X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=71348ef9bf5349dc212d042d9ec6c9d5842aad14;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=ce366c83fd2005db916e60547264d0513dba13c3;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index ce366c8..71348ef 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,154 +1,421 @@
/*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 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.util.List;
import java.awt.*;
import java.awt.event.*;
+
import javax.swing.*;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import com.stevesoft.pat.Regex;
-import MCview.*;
import jalview.datamodel.*;
import jalview.io.*;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+import java.awt.BorderLayout;
-public class SequenceFetcher
- extends JPanel implements Runnable
+public class SequenceFetcher extends JPanel implements Runnable
{
+ // ASequenceFetcher sfetch;
JInternalFrame frame;
+
+ IProgressIndicator guiWindow;
+
AlignFrame alignFrame;
+
StringBuffer result;
+
final String noDbSelected = "-- Select Database --";
- public SequenceFetcher(AlignFrame af)
+
+ private static jalview.ws.SequenceFetcher sfetch = null;
+
+ private static long lastDasSourceRegistry = -3;
+
+ private static DasSourceRegistryI dasRegistry = null;
+
+ private static boolean _initingFetcher = false;
+
+ private static Thread initingThread = null;
+
+ /**
+ * Blocking method that initialises and returns the shared instance of the
+ * SequenceFetcher client
+ *
+ * @param guiWindow
+ * - where the initialisation delay message should be shown
+ * @return the singleton instance of the sequence fetcher client
+ */
+ public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
+ final IProgressIndicator guiWindow)
+ {
+ if (_initingFetcher && initingThread != null && initingThread.isAlive())
+ {
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(
+ MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
+ Thread.currentThread().hashCode());
+ }
+ // initting happening on another thread - so wait around to see if it
+ // finishes.
+ while (_initingFetcher && initingThread != null
+ && initingThread.isAlive())
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(
+ MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
+ Thread.currentThread().hashCode());
+ }
+ }
+ if (sfetch == null
+ || dasRegistry != jalview.bin.Cache.getDasSourceRegistry()
+ || lastDasSourceRegistry != (jalview.bin.Cache
+ .getDasSourceRegistry().getDasRegistryURL() + jalview.bin.Cache
+ .getDasSourceRegistry().getLocalSourceString())
+ .hashCode())
+ {
+ _initingFetcher = true;
+ initingThread = Thread.currentThread();
+ /**
+ * give a visual indication that sequence fetcher construction is occuring
+ */
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
+ Thread.currentThread().hashCode());
+ }
+ dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
+ dasRegistry.refreshSources();
+
+ jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
+ Thread.currentThread().hashCode());
+ }
+ lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
+ .getLocalSourceString()).hashCode();
+ sfetch = sf;
+ _initingFetcher = false;
+ initingThread = null;
+ }
+ return sfetch;
+ }
+
+ public SequenceFetcher(IProgressIndicator guiIndic)
+ {
+ final IProgressIndicator guiWindow = guiIndic;
+ final SequenceFetcher us = this;
+ // launch initialiser thread
+ Thread sf = new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ if (getSequenceFetcherSingleton(guiWindow) != null)
+ {
+ us.initGui(guiWindow);
+ }
+ else
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager.getString("label.couldnt_create_sequence_fetcher"),
+ JOptionPane.ERROR_MESSAGE);
+ }
+ });
+
+ // raise warning dialog
+ }
+ }
+ });
+ sf.start();
+ }
+
+ private class DatabaseAuthority extends DefaultMutableTreeNode
+ {
+
+ };
+
+ private class DatabaseSource extends DefaultMutableTreeNode
{
- alignFrame = af;
- database.addItem(noDbSelected);
- database.addItem("Uniprot");
- database.addItem("EMBL");
- database.addItem("EMBLCDS");
- database.addItem("PDB");
- database.addItem("PFAM");
+ };
+
+ /**
+ * called by thread spawned by constructor
+ *
+ * @param guiWindow
+ */
+ private void initGui(IProgressIndicator guiWindow)
+ {
+ this.guiWindow = guiWindow;
+ if (guiWindow instanceof AlignFrame)
+ {
+ alignFrame = (AlignFrame) guiWindow;
+ }
+ database = new JDatabaseTree(sfetch);
try
{
jbInit();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
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);
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
}
else
{
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
}
}
private String getFrameTitle()
{
- return ( (alignFrame == null) ? "New " : "Additional ") +
- "Sequence Fetcher";
+ return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher"));
}
- private void jbInit()
- throws Exception
+ private void jbInit() 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));
+ database.setFont(JvSwingUtils.getLabelFont());
+ dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
- jLabel1.setText(
- "Separate multiple accession ids with semi colon \";\"");
- ok.setText("OK");
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+ jLabel1.setText(MessageManager
+ .getString("label.separate_multiple_accession_ids"));
