X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=1b1e76577485cab08941e9f966afa91616b4ae02;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=35bc29ad3eae2d53cc4d84987f425e87f7f354b3;hpb=10b903bf6b22d53e8920091efb2145d6b6a677ba;p=jalview.git diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index 35bc29a..1b1e765 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,28 +20,80 @@ */ 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; @@ -62,6 +114,8 @@ 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 @@ -77,9 +131,11 @@ public class SequenceFetcher extends JPanel implements Runnable { if (guiWindow != null) { - guiWindow.setProgressBar( - MessageManager.getString("status.waiting_sequence_database_fetchers_init"), - 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. @@ -96,9 +152,11 @@ public class SequenceFetcher extends JPanel implements Runnable } if (guiWindow != null) { - guiWindow.setProgressBar( - MessageManager.getString("status.waiting_sequence_database_fetchers_init"), - Thread.currentThread().hashCode()); + guiWindow + .setProgressBar( + MessageManager + .getString("status.waiting_sequence_database_fetchers_init"), + Thread.currentThread().hashCode()); } } if (sfetch == null @@ -115,7 +173,8 @@ public class SequenceFetcher extends JPanel implements Runnable */ if (guiWindow != null) { - guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"), + guiWindow.setProgressBar(MessageManager + .getString("status.init_sequence_database_fetchers"), Thread.currentThread().hashCode()); } dasRegistry = jalview.bin.Cache.getDasSourceRegistry(); @@ -124,8 +183,7 @@ public class SequenceFetcher extends JPanel implements Runnable jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher(); if (guiWindow != null) { - guiWindow.setProgressBar(MessageManager.getString("status.init_sequence_database_fetchers"), - Thread.currentThread().hashCode()); + guiWindow.setProgressBar(null, Thread.currentThread().hashCode()); } lastDasSourceRegistry = (dasRegistry.getDasRegistryURL() + dasRegistry .getLocalSourceString()).hashCode(); @@ -136,9 +194,11 @@ 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() @@ -147,9 +207,9 @@ 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 { @@ -161,8 +221,10 @@ public class SequenceFetcher extends JPanel implements Runnable JOptionPane .showInternalMessageDialog( Desktop.desktop, - MessageManager.getString("warn.couldnt_create_sequence_fetcher_client"), - MessageManager.getString("label.couldnt_create_sequence_fetcher"), + MessageManager + .getString("warn.couldnt_create_sequence_fetcher_client"), + MessageManager + .getString("label.couldnt_create_sequence_fetcher"), JOptionPane.ERROR_MESSAGE); } }); @@ -219,7 +281,9 @@ public class SequenceFetcher extends JPanel implements Runnable private String getFrameTitle() { - return ((alignFrame == null) ? MessageManager.getString("label.new_sequence_fetcher") : MessageManager.getString("label.additional_sequence_fetcher")); + return ((alignFrame == null) ? MessageManager + .getString("label.new_sequence_fetcher") : MessageManager + .getString("label.additional_sequence_fetcher")); } private void jbInit() throws Exception @@ -283,7 +347,9 @@ public class SequenceFetcher extends JPanel implements Runnable public void keyPressed(KeyEvent e) { if (e.getKeyCode() == KeyEvent.VK_ENTER) + { ok_actionPerformed(); + } } }); jPanel3.setLayout(borderLayout1); @@ -298,39 +364,24 @@ public class SequenceFetcher extends JPanel implements Runnable 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(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) + 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); @@ -347,6 +398,43 @@ 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; @@ -365,42 +453,6 @@ 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) { try @@ -493,8 +545,13 @@ public class SequenceFetcher extends JPanel implements Runnable try { // update status - guiWindow.setProgressBar(MessageManager.formatMessage("status.fetching_sequence_queries_from", new String[]{Integer.valueOf(nqueries).toString(),proxy.getDbName()}), Thread - .currentThread().hashCode()); + 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) { @@ -691,11 +748,15 @@ public class SequenceFetcher extends JPanel implements Runnable presultTitle.add(titl); } } - guiWindow.setProgressBar(MessageManager.getString("status.finshed_querying"), Thread.currentThread() + guiWindow.setProgressBar(MessageManager + .getString("status.finshed_querying"), Thread.currentThread() .hashCode()); } - guiWindow.setProgressBar((presult.size() > 0) ? MessageManager.getString("status.parsing_results") - : MessageManager.getString("status.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) { @@ -730,7 +791,7 @@ public class SequenceFetcher extends JPanel implements Runnable AlignmentI parseResult(String result, String title) { String format = new IdentifyFile().Identify(result, "Paste"); - Alignment sequences = null; + AlignmentI sequences = null; if (FormatAdapter.isValidFormat(format)) { sequences = null; @@ -772,6 +833,10 @@ 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, @@ -784,17 +849,13 @@ 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) { @@ -821,21 +882,7 @@ 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; @@ -855,4 +902,14 @@ public class SequenceFetcher extends JPanel implements Runnable } }); } + + public IProgressIndicator getProgressIndicator() + { + return progressIndicator; + } + + public void setProgressIndicator(IProgressIndicator progressIndicator) + { + this.progressIndicator = progressIndicator; + } }