X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FFinder.java;h=1cbe6ab2a09a9639ace0692822b338241dab7123;hb=ca87cef11606dd9b1ba66222cea87e000e556817;hp=cc91ebfbecd90eeebbf3ffc6e74486c61302f5b5;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index cc91ebf..1cbe6ab 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * 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. * @@ -20,20 +20,32 @@ */ package jalview.gui; -import jalview.datamodel.SearchResults; +import jalview.api.AlignViewportI; +import jalview.datamodel.SearchResultMatchI; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.jbgui.GFinder; import jalview.util.MessageManager; +import jalview.viewmodel.AlignmentViewport; +import java.awt.Dimension; import java.awt.event.ActionEvent; +import java.awt.event.KeyEvent; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; import java.util.Vector; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; +import javax.swing.AbstractAction; +import javax.swing.JComponent; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; -import javax.swing.JOptionPane; +import javax.swing.KeyStroke; +import javax.swing.event.InternalFrameEvent; /** * Performs the menu option for searching the alignment, for the next or all @@ -48,21 +60,33 @@ import javax.swing.JOptionPane; */ public class Finder extends GFinder { - private static final int HEIGHT = 110; + private static final int MIN_WIDTH = 350; - private static final int WIDTH = 340; + private static final int MIN_HEIGHT = 120; - AlignViewport av; + private static final int MY_HEIGHT = 120; - AlignmentPanel ap; + private static final int MY_WIDTH = 400; - JInternalFrame frame; + private AlignViewportI av; - int seqIndex = 0; + private AlignmentPanel ap; - int resIndex = -1; + private JInternalFrame frame; - SearchResults searchResults; + /* + * sequence and column position of the last match, + * as currently used, and saved for each viewport + */ + private int seqIndex = 0; + + private int resIndex = -1; + + Map seqIndices; + + Map resIndices; + + private SearchResultsI searchResults; /** * Creates a new Finder object with no associated viewport or panel. @@ -80,18 +104,47 @@ public class Finder extends GFinder * @param viewport * @param alignPanel */ - public Finder(AlignViewport viewport, AlignmentPanel alignPanel) + public Finder(AlignmentViewport viewport, AlignmentPanel alignPanel) { av = viewport; ap = alignPanel; + seqIndices = new HashMap<>(); + resIndices = new HashMap<>(); focusfixed = true; frame = new JInternalFrame(); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); + frame.addInternalFrameListener( + new javax.swing.event.InternalFrameAdapter() + { + @Override + public void internalFrameClosing(InternalFrameEvent e) + { + closeAction(); + } + }); + addEscapeHandler(); Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), - WIDTH, HEIGHT); + MY_WIDTH, MY_HEIGHT); + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); + searchBox.requestFocus(); + } - textfield.requestFocus(); + /** + * Add a handler for the Escape key when the window has focus + */ + private void addEscapeHandler() + { + getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW) + .put(KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel"); + getRootPane().getActionMap().put("Cancel", new AbstractAction() + { + @Override + public void actionPerformed(ActionEvent e) + { + closeAction(); + } + }); } /** @@ -99,6 +152,7 @@ public class Finder extends GFinder * * @param e */ + @Override public void findNext_actionPerformed(ActionEvent e) { if (getFocusedViewport()) @@ -112,6 +166,7 @@ public class Finder extends GFinder * * @param e */ + @Override public void findAll_actionPerformed(ActionEvent e) { if (getFocusedViewport()) @@ -150,11 +205,27 @@ public class Finder extends GFinder JInternalFrame[] frames = Desktop.desktop.getAllFrames(); for (int f = 0; f < frames.length; f++) { - JInternalFrame frame = frames[f]; - if (frame != null && frame instanceof AlignFrame) + JInternalFrame alignFrame = frames[f]; + if (alignFrame != null && alignFrame instanceof AlignFrame + && !alignFrame.isIcon()) { - av = ((AlignFrame) frame).viewport; - ap = ((AlignFrame) frame).alignPanel; + av = ((AlignFrame) alignFrame).viewport; + ap = ((AlignFrame) alignFrame).alignPanel; + + /* + * restore search position if switching to a + * panel where we have previously searched + */ + seqIndex = 0; + resIndex = -1; + if (seqIndices.containsKey(av)) + { + seqIndex = seqIndices.get(av).intValue(); + } + if (resIndices.containsKey(av)) + { + resIndex = resIndices.get(av).intValue(); + } return true; } } @@ -162,29 +233,37 @@ public class Finder extends GFinder } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Opens a dialog that allows the user to create sequence features for the + * find match results. */ - public void createNewGroup_actionPerformed(ActionEvent e) + @Override + public void createFeatures_actionPerformed() { - SequenceI[] seqs = new SequenceI[searchResults.getSize()]; - SequenceFeature[] features = new SequenceFeature[searchResults - .getSize()]; + List seqs = new ArrayList<>(); + List features = new ArrayList<>(); - for (int i = 0; i < searchResults.getSize(); i++) - { - seqs[i] = searchResults.getResultSequence(i).getDatasetSequence(); + String searchString = searchBox.getEditor().getItem().toString().trim(); + String desc = "Search Results"; - features[i] = new SequenceFeature(textfield.getText().trim(), - "Search Results", null, searchResults.getResultStart(i), - searchResults.getResultEnd(i), "Search Results"); + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ + for (SearchResultMatchI match : searchResults.getResults()) + { + seqs.add(match.getSequence().getDatasetSequence()); + features.add(new SequenceFeature(searchString, desc, + match + .getStart(), match.getEnd(), desc)); } - if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) { + /* + * ensure feature display is turned on to show the new features, + * and remove them as highlighted regions + */ ap.alignFrame.showSeqFeatures.setSelected(true); av.setShowSequenceFeatures(true); ap.highlightSearchResults(null); @@ -195,13 +274,13 @@ public class Finder extends GFinder * Search the alignment for the next or all matches. If 'all matches', a * dialog is shown with the number of sequence ids and subsequences matched. * - * @param findAll + * @param doFindAll */ - void doSearch(boolean findAll) + void doSearch(boolean doFindAll) { - createNewGroup.setEnabled(false); + createFeatures.setEnabled(false); - String searchString = textfield.getText().trim(); + String searchString = searchBox.getUserInput().trim(); if (isInvalidSearchString(searchString)) { @@ -214,58 +293,48 @@ public class Finder extends GFinder jalview.analysis.Finder finder = new jalview.analysis.Finder( av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex); finder.setCaseSensitive(caseSensitive.isSelected()); - finder.setFindAll(findAll); + finder.setIncludeDescription(searchDescription.isSelected()); + + finder.setFindAll(doFindAll); - finder.find(searchString); // returns true if anything was actually found + finder.find(searchString); seqIndex = finder.getSeqIndex(); resIndex = finder.getResIndex(); + seqIndices.put(av, seqIndex); + resIndices.put(av, resIndex); - searchResults = finder.getSearchResults(); // find(regex, - // caseSensitive.isSelected(), ) - Vector idMatch = finder.getIdMatch(); - boolean haveResults = false; - // set or reset the GUI - if ((idMatch.size() > 0)) - { - haveResults = true; - ap.idPanel.highlightSearchResults(idMatch); - } - else - { - ap.idPanel.highlightSearchResults(null); - } + searchResults = finder.getSearchResults(); + Vector idMatch = finder.getIdMatch(); + ap.getIdPanel().highlightSearchResults(idMatch); - if (searchResults.getSize() > 0) + if (searchResults.isEmpty()) { - haveResults = true; - createNewGroup.setEnabled(true); + searchResults = null; } else { - searchResults = null; + createFeatures.setEnabled(true); } - // if allResults is null, this effectively switches displaySearch flag in - // seqCanvas ap.highlightSearchResults(searchResults); // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or // 'SelectRegion' selection - if (!haveResults) + if (idMatch.isEmpty() && searchResults == null) { - JOptionPane.showInternalMessageDialog(this, + JvOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"), null, - JOptionPane.INFORMATION_MESSAGE); + JvOptionPane.INFORMATION_MESSAGE); resIndex = -1; seqIndex = 0; } else { - if (findAll) + if (doFindAll) { // then we report the matches that were found - String message = (idMatch.size() > 0) ? "" + idMatch.size() - + " IDs" : ""; + String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs" + : ""; if (searchResults != null) { if (idMatch.size() > 0 && searchResults.getSize() > 0) @@ -275,13 +344,13 @@ public class Finder extends GFinder message += searchResults.getSize() + " subsequence matches found."; } - JOptionPane.showInternalMessageDialog(this, message, null, - JOptionPane.INFORMATION_MESSAGE); + JvOptionPane.showInternalMessageDialog(this, message, null, + JvOptionPane.INFORMATION_MESSAGE); resIndex = -1; seqIndex = 0; } } - + searchBox.updateCache(); } /** @@ -298,9 +367,9 @@ public class Finder extends GFinder { return false; } - JOptionPane.showInternalMessageDialog(this, error, + JvOptionPane.showInternalMessageDialog(this, error, MessageManager.getString("label.invalid_search"), // $NON-NLS-1$ - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); return true; } @@ -333,4 +402,15 @@ public class Finder extends GFinder } return error; } + + protected void closeAction() + { + frame.setVisible(false); + frame.dispose(); + searchBox.persistCache(); + if (getFocusedViewport()) + { + ap.alignFrame.requestFocus(); + } + } }