/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
* This file is part of Jalview.
- *
+ *
* Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * 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 <http://www.gnu.org/licenses/>.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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 jalview.datamodel.*;
-import jalview.io.*;
+import jalview.api.FeatureSettingsModelI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
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;
public class SequenceFetcher extends JPanel implements Runnable
{
- // ASequenceFetcher sfetch;
+ 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;
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
{
if (guiWindow != null)
{
- guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
- Thread.currentThread().hashCode());
+ 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.
}
if (guiWindow != null)
{
- guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
- Thread.currentThread().hashCode());
+ guiWindow
+ .setProgressBar(
+ MessageManager
+ .getString("status.waiting_sequence_database_fetchers_init"),
+ Thread.currentThread().hashCode());
}
}
if (sfetch == null
*/
if (guiWindow != null)
{
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ guiWindow.setProgressBar(MessageManager
+ .getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
dasRegistry = jalview.bin.Cache.getDasSourceRegistry();
jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
if (guiWindow != null)
{
- guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
- Thread.currentThread().hashCode());
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
}
lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
.getLocalSourceString()).hashCode();
return sfetch;
}
+ private IProgressIndicator progressIndicator;
+
public SequenceFetcher(IProgressIndicator guiIndic)
{
- final IProgressIndicator guiWindow = guiIndic;
+ this.progressIndicator = guiIndic;
final SequenceFetcher us = this;
// launch initialiser thread
Thread sf = new Thread(new Runnable()
@Override
public void run()
{
- if (getSequenceFetcherSingleton(guiWindow) != null)
+ if (getSequenceFetcherSingleton(progressIndicator) != null)
{
- us.initGui(guiWindow);
+ us.initGui(progressIndicator);
}
else
{
JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Could not create the sequence fetcher client. Check error logs for details.",
- "Couldn't create SequenceFetcher",
+ MessageManager
+ .getString("warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager
+ .getString("label.couldnt_create_sequence_fetcher"),
JOptionPane.ERROR_MESSAGE);
}
});
/**
* called by thread spawned by constructor
- *
+ *
* @param guiWindow
*/
private void initGui(IProgressIndicator guiWindow)
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
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("Separate multiple accession ids with semi colon \";\"");
+ 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("Replace commas with semi-colons");
- ok.setText("OK");
+ replacePunctuation.setText(MessageManager
+ .getString("label.replace_commas_semicolons"));
+ ok.setText(MessageManager.getString("action.ok"));
ok.addActionListener(new ActionListener()
{
@Override
ok_actionPerformed();
}
});
- clear.setText("Clear");
+ clear.setText(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
@Override
}
});
- example.setText("Example");
+ example.setText(MessageManager.getString("label.example"));
example.addActionListener(new ActionListener()
{
@Override
example_actionPerformed();
}
});
- close.setText("Close");
+ close.setText(MessageManager.getString("action.close"));
close.addActionListener(new ActionListener()
{
@Override
public void keyPressed(KeyEvent e)
{
if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
ok_actionPerformed();
+ }
}
});
jPanel3.setLayout(borderLayout1);
databaseButt.setFont(JvSwingUtils.getLabelFont());
database.addActionListener(new ActionListener()
{
-
@Override
public void actionPerformed(ActionEvent e)
{
- try
+ debounceTrap++;
+ String currentSelection = database.getSelectedItem();
+ if (!currentSelection.equalsIgnoreCase("pdb"))
{
- databaseButt.setText(database.getSelectedItem()
- + (database.getSelectedSources().size() > 1 ? " (and "
- + database.getSelectedSources().size()
- + " others)" : ""));
- String eq = database.getExampleQueries();
- dbeg.setText("Example query: " + 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)
+ otherSourceAction();
+ }
+ if (currentSelection.equalsIgnoreCase("pdb")
+ && (database.action == KeyEvent.VK_ENTER || ((debounceTrap % 2) == 0)))
{
- dbeg.setText("");
- replacePunctuation.setEnabled(true);
+ pdbSourceAction();
}
- jPanel2.repaint();
+ database.action = -1;
}
});
+
dbeg.setText("");
jPanel2.add(databaseButt, java.awt.BorderLayout.NORTH);
jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
}
+ 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;
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();
-
- 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
public void ok_actionPerformed()
{
- database.setEnabled(false);
+ databaseButt.setEnabled(false);
+ example.setEnabled(false);
textArea.setEnabled(false);
ok.setEnabled(false);
close.setEnabled(false);
private void resetDialog()
{
- database.setEnabled(true);
+ databaseButt.setEnabled(true);
+ example.setEnabled(true);
textArea.setEnabled(true);
ok.setEnabled(true);
close.setEnabled(true);
resetDialog();
return;
}
+ // TODO: Refactor to GUI independent code and write tests.
