X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=3d09f9963248dd4dabf29a00065e151228f3d103;hb=0751c58086542f9e0466201b624f84d1efd547bb;hp=435d21820c30c8d6bf2048a884a91506bf93c35b;hpb=cb5d856b1304448cae13a333cbd9017f81520d90;p=jalview.git
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 435d218..3d09f99 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1,242 +1,220 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * 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 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 jalview.datamodel.*;
-import jalview.io.*;
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+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.uniprot.UniprotFTSPanel;
+import jalview.io.FileFormatI;
+import jalview.io.gff.SequenceOntologyI;
import jalview.util.DBRefUtils;
import jalview.util.MessageManager;
-import jalview.ws.dbsources.das.api.DasSourceRegistryI;
+import jalview.util.Platform;
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.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;
+
+/**
+ * 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
{
- // ASequenceFetcher sfetch;
- JInternalFrame frame;
+ private static jalview.ws.SequenceFetcher sfetch = null;
- IProgressIndicator guiWindow;
+ JLabel exampleAccession;
- AlignFrame alignFrame;
+ JComboBox database;
- StringBuffer result;
+ JCheckBox replacePunctuation;
- final String noDbSelected = "-- Select Database --";
+ JButton okBtn;
- private static jalview.ws.SequenceFetcher sfetch = null;
+ JButton exampleBtn;
+
+ JButton closeBtn;
+
+ JButton backBtn;
+
+ JTextArea textArea;
+
+ JInternalFrame frame;
+
+ IProgressIndicator guiWindow;
- private static long lastDasSourceRegistry = -3;
+ AlignFrame alignFrame;
- private static DasSourceRegistryI dasRegistry = null;
+ GFTSPanel parentSearchPanel;
- private static boolean _initingFetcher = false;
+ IProgressIndicator progressIndicator;
- private static Thread initingThread = null;
+ volatile boolean _isConstructing = false;
/**
- * Blocking method that initialises and returns the shared instance of the
- * SequenceFetcher client
+ * 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
+ * @return
*/
- public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
- final IProgressIndicator guiWindow)
+ public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton()
{
- if (_initingFetcher && initingThread != null && initingThread.isAlive())
+ if (sfetch == null)
{
- if (guiWindow != null)
- {
- guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
- 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(
- "Waiting for Sequence Database Fetchers to initialise",
- 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("Initialising 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("Initialising Sequence Database Fetchers",
- Thread.currentThread().hashCode());
- }
- lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
- .getLocalSourceString()).hashCode();
- sfetch = sf;
- _initingFetcher = false;
- initingThread = null;
+ sfetch = new jalview.ws.SequenceFetcher();
}
return sfetch;
}
+ /**
+ * Constructor given a client to receive any status or progress messages
+ * (currently either the Desktop, or an AlignFrame panel)
+ *
+ * @param guiIndic
+ */
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,
- "Could not create the sequence fetcher client. Check error logs for details.",
- "Couldn't create SequenceFetcher",
- JOptionPane.ERROR_MESSAGE);
- }
- });
-
- // raise warning dialog
- }
- }
- });
- sf.start();
+ this(guiIndic, null, null);
}
- private class DatabaseAuthority extends DefaultMutableTreeNode
- {
-
- };
-
- private class DatabaseSource extends DefaultMutableTreeNode
- {
-
- };
-
/**
- * called by thread spawned by constructor
+ * Constructor with specified database and accession(s) to retrieve
*
- * @param guiWindow
+ * @param guiIndic
+ * @param selectedDb
+ * @param queryString
*/
- private void initGui(IProgressIndicator guiWindow)
+ public SequenceFetcher(IProgressIndicator guiIndic,
+ final String selectedDb, final String queryString)
{
- this.guiWindow = guiWindow;
- if (guiWindow instanceof AlignFrame)
- {
- alignFrame = (AlignFrame) guiWindow;
- }
- database = new JDatabaseTree(sfetch);
- try
- {
- jbInit();
- } catch (Exception ex)
+ this.progressIndicator = guiIndic;
+ getSequenceFetcherSingleton();
+ this.guiWindow = progressIndicator;
+
+ if (progressIndicator instanceof AlignFrame)
{
- ex.printStackTrace();
+ alignFrame = (AlignFrame) progressIndicator;
}
+ jbInit(selectedDb);
+ textArea.setText(queryString);
+
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);
- }
+ Desktop.addInternalFrame(frame, getFrameTitle(), Desktop.FRAME_MAKE_VISIBLE, 400,
+ Platform.isAMacAndNotJS() ? 240 : 180, Desktop.FRAME_ALLOW_RESIZE, Desktop.FRAME_SET_MIN_SIZE_300);
}
