X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=f8d3734dcee1eccc9ecbf8824ff3736ea56dc9da;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=498489d1902f15837bdebb04123fa04720363233;hpb=4f01ddc72d2297c48c57d4f9c25af45b300df154;p=jalview.git
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 498489d..f8d3734 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,460 +1,915 @@
-/*
- * 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.HORIZONTAL,
- new Insets(0, 0, 0, 6), 200, 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"))
- {
- EBIFetchClient dbFetch = new EBIFetchClient();
- String[] reply = dbFetch.fetchData(
- database.getSelectedItem().toString().toLowerCase(
- ) + ":" + textfield.getText(),
- "fasta", "raw");
-
- if(reply!=null)
- {
- for (int i = 0; i < reply.length; i++)
- result.append(reply[i] + "\n");
-
- 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);
- SequenceFeatureFetcher sff = new SequenceFeatureFetcher();
- Vector entries = sff.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.getProteinName() != null)
- name.append(" " + entry.getProteinName().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);
- sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());
-
- }
- }
- }
-
- 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[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");
- if (reply == null)
- return null;
- try
- {
- PDBfile pdbfile = new PDBfile(reply);
- 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 = 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("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(String error)
- {
- resetDialog();
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- error, "Error Retrieving Data",
- JOptionPane.WARNING_MESSAGE);
- return;
- }
-}
-
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.FormatAdapter;
+import jalview.io.IdentifyFile;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+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.Iterator;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingConstants;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import com.stevesoft.pat.Regex;
+
+public class SequenceFetcher extends JPanel implements Runnable
+{
+ 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();
+
+ 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();
+
+ JInternalFrame frame;
+
+ IProgressIndicator guiWindow;
+
+ AlignFrame alignFrame;
+
+ StringBuffer result;
+
+ final String noDbSelected = "-- Select Database --";
+
+ 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;
+
+ int debounceTrap = 0;
+
+ /**
+ * 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(null, Thread.currentThread().hashCode());
+ }
+ lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
+ .getLocalSourceString()).hashCode();
+ sfetch = sf;
+ _initingFetcher = false;
+ initingThread = null;
+ }
+ return sfetch;
+ }
+
+ private IProgressIndicator progressIndicator;
+
+ public SequenceFetcher(IProgressIndicator guiIndic)
+ {
+ this.progressIndicator = guiIndic;
+ final SequenceFetcher us = this;
+ // launch initialiser thread
+ Thread sf = new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ if (getSequenceFetcherSingleton(progressIndicator) != null)
+ {
+ us.initGui(progressIndicator);
+ }
+ 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
+ {
+
+ };
+
+ /**
+ * 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)
+ {
+ ex.printStackTrace();
+ }
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (new jalview.util.Platform().isAMac())
+ {
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
+ }
+ }
+
+ private String getFrameTitle()
+ {
+ return ((alignFrame == null) ? MessageManager
+ .getString("label.new_sequence_fetcher") : MessageManager
+ .getString("label.additional_sequence_fetcher"));
+ }
+
+ private void jbInit() throws Exception
+ {
+ this.setLayout(borderLayout2);
+
+ 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.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)
+ {
+ clear_actionPerformed();
+ }
+ });
+
+ 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);
+ }
+ });
+ textArea.setFont(JvSwingUtils.getLabelFont());
+ textArea.setLineWrap(true);
+ textArea.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent 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);
+ 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)
+ {
+ debounceTrap++;
+ String currentSelection = database.getSelectedItem();
+ if (!currentSelection.equalsIgnoreCase("pdb"))
+ {
+ otherSourceAction();
+ }
+ if (currentSelection.equalsIgnoreCase("pdb")
+ && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
+ {
+ pdbSourceAction();
+ }