+
+ replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
+ replacePunctuation
+ .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ replacePunctuation.setText(MessageManager
+ .getString("label.replace_commas_semicolons"));
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed();
+ }
+ });
+ clear.setText(MessageManager.getString("action.clear"));
+ clear.addActionListener(new ActionListener()
+ {
+ @Override
public void actionPerformed(ActionEvent e)
{
- ok_actionPerformed(e);
+ clear_actionPerformed();
}
});
- close.setText("Close");
+
+ example.setText(MessageManager.getString("label.example"));
+ example.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ example_actionPerformed();
+ }
+ });
+ close.setText(MessageManager.getString("action.close"));
close.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
close_actionPerformed(e);
}
});
- textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- textfield.addActionListener(new ActionListener()
+ textArea.setFont(JvSwingUtils.getLabelFont());
+ textArea.setLineWrap(true);
+ textArea.addKeyListener(new KeyAdapter()
{
- public void actionPerformed(ActionEvent e)
+ @Override
+ 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(example);
+ jPanel1.add(clear);
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.CENTER);
+ jPanel2.setLayout(borderLayout3);
+ databaseButt = database.getDatabaseSelectorButton();
+ databaseButt.setFont(JvSwingUtils.getLabelFont());
+ database.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ databaseButt.setText(database.getSelectedItem()
+ + (database.getSelectedSources().size() > 1 ? " (and "
+ + database.getSelectedSources().size()
+ + " others)" : ""));
+ String eq = database.getExampleQueries();
+ dbeg.setText(MessageManager.formatMessage(
+ "label.example_query_param", new String[]
+ { eq }));
+ boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
+ for (DbSourceProxy dbs : database.getSelectedSources())
+ {
+ if (dbs instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+ {
+ enablePunct = false;
+ break;
+ }
+ }
+ replacePunctuation.setEnabled(enablePunct);
+
+ } catch (Exception ex)
+ {
+ dbeg.setText("");
+ replacePunctuation.setEnabled(true);
+ }
+ jPanel2.repaint();
+ }
+ });
+ dbeg.setText("");
+ jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
+ jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
+ JPanel jPanel2a = new JPanel(new BorderLayout());
+ jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
+ jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
+ jPanel2.add(jPanel2a, 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);
+ jScrollPane1.getViewport().add(textArea);
+
+ }
+
+ protected void example_actionPerformed()
+ {
+ DbSourceProxy db = null;
+ try
+ {
+ textArea.setText(database.getExampleQueries());
+ } catch (Exception ex)
+ {
+ }
+ jPanel3.repaint();
}
- JComboBox database = new JComboBox();
+ protected void clear_actionPerformed()
+ {
+ textArea.setText("");
+ jPanel3.repaint();
+ }
+
+ JLabel dbeg = new JLabel();
+
+ JDatabaseTree database;
+
+ JButton databaseButt;
+
JLabel jLabel1 = new JLabel();
+
+ JCheckBox replacePunctuation = new JCheckBox();
+
JButton ok = new JButton();
+
+ JButton clear = new JButton();
+
+ JButton example = 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();
+
+ JPanel jPanel4 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ BorderLayout borderLayout2 = new BorderLayout();
+
+ BorderLayout borderLayout3 = new BorderLayout();
+
public void close_actionPerformed(ActionEvent e)
{
try
{
frame.setClosed(true);
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
}
- public void ok_actionPerformed(ActionEvent e)
+ public void ok_actionPerformed()
{
- database.setEnabled(false);
- textfield.setEnabled(false);
+ databaseButt.setEnabled(false);
+ example.setEnabled(false);
+ textArea.setEnabled(false);
ok.setEnabled(false);
close.setEnabled(false);
@@ -158,22 +425,38 @@ public class SequenceFetcher
private void resetDialog()
{
- database.setEnabled(true);
- textfield.setEnabled(true);
+ databaseButt.setEnabled(true);
+ example.setEnabled(true);
+ textArea.setEnabled(true);
ok.setEnabled(true);
close.setEnabled(true);
}
+ @Override
public void run()
{
String error = "";
- if (database.getSelectedItem().equals(noDbSelected))
+ if (!database.hasSelection())
{
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)
+ // TODO: make this transformation more configurable
+ com.stevesoft.pat.Regex empty;
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+ {
+ empty = new com.stevesoft.pat.Regex(
+ // replace commas and spaces with a semicolon
+ "(\\s|[,; ])+", ";");
+ }
+ else
+ {
+ // just turn spaces and semicolons into single semicolons
+ empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
+ }
+ textArea.setText(empty.replaceAll(textArea.getText()));
+ // see if there's anthing to search with
+ if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
+ .getText()))
{
error += "Please enter a (semi-colon separated list of) database id(s)";
}
@@ -183,268 +466,268 @@ public class SequenceFetcher
resetDialog();
return;
}
-
- result = new StringBuffer();
- if (database.getSelectedItem().equals("Uniprot"))
+ // indicate if successive sources should be merged into one alignment.