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(String selectedDb)
{
- this.setLayout(borderLayout2);
+ this.setLayout(new BorderLayout());
+ database = new JComboBox<>();
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()
+ database.setPrototypeDisplayValue("ENSEMBLGENOMES ");
+ String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb();
+ Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
+ database.addItem(MessageManager.getString("action.select_ddbb"));
+ for (String source : sources)
+ {
+ database.addItem(source);
+ }
+ database.setSelectedItem(selectedDb);
+ if (database.getSelectedIndex() == -1)
+ {
+ database.setSelectedIndex(0);
+ }
+ database.setMaximumRowCount(database.getItemCount());
+ database.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ String currentSelection = (String) database.getSelectedItem();
+ updateExampleQuery(currentSelection);
+
+ if ("pdb".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new PDBFTSPanel(SequenceFetcher.this);
+ }
+ else if ("uniprot".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new UniprotFTSPanel(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)
@@ -244,7 +222,7 @@ public class SequenceFetcher extends JPanel implements Runnable
ok_actionPerformed();
}
});
- clear.setText(MessageManager.getString("action.clear"));
+ JButton clear = new JButton(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
@Override
@@ -254,8 +232,8 @@ public class SequenceFetcher extends JPanel implements Runnable
}
});
- example.setText(MessageManager.getString("label.example"));
- example.addActionListener(new ActionListener()
+ exampleBtn = new JButton(MessageManager.getString("label.example"));
+ exampleBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
@@ -263,8 +241,8 @@ public class SequenceFetcher extends JPanel implements Runnable
example_actionPerformed();
}
});
- close.setText(MessageManager.getString("action.close"));
- close.addActionListener(new ActionListener()
+ closeBtn = new JButton(MessageManager.getString("action.cancel"));
+ closeBtn.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
@@ -272,6 +250,19 @@ public class SequenceFetcher extends JPanel implements Runnable
close_actionPerformed(e);
}
});
+ backBtn = new JButton(MessageManager.getString("action.back"));
+ backBtn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ parentSearchPanel.btn_back_ActionPerformed();
+ }
+ });
+ // back not visible unless embedded
+ backBtn.setVisible(false);
+
+ textArea = new JTextArea();
textArea.setFont(JvSwingUtils.getLabelFont());
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
@@ -280,139 +271,184 @@ public class SequenceFetcher extends JPanel implements Runnable
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)
- {
- 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);
+ 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);
- } catch (Exception ex)
+ 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);
+ }
+
+ /**
+ * Answers a semi-colon-delimited string with the example query or queries for
+ * the selected database
+ *
+ * @param db
+ * @return
+ */
+ protected String getExampleQueries(String db)
+ {
+ 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)
{
- dbeg.setText("");
- replacePunctuation.setEnabled(true);
+ sb.append(";");
}
- jPanel2.repaint();
+ sb.append(tq);
}
- });
- 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);
-
+ }
+ return sb.toString();
}
- protected void example_actionPerformed()
+ /**
+ * 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()
{
- DbSourceProxy db = null;
try
{
- textArea.setText(database.getExampleQueries());
+ 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);
}
- jPanel3.repaint();
+ repaint();
}
- protected void clear_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)
{
- textArea.setText("");
- jPanel3.repaint();
+ String eq = getExampleQueries(selectedDatabase);
+ exampleAccession.setText(MessageManager
+ .formatMessage("label.example_query_param", new String[]
+ { eq }));
+ return eq;
}
- 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();
+ /**
+ * 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((String) database.getSelectedItem());
+ textArea.setText(eq);
+ repaint();
+ }
- BorderLayout borderLayout3 = new BorderLayout();
+ /**
+ * Clears the query input field
+ */
+ protected void clear_actionPerformed()
+ {
+ textArea.setText("");
+ repaint();
+ }
- public void close_actionPerformed(ActionEvent e)
+ /**
+ * 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)
{
try
{
frame.setClosed(true);
+ if (parentSearchPanel != null)
+ {
+ parentSearchPanel.btn_cancel_ActionPerformed();
+ }
} catch (Exception ex)
{
}
}
+ /**
+ * Action on OK is to start the fetch for entered accession(s)
+ */
public void ok_actionPerformed()
{
- databaseButt.setEnabled(false);
- example.setEnabled(false);
+ /*