// indicate if successive sources should be merged into one alignment.
- boolean addToLast=false;
+ boolean addToLast = false;
ArrayList<String> aresultq = new ArrayList<String>(), presultTitle = new ArrayList<String>();
ArrayList<AlignmentI> presult = new ArrayList<AlignmentI>(), aresult = new ArrayList<AlignmentI>();
Iterator<DbSourceProxy> proxies = database.getSelectedSources()
.split(";"));
Iterator<String> en = Arrays.asList(new String[0]).iterator();
int nqueries = qries.length;
+
+ FeatureSettingsModelI preferredFeatureColours = null;
while (proxies.hasNext() && (en.hasNext() || nextfetch.size() > 0))
{
if (!en.hasNext() && nextfetch.size() > 0)
try
{
// update status
- guiWindow.setProgressBar("Fetching " + nqueries
- + " sequence queries from " + proxy.getDbName(), Thread
- .currentThread().hashCode());
- isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
+ guiWindow
+ .setProgressBar(MessageManager.formatMessage(
+ "status.fetching_sequence_queries_from",
+ new String[] {
+ Integer.valueOf(nqueries).toString(),
+ proxy.getDbName() }), Thread.currentThread()
+ .hashCode());
+ isAliSource = proxy.isAlignmentSource();
if (proxy.getAccessionSeparator() == null)
{
while (en.hasNext())
{
DBRefEntry dbr = new DBRefEntry(), found[] = null;
dbr.setSource(proxy.getDbSource());
+ dbr.setVersion(null);
+ String accId = proxy.getAccessionIdFromQuery(q);
+ dbr.setAccessionId(accId);
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)
+ if (rs[r] != null)
{
- rfound = true;
- rs[r] = null;
- continue;
+ found = DBRefUtils.searchRefs(rs[r].getDBRefs(), accId);
+ if (found != null && found.length > 0)
+ {
+ rfound = true;
+ rs[r] = null;
+ }
}
}
if (!rfound)
// 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)
{
- addToLast=false;
+ addToLast = false;
// new window for each result
while (aresult.size() > 0)
{
}
else
{
- String titl=null;
- if (addToLast && presult.size()>0)
+ String titl = null;
+ if (addToLast && presult.size() > 0)
{
- ar=presult.remove(presult.size()-1);
- titl=presultTitle.remove(presultTitle.size()-1);
+ ar = presult.remove(presult.size() - 1);
+ titl = presultTitle.remove(presultTitle.size() - 1);
}
// concatenate all results in one window
while (aresult.size() > 0)
}
;
}
- addToLast=true;
+ 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());
sb.append("Didn't retrieve the following "
+ (nextfetch.size() == 1 ? "query" : nextfetch.size()
+ " queries") + ": \n");
- int l = sb.length(),lr=0;
+ int l = sb.length(), lr = 0;
for (String s : nextfetch)
{
if (l != sb.length())
{
sb.append("; ");
}
- if (lr-sb.length()>40)
+ if (lr - sb.length() > 40)
{
sb.append("\n");
}
resetDialog();
}
- AlignmentI parseResult(String result, String title)
- {
- String format = new IdentifyFile().Identify(result, "Paste");
- Alignment 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
*/
}
AlignmentI parseResult(AlignmentI al, String title,
- String currentFileFormat)
+ String 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,
// Alignments?
}
- if (title == null)
- {
- title = getDefaultRetrievalTitle();
- }
SequenceFeature[] sfs = null;
List<SequenceI> alsqs;
synchronized (alsqs = al.getSequences())
{
for (SequenceI sq : alsqs)
{
- if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null)
+ if ((sfs = sq.getSequenceFeatures()) != null)
{
if (sfs.length > 0)
{
}
}
+
+ if (preferredFeatureColours != null)
+ {
+ af.viewport.applyFeaturesStyle(preferredFeatureColours);
+ }
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
{
}
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;
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
- "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.error_retrieving_data"),
+ JOptionPane.WARNING_MESSAGE);
}
});
}
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
}