-package jalview.gui;\r
-\r
-import jalview.jbgui.GFinder;\r
-import jalview.datamodel.*;\r
-import java.awt.event.*;\r
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-import java.util.*;\r
-import java.awt.*;\r
-\r
-public class Finder extends GFinder\r
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- JInternalFrame frame;\r
- SuperGroup searchGroup;\r
- Vector searchResults;\r
-\r
- int seqIndex = 0;\r
- int resIndex = 0;\r
- public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)\r
- {\r
- this.av = av;\r
- this.ap = ap;\r
- frame = f;\r
-\r
- // all a big pain, but we need to wait until the frame is visible before the textfield can\r
- // obtain the focus/////////////////////////\r
- frame.addInternalFrameListener(new InternalFrameAdapter()\r
- {\r
- public void internalFrameOpened(InternalFrameEvent evt)\r
- {\r
- SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- { textfield.requestFocus(); }\r
- });\r
- }\r
-\r
- public void internalFrameClosing(InternalFrameEvent evt)\r
- {\r
- cancel_actionPerformed(null);\r
- }\r
-});\r
-\r
- }\r
-\r
- public void textfield_actionPerformed(ActionEvent e)\r
- {\r
- doSearch(false);\r
- }\r
-\r
- public void findNext_actionPerformed(ActionEvent e)\r
- {\r
- doSearch(false);\r
- }\r
-\r
- public void findAll_actionPerformed(ActionEvent e)\r
- {\r
- resIndex=0;\r
- seqIndex=0;\r
- doSearch(true);\r
- }\r
-\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults( null );\r
- ap.idPanel.highlightSearchResults( null );\r
- // frame.setClosed(true);\r
- }catch(Exception ex){ }\r
- }\r
-\r
-\r
- public void createNewGroup_actionPerformed(ActionEvent e)\r
- {\r
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
- Color [] newColors = new Color[24];\r
- for(int i=0; i<24; i++)\r
- newColors[i] = new Color(60,160,115);\r
-\r
- ucs.setColourScheme(newColors);\r
- String searchString = textfield.getText();\r
-\r
- searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
-\r
-\r
- for(int i=0; i<searchResults.size(); i+=3)\r
- {\r
- // its possible edits may have occurred since search was performed\r
- // account for this here\r
-\r
- SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );\r
- int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;\r
- int endRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;\r
-\r
- SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes );\r
- sg.addSequence(seq);\r
- av.alignment.addGroup(sg);\r
- searchGroup.addGroup( sg );\r
-\r
- }\r
-\r
- ap.av.alignment.addSuperGroup(searchGroup);\r
- ap.highlightSearchResults( null );\r
- }\r
-\r
-\r
- void doSearch(boolean findAll)\r
- {\r
- createNewGroup.setEnabled(false);\r
-\r
- String searchString = textfield.getText().toUpperCase();\r
-\r
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
-\r
- searchResults = new Vector();\r
- int [] allResults = null;\r
-\r
- Sequence seq;\r
- String item=null;\r
- boolean found = false;\r
-\r
- ////// is the searchString a residue number?\r
- try{\r
- int res = Integer.parseInt(searchString);\r
- found = true;\r
-\r
- if(av.getSelectionGroup().getSize()>0)\r
- seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));\r
- else\r
- seq = (Sequence)av.getAlignment().getSequenceAt(0);\r
-\r
- searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );\r
- searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
- searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
-\r
- }catch(NumberFormatException ex){}\r
- ///////////////////////////////////////////////\r
-\r
-\r
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
- Color [] newColors = new Color[24];\r
- for(int i=0; i<24; i++)\r
- newColors[i] = new Color(60,160,115);\r
-\r
- ucs.setColourScheme(newColors);\r
-\r
- searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
-\r
- int end = av.alignment.getHeight();\r
-\r
- SequenceGroup selection = av.getSelectionGroup();\r
