimension())
- jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel3, java.awt.BorderLayout.CENTER);
- this.add(jPanel2,java.awt.BorderLayout.NORTH);
+
+ JPanel actionPanel = new JPanel();
+ actionPanel.add(backBtn);
+ actionPanel.add(exampleBtn);
+ actionPanel.add(clear);
+ actionPanel.add(okBtn);
+ actionPanel.add(closeBtn);
+
+ JPanel databasePanel = new JPanel();
+ databasePanel.setLayout(new BorderLayout());
+ databasePanel.add(database, BorderLayout.NORTH);
+ databasePanel.add(exampleAccession, BorderLayout.CENTER);
+ JPanel jPanel2a = new JPanel(new BorderLayout());
+ jPanel2a.add(jLabel1, BorderLayout.NORTH);
+ jPanel2a.add(replacePunctuation, BorderLayout.SOUTH);
+ databasePanel.add(jPanel2a, BorderLayout.SOUTH);
+
+ JPanel idsPanel = new JPanel();
+ idsPanel.setLayout(new BorderLayout(0, 5));
+ JScrollPane jScrollPane1 = new JScrollPane();
jScrollPane1.getViewport().add(textArea);
-
+ idsPanel.add(jScrollPane1, BorderLayout.CENTER);
+ this.add(actionPanel, BorderLayout.SOUTH);
+ this.add(idsPanel, BorderLayout.CENTER);
+ this.add(databasePanel, BorderLayout.NORTH);
}
- protected void example_actionPerformed()
+
+ private void setDatabaseSelectedItem(String db)
{
- DbSourceProxy db=null;
- try {
- db = sfetch.getSourceProxy((String)sources.get(database.getSelectedItem()));
- textArea.setText(db.getTestQuery());
- } catch (Exception ex)
+ for (int i = 0; i < database.getItemCount(); i++)
{
+ StringPair sp = database.getItemAt(i);
+ if (sp != null && db != null && db.equals(sp.getKey()))
+ {
+ database.setSelectedIndex(i);
+ return;
+ }
}
- jPanel3.repaint();
}
- protected void clear_actionPerformed()
+ /**
+ * Answers a semi-colon-delimited string with the example query or queries for
+ * the selected database
+ *
+ * @param db
+ * @return
+ */
+ protected String getExampleQueries(String db)
{
- textArea.setText("");
- jPanel3.repaint();
+ StringBuilder sb = new StringBuilder();
+ HashSet hs = new HashSet<>();
+ for (DbSourceProxy dbs : sfetch.getSourceProxy(db))
+ {
+ String tq = dbs.getTestQuery();
+ if (hs.add(tq)) // not a duplicate source
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(";");
+ }
+ sb.append(tq);
+ }
+ }
+ return sb.toString();
}
- JLabel dbeg = new JLabel();
- JComboBox database = new JComboBox();
- JLabel jLabel1 = new JLabel();
- JButton ok = new JButton();
- JButton clear = new JButton();
- JButton example = new JButton();
- JButton close = new JButton();
- JPanel jPanel1 = new JPanel();
- JTextArea textArea = new JTextArea();
- JScrollPane jScrollPane1 = new JScrollPane();
- JPanel jPanel2 = new JPanel();
- JPanel jPanel3 = new JPanel();
- JPanel jPanel4 = new JPanel();
-
- BorderLayout borderLayout1 = new BorderLayout();
- BorderLayout borderLayout2 = new BorderLayout();
- BorderLayout borderLayout3 = new BorderLayout();
- public void close_actionPerformed(ActionEvent e)
+
+ /**
+ * Action on selecting a database other than Uniprot or PDB is to enable or
+ * disable 'Replace commas', and await input in the query field
+ */
+ protected void otherSourceAction()
{
try
{
- frame.setClosed(true);
+ String eq = exampleAccession.getText();
+ // TODO this should be a property of the SequenceFetcher whether commas
+ // are allowed in the IDs...