+ * tidy inputs and check there is something to search for
+ */
+ String t0 = textArea.getText();
+ String text = t0.trim();
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+ {
+ text = text.replace(",", ";");
+ }
+ text = text.replaceAll("(\\s|[; ])+", ";");
+ if (!t0.equals(text))
+ {
+ textArea.setText(text);
+ }
+ if (text.isEmpty())
+ {
+ // todo i18n
+ showErrorMessage(
+ "Please enter a (semi-colon separated list of) database id(s)");
+ resetDialog();
+ return;
+ }
+ if (database.getSelectedIndex() == 0)
+ {
+ // todo i18n
+ showErrorMessage("Please choose a database");
+ resetDialog();
+ return;
+ }
+
+ exampleBtn.setEnabled(false);
textArea.setEnabled(false);
- ok.setEnabled(false);
- close.setEnabled(false);
+ okBtn.setEnabled(false);
+ closeBtn.setEnabled(false);
+ backBtn.setEnabled(false);
Thread worker = new Thread(this);
worker.start();
@@ -420,211 +456,75 @@ public class SequenceFetcher extends JPanel implements Runnable
private void resetDialog()
{
- databaseButt.setEnabled(true);
- example.setEnabled(true);
+ exampleBtn.setEnabled(true);
textArea.setEnabled(true);
- ok.setEnabled(true);
- close.setEnabled(true);
+ okBtn.setEnabled(true);
+ closeBtn.setEnabled(true);
+ backBtn.setEnabled(parentSearchPanel != null);
}
@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(";"));
+ List aresultq = new ArrayList<>();
+ List presultTitle = new ArrayList<>();
+ List presult = new ArrayList<>();
+ List aresult = new ArrayList<>();
+ List sources = sfetch
+ .getSourceProxy((String) database.getSelectedItem());
+ 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;
- while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
+
+ FeatureSettingsModelI preferredFeatureColours = null;
+ while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
{
- if (!en.hasNext() && nextfetch.size() > 0)
+ if (!en.hasNext() && nextFetch.size() > 0)
{
- en = nextfetch.iterator();
- nqueries = nextfetch.size();
+ en = nextFetch.iterator();
+ nqueries = nextFetch.size();
// save the remaining queries in the original array
- qries = nextfetch.toArray(new String[nqueries]);
- nextfetch = new ArrayList();
+ qries = nextFetch.toArray(new String[nqueries]);
+ nextFetch = new ArrayList<>();
}
DbSourceProxy proxy = proxies.next();
- boolean isAliSource = false;
try
{
// update status
- guiWindow.setProgressBar("Fetching " + nqueries
- + " sequence queries from " + proxy.getDbName(), Thread
- .currentThread().hashCode());
- isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
- if (proxy.getAccessionSeparator() == null)
+ 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 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)
+ String acc = en.next();
+ if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
{
- jalview.bin.Cache.log.info("Error retrieving " + item
- + " from " + proxy.getDbName(), e);
- nextfetch.add(item);
+ nextFetch.add(acc);
}
}
}
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);
- }
+ /*
+ * proxy can fetch multiple accessions at one time
+ */
+ fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
}
-
} catch (Exception e)
{
- showErrorMessage("Error retrieving " + textArea.getText()
- + " from " + database.getSelectedItem());
+ showErrorMessage("Error retrieving " + textArea.getText() + " from "
+ + database.getSelectedItem());
// error
// +="Couldn't retrieve sequences from "+database.getSelectedItem();
System.err.println("Retrieval failed for source ='"
@@ -633,11 +533,8 @@ public class SequenceFetcher extends JPanel implements Runnable
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()
+ + 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)
@@ -646,19 +543,27 @@ public class SequenceFetcher extends JPanel implements Runnable
+ " from " + database.getSelectedItem());
e.printStackTrace();
}
+
// Stack results ready for opening in alignment windows
if (aresult != null && aresult.size() > 0)
{
+ FeatureSettingsModelI proxyColourScheme = proxy
+ .getFeatureColourScheme();
+ if (proxyColourScheme != null)
+ {
+ preferredFeatureColours = proxyColourScheme;
+ }
+
AlignmentI ar = null;
- if (isAliSource)
+ if (proxy.isAlignmentSource())
{
addToLast = false;
// new window for each result
while (aresult.size() > 0)
{
presult.add(aresult.remove(0));
- presultTitle.add(aresultq.remove(0) + " "
- + getDefaultRetrievalTitle());
+ presultTitle.add(
+ aresultq.remove(0) + " " + getDefaultRetrievalTitle());
}
}
else
@@ -680,33 +585,40 @@ public class SequenceFetcher extends JPanel implements Runnable
{
ar.append(aresult.remove(0));
}
- ;
}
addToLast = true;
presult.add(ar);
presultTitle.add(titl);
}
}
- guiWindow.setProgressBar("Finished querying", Thread.currentThread()
- .hashCode());
+ guiWindow.setProgressBar(
+ MessageManager.getString("status.finshed_querying"),
+ Thread.currentThread().hashCode());
}
- guiWindow.setProgressBar((presult.size() > 0) ? "Parsing results."