+ boolean addToLast = false;
+ ArrayList aresultq = new ArrayList(), presultTitle = new ArrayList();
+ ArrayList presult = new ArrayList(), aresult = new ArrayList();
+ Iterator proxies = database.getSelectedSources()
+ .iterator();
+ String[] qries;
+ List nextfetch = Arrays.asList(qries = textArea.getText()
+ .split(";"));
+ Iterator en = Arrays.asList(new String[0]).iterator();
+ int nqueries = qries.length;
+ while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
{
- getUniprotFile(textfield.getText());
- }
- else if (database.getSelectedItem().equals("EMBL")
- || database.getSelectedItem().equals("EMBLCDS"))
- {
- StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
- while (st.hasMoreTokens())
+ if (!en.hasNext() && nextfetch.size() > 0)
{
- EBIFetchClient dbFetch = new EBIFetchClient();
-
- String[] reply = dbFetch.fetchData(
- database.getSelectedItem().toString().toLowerCase(
- ) + ":" + st.nextToken(),
- "fasta", "raw");
-//
- if (reply != null)
+ 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();
+ boolean isAliSource = false;
+ try
+ {
+ // update status
+ guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread
+ .currentThread().hashCode());
+ isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
+ if (proxy.getAccessionSeparator() == null)
{
- for (int i = 0; i < reply.length; i++)
+ while (en.hasNext())
{
- result.append(reply[i] + "\n");
+ String item = en.next();
+ try
+ {
+ if (aresult != null)
+ {
+ try
+ {
+ // give the server a chance to breathe
+ Thread.sleep(5);
+ } catch (Exception e)
+ {
+ //
+ }
+
+ }
+
+ AlignmentI indres = null;
+ try
+ {
+ indres = proxy.getSequenceRecords(item);
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + item + " from "
+ + proxy.getDbName(), oome, this);
+ }
+ if (indres != null)
+ {
+ aresultq.add(item);
+ aresult.add(indres);
+ }
+ else
+ {
+ nextfetch.add(item);
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.info("Error retrieving " + item
+ + " from " + proxy.getDbName(), e);
+ nextfetch.add(item);
+ }
}
}
- }
-
- if (result != null && result.length() > 1) // arbitrary minimum length for a seuqence file
- {
- System.out.println(result.toString());
-
- parseResult(result.toString(), null);
- }
- }
- else if (database.getSelectedItem().equals("PDB"))
- {
- StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");
- String query;
- SequenceI[] seqs = null;
- while (qset.hasMoreTokens() && ( (query = qset.nextToken()) != null))
- {
- SequenceI[] seqparts = getPDBFile(query.toUpperCase());
- if (seqparts != null)
+ else
{
- if (seqs == null)
+ StringBuffer multiacc = new StringBuffer();
+ ArrayList tosend = new ArrayList();
+ while (en.hasNext())
{
- seqs = seqparts;
+ String nel = en.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (en.hasNext())
+ {
+ multiacc.append(proxy.getAccessionSeparator());
+ }
}
- else
+ try
{
- SequenceI[] newseqs = new SequenceI[seqs.length + seqparts.length];
- int i = 0;
- for (; i < seqs.length; i++)
+ AlignmentI rslt;
+ SequenceI[] rs;
+ List nores = new ArrayList();
+ rslt = proxy.getSequenceRecords(multiacc.toString());
+ if (rslt == null || rslt.getHeight() == 0)
{
- newseqs[i] = seqs[i];
- seqs[i] = null;
+ // no results - pass on all queries to next source
+ nextfetch.addAll(tosend);
}
- for (int j = 0; j < seqparts.length; i++, j++)
+ else
{
- newseqs[i] = seqparts[j];
+ aresultq.add(multiacc.toString());
+ aresult.add(rslt);
+
+ rs = rslt.getSequencesArray();
+ // search for each query in the dbrefs associated with each
+ // sequence
+ // returned.
