/*
- * 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 2.8.2)
+ * 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.
- *
+ * 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 javax.swing.tree.MutableTreeNode;
-import javax.swing.tree.TreeModel;
-
-import jalview.datamodel.*;
-import jalview.io.*;
+import jalview.datamodel.Alignment;
+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
{
if (guiWindow != null)
{
guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
+ MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
Thread.currentThread().hashCode());
}
// initting happening on another thread - so wait around to see if it
if (guiWindow != null)
{
guiWindow.setProgressBar(
- "Waiting for Sequence Database Fetchers to initialise",
+ MessageManager.getString("status.waiting_sequence_database_fetchers_init"),
Thread.currentThread().hashCode());
}
}
*/
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",
+ guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"),
Thread.currentThread().hashCode());
}
lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry
Thread sf = new Thread(new Runnable()
{
+ @Override
public void run()
{
if (getSequenceFetcherSingleton(guiWindow) != null)
{
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",
+ MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"),
+ MessageManager.getString("label.couldnt_create_sequence_fetcher"),
JOptionPane.ERROR_MESSAGE);
}
});
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
public void actionPerformed(ActionEvent e)
{
ok_actionPerformed();
}
});
- clear.setText("Clear");
+ clear.setText(MessageManager.getString("action.clear"));
clear.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
clear_actionPerformed();
}
});
- example.setText("Example");
+ example.setText(MessageManager.getString("label.example"));
example.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
example_actionPerformed();
}
});
- close.setText("Close");
+ close.setText(MessageManager.getString("action.close"));
close.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
close_actionPerformed(e);
textArea.setLineWrap(true);
textArea.addKeyListener(new KeyAdapter()
{
+ @Override
public void keyPressed(KeyEvent e)
{
if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
ok_actionPerformed();
+ }
}
});
jPanel3.setLayout(borderLayout1);
database.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent e)
{
- DbSourceProxy db = null;
try
{
databaseButt.setText(database.getSelectedItem()
+ database.getSelectedSources().size()
+ " others)" : ""));
String eq = database.getExampleQueries();
- dbeg.setText("Example query: " + eq);
- replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
+ 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("");
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);
}
+ @Override
public void run()
{
String error = "";
return;
}
// 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()
try
{
// update status
- guiWindow.setProgressBar("Fetching " + nqueries
- + " sequence queries from " + proxy.getDbName(), Thread
+ 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)
{
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++)
{
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)
{
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");
}
title = getDefaultRetrievalTitle();
}
SequenceFeature[] sfs = null;
- for (Enumeration sq = al.getSequences().elements(); sq
- .hasMoreElements();)
+ List<SequenceI> alsqs;
+ synchronized (alsqs = al.getSequences())
{
- if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence()
- .getSequenceFeatures()) != null)
+ for (SequenceI sq : alsqs)
{
- if (sfs.length > 0)
+ if ((sfs = sq.getSequenceFeatures()) != null)
{
- af.setShowSeqFeatures(true);
- break;
+ if (sfs.length > 0)
+ {
+ af.setShowSeqFeatures(true);
+ break;
+ }
}
- }
+ }
}
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
{
resetDialog();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop, error,
- "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);
+ MessageManager.getString("label.error_retrieving_data"),
+ JOptionPane.WARNING_MESSAGE);
}
});
}
git://source.jalview.org / jalview.git / blobdiff