+
+ boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
+ replacePunctuation.setEnabled(enablePunct);
+
+ } catch (Exception ex)
+ {
+ exampleAccession.setText("");
+ replacePunctuation.setEnabled(true);
}
- catch (Exception ex)
- {}
+ repaint();
}
- public void ok_actionPerformed()
+ /**
+ * Sets the text of the example query to incorporate the example accession
+ * provided by the selected database source
+ *
+ * @param selectedDatabase
+ * @return
+ */
+ protected String updateExampleQuery(String selectedDatabase)
{
- database.setEnabled(false);
- textArea.setEnabled(false);
- ok.setEnabled(false);
- close.setEnabled(false);
+ String eq = getExampleQueries(selectedDatabase);
+ exampleAccession.setText(MessageManager
+ .formatMessage("label.example_query_param", new String[]
+ { eq }));
+ return eq;
+ }
- Thread worker = new Thread(this);
- worker.start();
+ /**
+ * Action on clicking the 'Example' button is to write the example accession
+ * as the query text field value
+ */
+ protected void example_actionPerformed()
+ {
+ String eq = getExampleQueries(
+ ((StringPair) database.getSelectedItem()).getKey());
+ textArea.setText(eq);
+ repaint();
}
- private void resetDialog()
+ /**
+ * Clears the query input field
+ */
+ protected void clear_actionPerformed()
{
- database.setEnabled(true);
- textArea.setEnabled(true);
- ok.setEnabled(true);
- close.setEnabled(true);
+ textArea.setText("");
+ repaint();
}
- public void run()
+ /**
+ * Action on Close button is to close this frame, and also (if it is embedded
+ * in a search panel) to close the search panel
+ *
+ * @param e
+ */
+ protected void close_actionPerformed(ActionEvent e)
{
- 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+", "");
- textArea.setText(empty.replaceAll(textArea.getText()));
- if (textArea.getText().length() == 0)
+ try
{
- error += "Please enter a (semi-colon separated list of) database id(s)";
- }
- if (error.length() > 0)
+ frame.setClosed(true);
+ if (parentSearchPanel != null)
+ {
+ parentSearchPanel.btn_cancel_ActionPerformed();
+ }
+ } catch (Exception ex)
{
- showErrorMessage(error);
- resetDialog();
- return;
}
- AlignmentI aresult=null;
- try {
- guiWindow.setProgressBar("Fetching Sequences from "+database.getSelectedItem(), Thread.currentThread().hashCode());
- aresult = sfetch.getSourceProxy((String)sources.get(database.getSelectedItem()))
- .getSequenceRecords(textArea.getText());
-
- }
- catch (Exception e)
+ }
+
+ /**
+ * Action on OK is to start the fetch for entered accession(s)
+ */
+ public void ok_actionPerformed()
+ {
+ /*
+ * tidy inputs and check there is something to search for
+ */
+ String t0 = textArea.getText();
+ String text = t0.trim();
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
{
- showErrorMessage("Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
- //error +="Couldn't retrieve sequences from "+database.getSelectedItem();
- System.err.println("Retrieval failed for source ='"+database.getSelectedItem()+"' and query\n'"+textArea.getText()+"'\n");
- e.printStackTrace();
+ text = text.replace(",", ";");
}
- catch (OutOfMemoryError e)
+ text = text.replaceAll("(\\s|[; ])+", ";");
+ if (!t0.equals(text))
{
- showErrorMessage("Out of Memory when retrieving " + textArea.getText()
- + " from " + database.getSelectedItem()+"\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
- e.printStackTrace();
+ textArea.setText(text);
}
- catch (Error e)
+ if (text.isEmpty())
{
- showErrorMessage("Serious Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
- e.printStackTrace();
+ // todo i18n
+ showErrorMessage(
+ "Please enter a (semi-colon separated list of) database id(s)");
+ resetDialog();
+ return;
}
- guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
- if (aresult!=null)
+ if (database.getSelectedIndex() == 0)