+ // ones we do not find will be used to query next source (if any)
+ for (String q : tosend)
+ {
+ DBRefEntry dbr = new DBRefEntry(), found[] = null;
+ dbr.setSource(proxy.getDbSource());
+ dbr.setVersion(null);
+ if (proxy.getAccessionValidator() != null)
+ {
+ Regex vgr = proxy.getAccessionValidator();
+ vgr.search(q);
+ if (vgr.numSubs() > 0)
+ {
+ dbr.setAccessionId(vgr.stringMatched(1));
+ }
+ else
+ {
+ dbr.setAccessionId(vgr.stringMatched());
+ }
+ }
+ else
+ {
+ dbr.setAccessionId(q);
+ }
+ boolean rfound = false;
+ for (int r = 0; r < rs.length; r++)
+ {
+ if (rs[r] != null
+ && (found = DBRefUtils.searchRefs(
+ rs[r].getDBRef(), dbr)) != null
+ && found.length > 0)
+ {
+ rfound = true;
+ rs[r] = null;
+ continue;
+ }
+ }
+ if (!rfound)
+ {
+ nextfetch.add(q);
+ }
+ }
}
- seqs = newseqs;
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
}
- 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");
- }
- }
- }
- 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)
+ } catch (Exception e)
{
- 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())
+ 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();
+ } catch (OutOfMemoryError e)
{
- 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");
-
+ // resets dialog box - so we don't use OOMwarning here.
+ 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();
+ } catch (Error e)
+ {
+ showErrorMessage("Serious Error retrieving " + textArea.getText()
+ + " from " + database.getSelectedItem());
+ e.printStackTrace();
}
-
- //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++)
+ // Stack results ready for opening in alignment windows
+ if (aresult != null && aresult.size() > 0)
{
- UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
- Enumeration e = entry.getDbReference().elements();
- Vector onlyPdbEntries = new Vector();
- while (e.hasMoreElements())
+ AlignmentI ar = null;
+ if (isAliSource)
{
- PDBEntry pdb = (PDBEntry) e.nextElement();
- if (!pdb.getType().equals("PDB"))
+ addToLast = false;
+ // new window for each result
+ while (aresult.size() > 0)
{
- continue;
+ presult.add(aresult.remove(0));
+ presultTitle.add(aresultq.remove(0) + " "
+ + getDefaultRetrievalTitle());
}
-
- onlyPdbEntries.addElement(pdb);
}
-
- Enumeration en2 = entry.getAccession().elements();
- while (en2.hasMoreElements())
+ else
{
- al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
- DBRefSource.UNIPROT,
- "0",
- en2.nextElement().toString()));
- }
-
- al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
- if (entry.getFeature() != null)
- {
- e = entry.getFeature().elements();
- while (e.hasMoreElements())
+ String titl = null;
+ if (addToLast && presult.size() > 0)
+ {
+ ar = presult.remove(presult.size() - 1);
+ titl = presultTitle.remove(presultTitle.size() - 1);
+ }
+ // concatenate all results in one window
+ while (aresult.size() > 0)
{
- SequenceFeature sf = (SequenceFeature) e.nextElement();
- sf.setFeatureGroup("Uniprot");
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ if (ar == null)
+ {
+ ar = aresult.remove(0);
+ }
+ else
+ {
+ ar.append(aresult.remove(0));
+ }
+ ;
}
+ addToLast = true;
+ presult.add(ar);
+ presultTitle.add(titl);
}
}
+ guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread()
+ .hashCode());
}
- }
-
- SequenceI[] getPDBFile(String id)
- {
- 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)
+ guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results")
+ : MessageManager.getString("status.processing"), Thread.currentThread().hashCode());
+ // process results
+ while (presult.size() > 0)
{
- return null;
+ parseResult(presult.remove(0), presultTitle.remove(0), null);
}
- try
+ // only remove visual delay after we finished parsing.
