X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=a4d7ad0a824713414d616d4203f9ecc726fe6f0e;hb=a2926674d871f1e06760b677c4cc3b171d72902b;hp=d417136892d32c198733c9e6e88ad2c554247ae3;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index d417136..a4d7ad0 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 2.9.0b1) - * Copyright (C) 2015 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. * @@ -20,16 +20,23 @@ */ package jalview.gui; -import jalview.datamodel.SearchResults; +import jalview.api.AlignViewportI; +import jalview.api.FinderI; +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.Vector; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; @@ -37,8 +44,9 @@ 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.InternalFrameAdapter; +import javax.swing.event.InternalFrameEvent; /** * Performs the menu option for searching the alignment, for the next or all @@ -53,29 +61,39 @@ import javax.swing.KeyStroke; */ 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; - AlignmentViewport 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; + /* + * Finder agent per viewport searched + */ + private Map finders; + + private SearchResultsI searchResults; + + /* + * true if we only search a given alignment view + */ + private boolean focusfixed; /** - * Creates a new Finder object with no associated viewport or panel. + * Creates a new Finder object with no associated viewport or panel. Each Find + * or Find Next action will act on whichever viewport has focus at the time. */ public Finder() { this(null, null); - focusfixed = false; } /** @@ -89,15 +107,25 @@ public class Finder extends GFinder { av = viewport; ap = alignPanel; - focusfixed = true; + finders = new HashMap<>(); + focusfixed = viewport != null; frame = new JInternalFrame(); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); + frame.addInternalFrameListener( + new InternalFrameAdapter() + { + @Override + public void internalFrameClosing(InternalFrameEvent e) + { + closeAction(); + } + }); addEscapeHandler(); Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), - WIDTH, HEIGHT); - - textfield.requestFocus(); + MY_WIDTH, MY_HEIGHT); + frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); + searchBox.requestFocus(); } /** @@ -105,32 +133,23 @@ public class Finder extends GFinder */ private void addEscapeHandler() { - getRootPane().getInputMap(JComponent.WHEN_IN_FOCUSED_WINDOW).put( - KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0), "Cancel"); + 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) { - escapeActionPerformed(); + closeAction(); } }); } /** - * Close the panel on Escape key press + * Performs the 'Find Next' action on the alignment panel with focus */ - protected void escapeActionPerformed() - { - setVisible(false); - frame.dispose(); - } - - /** - * Performs the 'Find Next' action. - * - * @param e - */ - public void findNext_actionPerformed(ActionEvent e) + @Override + public void findNext_actionPerformed() { if (getFocusedViewport()) { @@ -139,26 +158,18 @@ public class Finder extends GFinder } /** - * Performs the 'Find All' action. - * - * @param e + * Performs the 'Find All' action on the alignment panel with focus */ - public void findAll_actionPerformed(ActionEvent e) + @Override + public void findAll_actionPerformed() { if (getFocusedViewport()) { - resIndex = -1; - seqIndex = 0; doSearch(true); } } /** - * do we only search a given alignment view ? - */ - private boolean focusfixed; - - /** * if !focusfixed and not in a desktop environment, checks that av and ap are * valid. Otherwise, gets the topmost alignment window and sets av and ap * accordingly @@ -181,11 +192,12 @@ 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; return true; } } @@ -193,29 +205,37 @@ 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.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); @@ -226,13 +246,13 @@ 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)) { @@ -242,63 +262,56 @@ public class Finder extends GFinder // other stuff // TODO: add switches to control what is searched - sequences, IDS, // descriptions, features - jalview.analysis.Finder finder = new jalview.analysis.Finder( - av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex); - finder.setCaseSensitive(caseSensitive.isSelected()); - finder.setIncludeDescription(searchDescription.isSelected()); - - finder.setFindAll(findAll); - - finder.find(searchString); // returns true if anything was actually found - - seqIndex = finder.getSeqIndex(); - resIndex = finder.getResIndex(); + FinderI finder = finders.get(av); + if (finder == null) + { + /* + * first time we've searched this viewport + */ + finder = new jalview.analysis.Finder(av); + finders.put(av, finder); + } - searchResults = finder.getSearchResults(); // find(regex, - // caseSensitive.isSelected(), ) - Vector idMatch = finder.getIdMatch(); - boolean haveResults = false; - // set or reset the GUI - if ((idMatch.size() > 0)) + boolean isCaseSensitive = caseSensitive.isSelected(); + boolean doSearchDescription = searchDescription.isSelected(); + if (doFindAll) { - haveResults = true; - ap.getIdPanel().highlightSearchResults(idMatch); + finder.findAll(searchString, isCaseSensitive, doSearchDescription); } else { - ap.getIdPanel().highlightSearchResults(null); + finder.findNext(searchString, isCaseSensitive, doSearchDescription); } - if (searchResults.getSize() > 0) + searchResults = finder.getSearchResults(); + List idMatch = finder.getIdMatches(); + ap.getIdPanel().highlightSearchResults(idMatch); + + 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); - resIndex = -1; - seqIndex = 0; + JvOptionPane.INFORMATION_MESSAGE); } 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) @@ -308,13 +321,11 @@ public class Finder extends GFinder message += searchResults.getSize() + " subsequence matches found."; } - JOptionPane.showInternalMessageDialog(this, message, null, - JOptionPane.INFORMATION_MESSAGE); - resIndex = -1; - seqIndex = 0; + JvOptionPane.showInternalMessageDialog(this, message, null, + JvOptionPane.INFORMATION_MESSAGE); } } - + searchBox.updateCache(); } /** @@ -331,9 +342,9 @@ 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; } @@ -366,4 +377,15 @@ public class Finder extends GFinder } return error; } + + protected void closeAction() + { + frame.setVisible(false); + frame.dispose(); + searchBox.persistCache(); + if (getFocusedViewport()) + { + ap.alignFrame.requestFocus(); + } + } }