- : "Processing ..", 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);
+ 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)
+ if (nextFetch.size() > 0)
{
StringBuffer sb = new StringBuffer();
sb.append("Didn't retrieve the following "
- + (nextfetch.size() == 1 ? "query" : nextfetch.size()
- + " queries") + ": \n");
+ + (nextFetch.size() == 1 ? "query"
+ : nextFetch.size() + " queries")
+ + ": \n");
int l = sb.length(), lr = 0;
- for (String s : nextfetch)
+ for (String s : nextFetch)
{
if (l != sb.length())
{
@@ -723,33 +635,157 @@ public class SequenceFetcher extends JPanel implements Runnable
resetDialog();
}
- AlignmentI parseResult(String result, String title)
+ /**
+ * 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
{
- String format = new IdentifyFile().Identify(result, "Paste");
- Alignment sequences = null;
- if (FormatAdapter.isValidFormat(format))
+ StringBuilder multiacc = new StringBuilder();
+ List tosend = new ArrayList<>();
+ while (accessions.hasNext())
{
- sequences = null;
- try
- {
- sequences = new FormatAdapter().readFile(result.toString(),
- "Paste", format);
- } catch (Exception ex)
+ String nel = accessions.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (accessions.hasNext())
{
+ multiacc.append(proxy.getAccessionSeparator());
}
+ }
- if (sequences != null)
+ try
+ {
+ String query = multiacc.toString();
+ AlignmentI rslt = proxy.getSequenceRecords(query);
+ if (rslt == null || rslt.getHeight() == 0)
{
- return parseResult(sequences, title, format);
+ // no results - pass on all queries to next source
+ nextFetch.addAll(tosend);
+ }
+ else
+ {
+ aresultq.add(query);
+ aresult.add(rslt);
+ if (tosend.size() > 1)
+ {
+ checkResultForQueries(rslt, tosend, nextFetch, proxy);
+ }
}
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
}
- else
+ }
+
+ /**
+ * 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)
+ {
+ boolean success = false;
+ try
{
- showErrorMessage("Error retrieving " + textArea.getText() + " from "
- + database.getSelectedItem());
+ if (aresult != null)
+ {
+ try
+ {
+ // give the server a chance to breathe
+ Thread.sleep(5);
+ } catch (Exception e)
+ {
+ //
+ }
+ }
+
+ AlignmentI indres = null;
+ try
+ {
+ indres = proxy.getSequenceRecords(accession);
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning(
+ "fetching " + accession + " from " + proxy.getDbName(),
+ oome, this);
+ }
+ if (indres != null)
+ {
+ aresultq.add(accession);
+ aresult.add(indres);
+ success = true;
+ }
+ } catch (Exception e)
+ {
+ Cache.log.info("Error retrieving " + accession + " from "
+ + proxy.getDbName(), e);
}
+ return success;
+ }
- return null;
+ /**
+ * 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)
+ {
+ 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++)
+ {
+ if (rs[r] != null)
+ {
+ List found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
+ accId);
+ if (!found.isEmpty())
+ {
+ rfound = true;
+ break;
+ }
+ }
+ }
+ if (!rfound)
+ {
+ nextFetch.add(q);
+ }
+ }
}
/**
@@ -763,74 +799,62 @@ public class SequenceFetcher extends JPanel implements Runnable
}
AlignmentI parseResult(AlignmentI al, String title,
- String currentFileFormat)
+ 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)
{
- af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT
- // FORMAT FOR
- // NON-FormatAdapter Sourced
- // Alignments?
+ af.currentFileFormat = currentFileFormat;
}
- if (title == null)
- {
- title = getDefaultRetrievalTitle();
- }
- SequenceFeature[] sfs = null;
- List alsqs;
- synchronized (alsqs = al.getSequences())
+ List alsqs = al.getSequences();
+ synchronized (alsqs)
{
for (SequenceI sq : alsqs)
{
- if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
+ if (sq.getFeatures().hasFeatures())
{
- if (sfs.length > 0)
- {
- af.setShowSeqFeatures(true);
- break;
- }
+ af.setShowSeqFeatures(true);
+ break;
}
-
}
}
+
+ if (preferredFeatureColours != null)
+ {
+ 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(MessageManager.getString("label.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)
{
}
}
else
{
- for (int i = 0; i < al.getHeight(); i++)
- {
- alignFrame.viewport.getAlignment().addSequence(
- al.getSequenceAt(i)); // this
- // also
- // creates
- // dataset
- // sequence
- // entries
- }
- alignFrame.viewport.setEndSeq(alignFrame.viewport.getAlignment()
- .getHeight());
- alignFrame.viewport.getAlignment().getWidth();
- alignFrame.viewport.firePropertyChange("alignment", null,
- alignFrame.viewport.getAlignment().getSequences());
+ alignFrame.viewport.addAlignment(al, title);
}
}
return al;
@@ -844,9 +868,49 @@ public class SequenceFetcher extends JPanel implements Runnable
@Override
public void run()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
- MessageManager.getString("label.error_retrieving_data"), JOptionPane.WARNING_MESSAGE);
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), 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;
+ }
}