{
- parseResult(aresult, null, null);
+ // todo i18n
+ showErrorMessage("Please choose a database");
+ resetDialog();
+ return;
}
- resetDialog();
+
+ exampleBtn.setEnabled(false);
+ textArea.setEnabled(false);
+ okBtn.setEnabled(false);
+ closeBtn.setEnabled(false);
+ backBtn.setEnabled(false);
+
+ Thread worker = new Thread(this);
+ worker.start();
}
- /*
- result = new StringBuffer();
- if (database.getSelectedItem().equals("Uniprot"))
- {
- getUniprotFile(textArea.getText());
- }
- else if (database.getSelectedItem().equals("EMBL")
- || database.getSelectedItem().equals("EMBLCDS"))
- {
- 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 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())
- {
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
- }
- 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 aresultq = new ArrayList<>();
+ List presultTitle = new ArrayList<>();
+ List presult = new ArrayList<>();
+ List aresult = new ArrayList<>();
+ List sources = sfetch.getSourceProxy(
+ ((StringPair) database.getSelectedItem()).getKey());
+ Iterator proxies = sources.iterator();
+ String[] qries = textArea.getText().trim().split(";");
+ List nextFetch = Arrays.asList(qries);
+ Iterator en = Arrays.asList(new String[0]).iterator();
+ int nqueries = qries.length;
+
+ FeatureSettingsModelI preferredFeatureColours = null;
+ while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
+ {
+ if (!en.hasNext() && nextFetch.size() > 0)
+ {
+ en = nextFetch.iterator();
+ nqueries = nextFetch.size();
+ // save the remaining queries in the original array
+ qries = nextFetch.toArray(new String[nqueries]);
+ nextFetch = new ArrayList<>();
+ }
+
+ DbSourceProxy proxy = proxies.next();
+ try
+ {
+ // update status
+ guiWindow.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_sequence_queries_from", new String[]
+ { Integer.valueOf(nqueries).toString(),
+ proxy.getDbName() }),
+ Thread.currentThread().hashCode());
+ if (proxy.getMaximumQueryCount() == 1)
+ {
+ /*
+ * proxy only handles one accession id at a time
+ */
+ while (en.hasNext())
+ {
+ String acc = en.next();
+ if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
+ {
+ nextFetch.add(acc);
}
}
- } else {
- result.append("# no response for "+qry);
}
- }
- if (seqs!=null && seqs.length>0) {
- if (parseResult(new Alignment(seqs), null, null)!=null)
+ else
{
- result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
+ /*
+ * proxy can fetch multiple accessions at one time
+ */
+ fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
}
+ } catch (Exception e)
+ {
+ showErrorMessage("Error retrieving " + textArea.getText() + " from "
+ + ((StringPair) database.getSelectedItem()).getDisplay());
+ // error
+ // +="Couldn't retrieve sequences from "+database.getSelectedItem();
+ System.err.println("Retrieval failed for source ='"
+ + ((StringPair) database.getSelectedItem()).getDisplay()
+ + "' and query\n'" + textArea.getText() + "'\n");
+ e.printStackTrace();
+ } catch (OutOfMemoryError e)
+ {
+ showErrorMessage("Out of Memory when retrieving "
+ + textArea.getText() + " from "
+ + ((StringPair) database.getSelectedItem()).getDisplay()
+ + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
+ e.printStackTrace();
+ } catch (Error e)
+ {
+ showErrorMessage("Serious Error retrieving " + textArea.getText()
+ + " from "
+ + ((StringPair) database.getSelectedItem()).getDisplay());
+ e.printStackTrace();
}
- }
- else if (database.getSelectedItem().equals("PDB"))
- {
- StringTokenizer qset = new StringTokenizer(textArea.getText(), ";");
- String query;
- SequenceI[] seqs = null;
- while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
+
+ // Stack results ready for opening in alignment windows
+ if (aresult != null && aresult.size() > 0)
{
- SequenceI[] seqparts = getPDBFile(query.toUpperCase());
