X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=d9200288ee0befcc890b5466bdaee5f0856b53a9;hb=15a454d6de78056c057ab64c5932dda788da979a;hp=94c4f6651f51acfed4ee1027b80181ae4643f732;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 94c4f66..d920028 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -1,45 +1,99 @@ /* - * 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.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 { - // 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; @@ -60,6 +114,7 @@ public class SequenceFetcher extends JPanel implements Runnable private static Thread initingThread = null; + int debounceTrap = 0; /** * Blocking method that initialises and returns the shared instance of the * SequenceFetcher client @@ -76,7 +131,7 @@ 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 @@ -95,7 +150,7 @@ 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()); } } @@ -113,7 +168,7 @@ 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(); @@ -122,8 +177,7 @@ public class SequenceFetcher extends JPanel implements Runnable jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher(); if (guiWindow != null) { - guiWindow.setProgressBar("Initialising Sequence Database Fetchers", - Thread.currentThread().hashCode()); + guiWindow.setProgressBar(null, Thread.currentThread().hashCode()); } lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry .getLocalSourceString()).hashCode(); @@ -134,9 +188,10 @@ public class SequenceFetcher extends JPanel implements Runnable 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() @@ -145,9 +200,9 @@ public class SequenceFetcher extends JPanel implements Runnable @Override public void run() { - if (getSequenceFetcherSingleton(guiWindow) != null) + if (getSequenceFetcherSingleton(progressIndicator) != null) { - us.initGui(guiWindow); + us.initGui(progressIndicator); } else { @@ -159,8 +214,8 @@ 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); } }); @@ -217,8 +272,7 @@ 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 @@ -229,13 +283,15 @@ 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 @@ -244,7 +300,7 @@ public class SequenceFetcher extends JPanel implements Runnable ok_actionPerformed(); } }); - clear.setText("Clear"); + clear.setText(MessageManager.getString("action.clear")); clear.addActionListener(new ActionListener() { @Override @@ -254,7 +310,7 @@ public class SequenceFetcher extends JPanel implements Runnable } }); - example.setText("Example"); + example.setText(MessageManager.getString("label.example")); example.addActionListener(new ActionListener() { @Override @@ -263,7 +319,7 @@ public class SequenceFetcher extends JPanel implements Runnable example_actionPerformed(); } }); - close.setText("Close"); + close.setText(MessageManager.getString("action.close")); close.addActionListener(new ActionListener() { @Override @@ -280,7 +336,9 @@ public class SequenceFetcher extends JPanel implements Runnable public void keyPressed(KeyEvent e) { if (e.getKeyCode() == KeyEvent.VK_ENTER) + { ok_actionPerformed(); + } } }); jPanel3.setLayout(borderLayout1); @@ -295,35 +353,21 @@ public class SequenceFetcher extends JPanel implements Runnable 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("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); + debounceTrap++; + String currentSelection = database.getSelectedItem(); - } catch (Exception ex) + if (!currentSelection.equalsIgnoreCase("pdb")) { - dbeg.setText(""); - replacePunctuation.setEnabled(true); + otherSourceAction(); } - jPanel2.repaint(); + if (currentSelection.equalsIgnoreCase("pdb") && ((debounceTrap % 2) == 0)) + { + pdbSourceAction(); + } + } }); dbeg.setText(""); @@ -342,6 +386,44 @@ public class SequenceFetcher extends JPanel implements Runnable } + 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; @@ -360,41 +442,7 @@ public class SequenceFetcher extends JPanel implements Runnable 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) { @@ -488,8 +536,7 @@ 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) @@ -687,11 +734,11 @@ 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) { @@ -768,6 +815,10 @@ 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, @@ -780,17 +831,13 @@ public class SequenceFetcher extends JPanel implements Runnable // Alignments? } - if (title == null) - { - title = getDefaultRetrievalTitle(); - } SequenceFeature[] sfs = null; List alsqs; synchronized (alsqs = al.getSequences()) { for (SequenceI sq : alsqs) { - if ((sfs = (sq).getDatasetSequence().getSequenceFeatures()) != null) + if ((sfs = sq.getSequenceFeatures()) != null) { if (sfs.length > 0) { @@ -804,7 +851,8 @@ 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 { @@ -816,21 +864,7 @@ 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; @@ -845,8 +879,19 @@ public class SequenceFetcher extends JPanel implements Runnable public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, error, - MessageManager.getString("label.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; + } }