X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=72a7167febb2c5e9b8d46e66fc943cb897e98858;hb=330289271fe2239a59fa318d6b2b19fdd319f8a4;hp=f9779ada427ba3b7cbd84eae73f7956516576bdf;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index f9779ad..72a7167 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -1,40 +1,62 @@ /* - * 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 . + * + * 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 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.*; -import java.awt.event.*; +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.*; +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; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.util.DBRefUtils; -import jalview.ws.dbsources.das.api.DasSourceRegistryI; -import jalview.ws.seqfetcher.DbSourceProxy; -import java.awt.BorderLayout; - public class SequenceFetcher extends JPanel implements Runnable { // ASequenceFetcher sfetch; @@ -74,7 +96,7 @@ 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 @@ -93,7 +115,7 @@ 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()); } } @@ -111,7 +133,7 @@ public class SequenceFetcher extends JPanel implements Runnable */ 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(); @@ -120,7 +142,7 @@ public class SequenceFetcher extends JPanel implements Runnable 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 @@ -157,8 +179,8 @@ public class SequenceFetcher extends JPanel implements Runnable 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); } }); @@ -215,8 +237,7 @@ public class SequenceFetcher extends JPanel implements Runnable 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 @@ -227,13 +248,15 @@ public class SequenceFetcher extends JPanel implements Runnable 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 @@ -242,7 +265,7 @@ public class SequenceFetcher extends JPanel implements Runnable ok_actionPerformed(); } }); - clear.setText("Clear"); + clear.setText(MessageManager.getString("action.clear")); clear.addActionListener(new ActionListener() { @Override @@ -252,7 +275,7 @@ public class SequenceFetcher extends JPanel implements Runnable } }); - example.setText("Example"); + example.setText(MessageManager.getString("label.example")); example.addActionListener(new ActionListener() { @Override @@ -261,7 +284,7 @@ public class SequenceFetcher extends JPanel implements Runnable example_actionPerformed(); } }); - close.setText("Close"); + close.setText(MessageManager.getString("action.close")); close.addActionListener(new ActionListener() { @Override @@ -278,7 +301,9 @@ public class SequenceFetcher extends JPanel implements Runnable public void keyPressed(KeyEvent e) { if (e.getKeyCode() == KeyEvent.VK_ENTER) + { ok_actionPerformed(); + } } }); jPanel3.setLayout(borderLayout1); @@ -304,7 +329,9 @@ public class SequenceFetcher extends JPanel implements Runnable + database.getSelectedSources().size() + " others)" : "")); String eq = database.getExampleQueries(); - dbeg.setText("Example query: " + eq); + dbeg.setText(MessageManager.formatMessage( + "label.example_query_param", new String[] + { eq })); boolean enablePunct = !(eq != null && eq.indexOf(",") > -1); for (DbSourceProxy dbs : database.getSelectedSources()) { @@ -406,7 +433,8 @@ public class SequenceFetcher extends JPanel implements Runnable public void ok_actionPerformed() { - database.setEnabled(false); + databaseButt.setEnabled(false); + example.setEnabled(false); textArea.setEnabled(false); ok.setEnabled(false); close.setEnabled(false); @@ -417,7 +445,8 @@ public class SequenceFetcher extends JPanel implements Runnable private void resetDialog() { - database.setEnabled(true); + databaseButt.setEnabled(true); + example.setEnabled(true); textArea.setEnabled(true); ok.setEnabled(true); close.setEnabled(true); @@ -484,8 +513,7 @@ public class SequenceFetcher extends JPanel implements Runnable 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) @@ -683,11 +711,11 @@ public class SequenceFetcher extends JPanel implements Runnable presultTitle.add(titl); } } - guiWindow.setProgressBar("Finished querying", Thread.currentThread() + 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) { @@ -764,6 +792,10 @@ public class SequenceFetcher extends JPanel implements Runnable if (al != null && al.getHeight() > 0) { + if (title == null) + { + title = getDefaultRetrievalTitle(); + } if (alignFrame == null) { AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, @@ -776,10 +808,6 @@ public class SequenceFetcher extends JPanel implements Runnable // Alignments? } - if (title == null) - { - title = getDefaultRetrievalTitle(); - } SequenceFeature[] sfs = null; List alsqs; synchronized (alsqs = al.getSequences()) @@ -800,7 +828,8 @@ public class SequenceFetcher extends JPanel implements Runnable 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 { @@ -812,21 +841,7 @@ public class SequenceFetcher extends JPanel implements Runnable } 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; @@ -841,7 +856,8 @@ public class SequenceFetcher extends JPanel implements Runnable public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, error, - "Error Retrieving Data", JOptionPane.WARNING_MESSAGE); + MessageManager.getString("label.error_retrieving_data"), + JOptionPane.WARNING_MESSAGE); } }); }