+ database.action = -1;
+ }
+ });
+
+ 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);
+
+ }
+
+ private void pdbSourceAction()
+ {
+ databaseButt.setText(database.getSelectedItem());
+ new PDBSearchPanel(this);
+ frame.dispose();
+ }
+
+ private void otherSourceAction()
+ {
+ 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();
+ }
+
+ protected void example_actionPerformed()
+ {
+ DbSourceProxy db = null;
+ try
+ {
+ textArea.setText(database.getExampleQueries());
+ } catch (Exception ex)
+ {
+ }
+ jPanel3.repaint();
+ }
+
+ protected void clear_actionPerformed()
+ {
+ textArea.setText("");
+ jPanel3.repaint();
+ }
+
+ public void close_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ public void ok_actionPerformed()
+ {
+ databaseButt.setEnabled(false);
+ example.setEnabled(false);
+ textArea.setEnabled(false);
+ ok.setEnabled(false);
+ close.setEnabled(false);
+
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ private void resetDialog()
+ {
+ databaseButt.setEnabled(true);
+ example.setEnabled(true);
+ textArea.setEnabled(true);
+ ok.setEnabled(true);
+ close.setEnabled(true);
+ }
+
+ @Override
+ public void run()
+ {
+ String error = "";
+ if (!database.hasSelection())
+ {
+ error += "Please select the source database\n";
+ }
+ // 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)";
+ }
+ if (error.length() > 0)
+ {
+ showErrorMessage(error);
+ resetDialog();
+ return;
+ }
+ // 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))
+ {
+ 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();
+ 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)
+ {
+ while (en.hasNext())
+ {
+ 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);
+ }
+ }
+ }
+ else
+ {
+ StringBuffer multiacc = new StringBuffer();
+ ArrayList tosend = new ArrayList();
+ while (en.hasNext())
+ {
+ String nel = en.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (en.hasNext())
+ {
+ multiacc.append(proxy.getAccessionSeparator());
+ }
+ }
+ try
+ {
+ AlignmentI rslt;
+ SequenceI[] rs;
+ List nores = new ArrayList();
+ rslt = proxy.getSequenceRecords(multiacc.toString());
+ if (rslt == null || rslt.getHeight() == 0)
+ {
+ // no results - pass on all queries to next source
+ nextfetch.addAll(tosend);
+ }
+ else
+ {
+ 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);
+ }
+ }
+ }
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
+ }
+ }
+
+ } catch (Exception e)
+ {
+ 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)
+ {
+ // 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();
+ }
+ // Stack results ready for opening in alignment windows
+ if (aresult != null && aresult.size() > 0)
+ {
+ AlignmentI ar = null;
+ if (isAliSource)
+ {
+ addToLast = false;
+ // new window for each result
+ while (aresult.size() > 0)
+ {
+ presult.add(aresult.remove(0));
+ presultTitle.add(aresultq.remove(0) + " "
+ + getDefaultRetrievalTitle());
+ }
+ }
+ else
+ {
+ 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)
+ {
+ 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());
+ }
+ 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);
+ }
+ // 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 (l != sb.length())
+ {
+ sb.append("; ");
+ }
+ if (lr - sb.length() > 40)
+ {
+ sb.append("\n");
+ }
+ sb.append(s);
+ }
+ showErrorMessage(sb.toString());
+ }
+ resetDialog();
+ }
+
+ AlignmentI parseResult(String result, String title)
+ {
+ String format = new IdentifyFile().Identify(result, "Paste");
+ AlignmentI sequences = null;
+ if (FormatAdapter.isValidFormat(format))
+ {
+ sequences = null;
+ 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;
+ }
+
+ /**
+ *
+ * @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 (title == null)
+ {
+ title = getDefaultRetrievalTitle();
+ }
+ if (alignFrame == 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?
+ }
+
+ SequenceFeature[] sfs = null;
+ List alsqs;
+ synchronized (alsqs = al.getSequences())
+ {
+ for (SequenceI sq : alsqs)
+ {
+ if ((sfs = sq.getSequenceFeatures()) != null)
+ {
+ if (sfs.length > 0)
+ {
+ af.setShowSeqFeatures(true);
+ break;
+ }
+ }
+
+ }
+ }
+ Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ af.statusBar.setText(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
+
+ try
+ {
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN",
+ false));
+ } catch (Exception ex)
+ {
+ }
+ }
+ else
+ {
+ alignFrame.viewport.addAlignment(al, title);
+ }
+ }
+ return al;
+ }
+
+ void showErrorMessage(final String error)
+ {
+ resetDialog();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+ MessageManager.getString("label.error_retrieving_data"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
+}