- if (seqparts != null)
+ FeatureSettingsModelI proxyColourScheme = proxy
+ .getFeatureColourScheme();
+ if (proxyColourScheme != null)
+ {
+ preferredFeatureColours = proxyColourScheme;
+ }
+
+ AlignmentI ar = null;
+ if (proxy.isAlignmentSource())
{
- if (seqs == null)
+ addToLast = false;
+ // new window for each result
+ while (aresult.size() > 0)
{
- seqs = seqparts;
+ presult.add(aresult.remove(0));
+ presultTitle.add(
+ aresultq.remove(0) + " " + getDefaultRetrievalTitle());
}
- else
+ }
+ else
+ {
+ String titl = null;
+ if (addToLast && presult.size() > 0)
{
- SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];
- int i=0;
- for (; i < seqs.length; i++)
+ ar = presult.remove(presult.size() - 1);
+ titl = presultTitle.remove(presultTitle.size() - 1);
+ }
+ // concatenate all results in one window
+ while (aresult.size() > 0)
+ {
+ if (ar == null)
{
- newseqs[i] = seqs[i];
- seqs[i] = null;
+ ar = aresult.remove(0);
}
- for (int j=0;j 0)
+ guiWindow.setProgressBar(
+ MessageManager.getString("status.finshed_querying"),
+ Thread.currentThread().hashCode());
+ }
+ guiWindow
+ .setProgressBar(
+ (presult.size() > 0)
+ ? MessageManager
+ .getString("status.parsing_results")
+ : MessageManager.getString("status.processing"),
+ Thread.currentThread().hashCode());
+ // process results
+ while (presult.size() > 0)
+ {
+ parseResult(presult.remove(0), presultTitle.remove(0), null,
+ preferredFeatureColours);
+ }
+ // only remove visual delay after we finished parsing.
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
+ if (nextFetch.size() > 0)
+ {
+ StringBuffer sb = new StringBuffer();
+ sb.append("Didn't retrieve the following "
+ + (nextFetch.size() == 1 ? "query"
+ : nextFetch.size() + " queries")
+ + ": \n");
+ int l = sb.length(), lr = 0;
+ for (String s : nextFetch)
{
- if (parseResult(new Alignment(seqs), null, null)!=null)
+ if (l != sb.length())
{
- result.append(
- "# Successfully parsed the PDB File Queries into an Alignment");
+ sb.append("; ");
}
- }
- }
- else if( database.getSelectedItem().equals("PFAM"))
- {
- try
- {
- result.append(new FastaFile(
- "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
- + textArea.getText().toUpperCase(), "URL").print()
- );
-
- if(result.length()>0)
+ if (lr - sb.length() > 40)
{
- parseResult( result.toString(), textArea.getText().toUpperCase() );
+ sb.append("\n");
}
-
- }
- catch (java.io.IOException ex)
- {
- result = null;
+ sb.append(s);
}
+ showErrorMessage(sb.toString());
}
-
- if (result == null || result.length() == 0)
- {
- showErrorMessage("Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
- }
-
resetDialog();
- return;
}
- void getUniprotFile(String id)
+ /**
+ * Tries to fetch one or more accession ids from the database proxy
+ *
+ * @param proxy
+ * @param accessions
+ * the queries to fetch
+ * @param aresultq
+ * a successful queries list to add to
+ * @param aresult
+ * a list of retrieved alignments to add to
+ * @param nextFetch
+ * failed queries are added to this list
+ * @throws Exception
+ */
+ void fetchMultipleAccessions(DbSourceProxy proxy,
+ Iterator accessions, List aresultq,
+ List aresult, List nextFetch) throws Exception
{
- EBIFetchClient ebi = new EBIFetchClient();
- File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
-
- DBRefFetcher dbref = new DBRefFetcher();
- Vector entries = dbref.getUniprotEntries(file);
+ StringBuilder multiacc = new StringBuilder();
+ List tosend = new ArrayList<>();
+ while (accessions.hasNext())
+ {
+ String nel = accessions.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (accessions.hasNext())
+ {
+ multiacc.append(proxy.getAccessionSeparator());
+ }
+ }
- if (entries != null)
+ try
{
- //First, make the new sequences
- Enumeration en = entries.elements();