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
+ if (nextfetch.size() > 0)
{
- PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
- for (int i = 0; i < pdbfile.chains.size(); i++)
+ 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 (chain == null ||
- ( (PDBChain) pdbfile.chains.elementAt(i)).id.
- toUpperCase().equals(chain))
+ if (l != sb.length())
+ {
+ sb.append("; ");
+ }
+ if (lr - sb.length() > 40)
{
- 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());
+ sb.append("\n");
}
+ sb.append(s);
}
+ showErrorMessage(sb.toString());
}
- catch (Exception ex) // Problem parsing PDB file
- {
- jalview.bin.Cache.log.warn("Exception when retrieving " +
- 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);
- }
- return results;
+ resetDialog();
}
- Alignment parseResult(String result, String title)
+ AlignmentI parseResult(String result, String title)
{
String format = new IdentifyFile().Identify(result, "Paste");
Alignment sequences = null;
@@ -453,11 +736,11 @@ public class SequenceFetcher
sequences = null;
try
{
- sequences = new FormatAdapter().readFile(result.toString(), "Paste",
- format);
+ sequences = new FormatAdapter().readFile(result.toString(),
+ "Paste", format);
+ } catch (Exception ex)
+ {
}
- catch (Exception ex)
- {}
if (sequences != null)
{
@@ -466,59 +749,93 @@ public class SequenceFetcher
}
else
{
- showErrorMessage("Error retrieving " + textfield.getText()
- + " from " + database.getSelectedItem());
+ showErrorMessage("Error retrieving " + textArea.getText() + " from "
+ + database.getSelectedItem());
}
return null;
}
- Alignment parseResult(Alignment al, String title, String currentFileFormat)
+ /**
+ *
+ * @return a standard title for any results retrieved using the currently
+ * selected source and settings
+ */
+ public String getDefaultRetrievalTitle()
+ {
+ return "Retrieved from " + database.getSelectedItem();
+ }
+
+ AlignmentI parseResult(AlignmentI al, String title,
+ String currentFileFormat)
{
if (al != null && al.getHeight() > 0)
{
if (alignFrame == null)
{
- AlignFrame af = new AlignFrame(al,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ 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; // WHAT IS THE DEFAULT
+ // FORMAT FOR
+ // NON-FormatAdapter Sourced
+ // Alignments?
}
if (title == null)
{
- title = "Retrieved from " + database.getSelectedItem();
+ title = getDefaultRetrievalTitle();
}
+ SequenceFeature[] sfs = null;
+ List alsqs;
+ synchronized (alsqs = al.getSequences())
+ {
+ for (SequenceI sq : alsqs)
+ {
+ if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
+ {
+ if (sfs.length > 0)
+ {
+ af.setShowSeqFeatures(true);
+ break;
+ }
+ }
- Desktop.addInternalFrame(af,
- title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ }
+ }
+ Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
- af.statusBar.setText("Successfully pasted alignment file");
+ af.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
try
{
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ af.setMaximum(jalview.bin.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.getAlignment().addSequence(
+ al.getSequenceAt(i)); // this
+ // also
+ // creates
+ // dataset
+ // sequence
+ // entries
}
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
- getHeight());
- alignFrame.viewport.alignment.getWidth();
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
+ .getHeight());
+ alignFrame.viewport.getAlignment().getWidth();
alignFrame.viewport.firePropertyChange("alignment", null,
- alignFrame.viewport.
- getAlignment().getSequences());
+ alignFrame.viewport.getAlignment().getSequences());
}
}
return al;
@@ -529,11 +846,12 @@ public class SequenceFetcher
resetDialog();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- error, "Error Retrieving Data",
- JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+ MessageManager.getString("label.error_retrieving_data"),
+ JOptionPane.WARNING_MESSAGE);
}
});
}