X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=a1693f713aca74250886bfe13b5a233d9dbc6827;hb=0a2ec403c08a1747b7e876f00f468867f8329d36;hp=1cbe6ab2a09a9639ace0692822b338241dab7123;hpb=ca87cef11606dd9b1ba66222cea87e000e556817;p=jalview.git diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java index 1cbe6ab..a1693f7 100755 --- a/src/jalview/gui/Finder.java +++ b/src/jalview/gui/Finder.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.api.AlignViewportI; +import jalview.api.FinderI; import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; @@ -29,14 +30,12 @@ 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; @@ -45,6 +44,7 @@ import javax.swing.JComponent; import javax.swing.JInternalFrame; import javax.swing.JLayeredPane; import javax.swing.KeyStroke; +import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; /** @@ -75,26 +75,24 @@ public class Finder extends GFinder private JInternalFrame frame; /* - * sequence and column position of the last match, - * as currently used, and saved for each viewport + * Finder agent per viewport searched */ - private int seqIndex = 0; - - private int resIndex = -1; - - Map seqIndices; - - Map resIndices; + 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; } /** @@ -108,14 +106,13 @@ public class Finder extends GFinder { av = viewport; ap = alignPanel; - seqIndices = new HashMap<>(); - resIndices = new HashMap<>(); - focusfixed = true; + finders = new HashMap<>(); + focusfixed = viewport != null; frame = new JInternalFrame(); frame.setContentPane(this); frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener( - new javax.swing.event.InternalFrameAdapter() + new InternalFrameAdapter() { @Override public void internalFrameClosing(InternalFrameEvent e) @@ -125,9 +122,8 @@ public class Finder extends GFinder }); addEscapeHandler(); Desktop.addInternalFrame(frame, MessageManager.getString("label.find"), - MY_WIDTH, MY_HEIGHT); - frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); - searchBox.requestFocus(); + true, MY_WIDTH, MY_HEIGHT, true, true); + searchBox.getComponent().requestFocus(); } /** @@ -148,12 +144,10 @@ public class Finder extends GFinder } /** - * Performs the 'Find Next' action. - * - * @param e + * Performs the 'Find Next' action on the alignment panel with focus */ @Override - public void findNext_actionPerformed(ActionEvent e) + public void findNext_actionPerformed() { if (getFocusedViewport()) { @@ -162,27 +156,18 @@ public class Finder extends GFinder } /** - * Performs the 'Find All' action. - * - * @param e + * Performs the 'Find All' action on the alignment panel with focus */ @Override - public void findAll_actionPerformed(ActionEvent e) + 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 @@ -211,21 +196,6 @@ public class Finder extends GFinder { 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; } } @@ -234,15 +204,19 @@ public class Finder extends GFinder /** * Opens a dialog that allows the user to create sequence features for the - * find match results. + * find match results */ @Override public void createFeatures_actionPerformed() { + if (searchResults.isEmpty()) + { + return; // shouldn't happen + } List seqs = new ArrayList<>(); List features = new ArrayList<>(); - String searchString = searchBox.getEditor().getItem().toString().trim(); + String searchString = searchBox.getUserInput(); String desc = "Search Results"; /* @@ -252,22 +226,11 @@ public class Finder extends GFinder for (SearchResultMatchI match : searchResults.getResults()) { seqs.add(match.getSequence().getDatasetSequence()); - features.add(new SequenceFeature(searchString, desc, - match - .getStart(), match.getEnd(), desc)); + 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); - } + new FeatureEditor(ap, seqs, features, true).showDialog(); } /** @@ -280,7 +243,7 @@ public class Finder extends GFinder { createFeatures.setEnabled(false); - String searchString = searchBox.getUserInput().trim(); + String searchString = searchBox.getUserInput(); if (isInvalidSearchString(searchString)) { @@ -290,22 +253,29 @@ 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(doFindAll); - - finder.find(searchString); + 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); + } - seqIndex = finder.getSeqIndex(); - resIndex = finder.getResIndex(); - seqIndices.put(av, seqIndex); - resIndices.put(av, resIndex); + boolean isCaseSensitive = caseSensitive.isSelected(); + boolean doSearchDescription = searchDescription.isSelected(); + if (doFindAll) + { + finder.findAll(searchString, isCaseSensitive, doSearchDescription); + } + else + { + finder.findNext(searchString, isCaseSensitive, doSearchDescription); + } searchResults = finder.getSearchResults(); - Vector idMatch = finder.getIdMatch(); + List idMatch = finder.getIdMatches(); ap.getIdPanel().highlightSearchResults(idMatch); if (searchResults.isEmpty()) @@ -317,6 +287,8 @@ public class Finder extends GFinder createFeatures.setEnabled(true); } + searchBox.updateCache(); + ap.highlightSearchResults(searchResults); // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or // 'SelectRegion' selection @@ -324,9 +296,7 @@ public class Finder extends GFinder { JvOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"), null, - JvOptionPane.INFORMATION_MESSAGE); - resIndex = -1; - seqIndex = 0; + JvOptionPane.PLAIN_MESSAGE); } else { @@ -345,12 +315,9 @@ public class Finder extends GFinder + " subsequence matches found."; } JvOptionPane.showInternalMessageDialog(this, message, null, - JvOptionPane.INFORMATION_MESSAGE); - resIndex = -1; - seqIndex = 0; + JvOptionPane.PLAIN_MESSAGE); } } - searchBox.updateCache(); } /**