- while (en.hasMoreElements())
+ String query = multiacc.toString();
+ AlignmentI rslt = proxy.getSequenceRecords(query);
+ if (rslt == null || rslt.getHeight() == 0)
{
- 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");
-
+ // no results - pass on all queries to next source
+ nextFetch.addAll(tosend);
}
-
- //Then read in the features and apply them to the dataset
- Alignment al = parseResult(result.toString(), null);
- for (int i = 0; i < entries.size(); i++)
+ else
{
- 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);
- }
-
- Enumeration en2 = entry.getAccession().elements();
- while (en2.hasMoreElements())
- {
- al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
- DBRefSource.UNIPROT,
- "0",
- en2.nextElement().toString()));
- }
-
-
-
-
- al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
- if (entry.getFeature() != null)
+ aresultq.add(query);
+ aresult.add(rslt);
+ if (tosend.size() > 1)
{
- e = entry.getFeature().elements();
- while (e.hasMoreElements())
- {
- SequenceFeature sf = (SequenceFeature) e.nextElement();
- sf.setFeatureGroup("Uniprot");
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
- }
+ checkResultForQueries(rslt, tosend, nextFetch, proxy);
}
}
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + ((StringPair) database.getSelectedItem()).getDisplay(),
+ oome, this);
}
}
- SequenceI[] getPDBFile(String id)
+ /**
+ * Query for a single accession id via the database proxy
+ *
+ * @param proxy
+ * @param accession
+ * @param aresultq
+ * a list of successful queries to add to
+ * @param aresult
+ * a list of retrieved alignments to add to
+ * @return true if the fetch was successful, else false
+ */
+ boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
+ List aresultq, List aresult)
{
- Vector result = new Vector();
- 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;
- }
+ boolean success = false;
try
{
- PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
- for (int i = 0; i < pdbfile.chains.size(); i++)
+ if (aresult != null)
{
- if (chain == null ||
- ( (PDBChain) pdbfile.chains.elementAt(i)).id.
- toUpperCase().equals(chain))
+ try
{
- 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());
+ // give the server a chance to breathe
+ Thread.sleep(5);
+ } catch (Exception e)
+ {
+ //
}
}
- if (result.size() < 1)
+ AlignmentI indres = null;
+ try
{
- throw new Exception("WsDBFetch for PDB id resulted in zero result size");
+ indres = proxy.getSequenceRecords(accession);
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning(
+ "fetching " + accession + " from " + proxy.getDbName(),
+ oome, this);
}
- }
- catch (Exception ex) // Problem parsing PDB file
+ if (indres != null)
+ {
+ aresultq.add(accession);
+ aresult.add(indres);
+ success = true;
+ }
+ } catch (Exception e)
{
- jalview.bin.Cache.log.warn("Exception when retrieving " +
- textArea.getText() + " from " +
- database.getSelectedItem(), ex);
- return null;
+ Console.info("Error retrieving " + accession + " from "
+ + proxy.getDbName(), e);
}
+ return success;
+ }
-
- 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;
- }*/
- AlignmentI parseResult(String result, String title)
+ /**
+ * Checks which of the queries were successfully retrieved by searching the
+ * DBRefs of the retrieved sequences for a match. Any not found are added to
+ * the 'nextFetch' list.
+ *
+ * @param rslt
+ * @param queries
+ * @param nextFetch
+ * @param proxy
+ */
+ void checkResultForQueries(AlignmentI rslt, List queries,
+ List nextFetch, DbSourceProxy proxy)
{
- String format = new IdentifyFile().Identify(result, "Paste");
- Alignment sequences = null;
- if (FormatAdapter.isValidFormat(format))
- {
- sequences = null;
- try
+ SequenceI[] rs = rslt.getSequencesArray();
+
+ for (String q : queries)
+ {
+ // BH 2019.01.25 dbr is never used.
+ // DBRefEntry dbr = new DBRefEntry();
+ // dbr.setSource(proxy.getDbSource());
+ // dbr.setVersion(null);
+ String accId = proxy.getAccessionIdFromQuery(q);
+ // dbr.setAccessionId(accId);
+ boolean rfound = false;
+ for (int r = 0, nr = rs.length; r < nr; r++)
{
- sequences = new FormatAdapter().readFile(result.toString(), "Paste",
- format);
+ if (rs[r] != null)
+ {
+ List found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
+ accId);
+ if (!found.isEmpty())
+ {
+ rfound = true;
+ break;
+ }
+ }
}
- catch (Exception ex)
- {}
-
- if (sequences!=null)
+ if (!rfound)
{
- return parseResult(sequences, title, format);
+ nextFetch.add(q);
}
}
- else
- {
- showErrorMessage("Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
- }
+ }
- return null;
+ /**
+ *
+ * @return a standard title for any results retrieved using the currently
+ * selected source and settings
+ */
+ public String getDefaultRetrievalTitle()
+ {
+ return "Retrieved from "
+ + ((StringPair) database.getSelectedItem()).getDisplay();
}
- AlignmentI parseResult(AlignmentI al, String title, String currentFileFormat)
+ /**
+ * constructs an alignment frame given the data and metadata
+ *
+ * @param al
+ * @param title
+ * @param currentFileFormat
+ * @param preferredFeatureColours
+ * @return the alignment
+ */
+ public AlignmentI parseResult(AlignmentI al, String title,
+ FileFormatI currentFileFormat,
+ FeatureSettingsModelI preferredFeatureColours)
{
if (al != null && al.getHeight() > 0)
{
+ if (title == null)
+ {
+ title = getDefaultRetrievalTitle();
+ }
if (alignFrame == null)
{
- AlignFrame af = new AlignFrame(al,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- if (currentFileFormat!=null)
+ AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (currentFileFormat != null)
{
- af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
+ af.currentFileFormat = currentFileFormat;
}
- if(title==null)
+ List alsqs = al.getSequences();
+ synchronized (alsqs)
{
- title = "Retrieved from " + database.getSelectedItem();
+ for (SequenceI sq : alsqs)
+ {
+ if (sq.getFeatures().hasFeatures())
+ {
+ af.setShowSeqFeatures(true);
+ break;
+ }
+ }
}
- Desktop.addInternalFrame(af,
- title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ af.getViewport().applyFeaturesStyle(preferredFeatureColours);
+ if (Cache.getDefault("HIDE_INTRONS", true))
+ {
+ af.hideFeatureColumns(SequenceOntologyI.EXON, false);
+ }
+ Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText("Successfully pasted alignment file");
+ af.setStatus(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
else
{
- 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());
+ alignFrame.viewport.addAlignment(al, title);
}
}
return al;
@@ -735,13 +947,52 @@ extends JPanel implements Runnable
resetDialog();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- error, "Error Retrieving Data",
- JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+ MessageManager.getString("label.error_retrieving_data"),
+ JvOptionPane.WARNING_MESSAGE);
}
});
}
-}
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
+
+ /**
+ * Hide this panel (on clicking the database button to open the database
+ * chooser)
+ */
+ void hidePanel()
+ {
+ frame.setVisible(false);
+ }
+
+ public void setQuery(String ids)
+ {
+ textArea.setText(ids);
+ }
+
+ /**
+ * Called to modify the search panel for embedding as an alternative tab of a
+ * free text search panel. The database choice list is hidden (since the
+ * choice has been made), and a Back button is made visible (which reopens the
+ * Sequence Fetcher panel).
+ *
+ * @param parentPanel
+ */
+ public void embedIn(GFTSPanel parentPanel)
+ {
+ database.setVisible(false);
+ backBtn.setVisible(true);
+ parentSearchPanel = parentPanel;
+ }
+}