- if(selection!=null)\r
- if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))\r
- selection = null;\r
-\r
- while( !found && seqIndex<end)\r
- {\r
- seq = (Sequence)av.alignment.getSequenceAt(seqIndex);\r
-\r
-\r
- if(selection!=null && !selection.sequences.contains(seq))\r
- {\r
- seqIndex++;\r
- resIndex=0;\r
- continue;\r
- }\r
-\r
- item = seq.getSequence().toUpperCase();\r
-\r
- if(selection!=null && selection.getEndRes()<av.alignment.getWidth())\r
- item = item.substring(0, selection.getEndRes()+1);\r
-\r
- ///Shall we ignore gaps????\r
- StringBuffer noGaps = new StringBuffer();\r
- int insertCount=0;\r
- Vector spaces = new Vector();\r
-\r
- for (int j=0; j < item.length(); j++)\r
- {\r
-\r
- if(!jalview.util.Comparison.isGap(item.charAt(j)))\r
- {\r
- noGaps.append(item.charAt(j));\r
- spaces.add(new Integer(insertCount));\r
- }\r
- else\r
- insertCount++;\r
- }\r
-\r
-\r
-\r
- for(int r = resIndex; r<noGaps.length(); r++)\r
- {\r
-\r
- if( regex.searchFrom( noGaps.toString(), r ) )\r
- {\r
- resIndex = regex.matchedFrom();\r
- if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())\r
- continue;\r
-\r
- searchResults.add( Integer.toString( seqIndex) );\r
-\r
- int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );\r
- int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );\r
-\r
- searchResults.addElement( sres+"" );\r
- searchResults.addElement( eres+"" );\r
-\r
- if(!findAll)\r
- {\r
- // thats enough, break and display the result\r
- found = true;\r
- resIndex++;\r
- break;\r
- }\r
-\r
- r=resIndex;\r
- }\r
- }\r
- if(!found)\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
- }\r
- }\r
-\r
-\r
- Vector idMatch = new Vector();\r
- for(int id = 0; id<av.alignment.getHeight(); id++)\r
- {\r
- if( regex.search( av.alignment.getSequenceAt(id).getName() ) )\r
- idMatch.add( av.alignment.getSequenceAt(id) );\r
- }\r
-\r
- if(searchResults.size()==0 && idMatch.size()>0)\r
- ap.idPanel.highlightSearchResults( idMatch );\r
-\r
-\r
- if(searchResults.size()>0)\r
- {\r
- allResults = new int[searchResults.size()];\r
- for(int i=0; i<searchResults.size(); i++)\r
- allResults[i] = Integer.parseInt(searchResults.get(i).toString());\r
-\r
- createNewGroup.setEnabled(true);\r
- }\r
- else\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);\r
- resIndex=0;\r
- seqIndex=0;\r
- }\r
-\r
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults( allResults );\r
-\r
- if (findAll)\r
- {\r
- String message = (searchResults.size()/3) + " matches found.";\r
- JOptionPane.showInternalMessageDialog(this, message, null,\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- }\r
-\r
-}\r
+/*
+ * 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.
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+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 java.awt.Dimension;
+import java.awt.Graphics;
+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.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.KeyStroke;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+/**
+ * Performs the menu option for searching the alignment, for the next or all
+ * matches. If matches are found, they are highlighted, and the user has the
+ * option to create a new feature on the alignment for the matched positions.
+ *
+ * Searches can be for a simple base sequence, or may use a regular expression.
+ * Any gaps are ignored.
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Finder extends GFinder
+{
+ private static final int MIN_WIDTH = 350;
+
+ private static final int MIN_HEIGHT = 120;
+
+ private static final int MY_HEIGHT = 150;
+
+ private static final int MY_WIDTH = 400;
+
+ private AlignViewportI av;
+
+ private AlignmentPanel ap;
+
+ private JInternalFrame frame;
+
+ /*
+ * Finder agent per viewport searched
+ */
+ private Map<AlignViewportI, FinderI> finders;
+
+ private SearchResultsI searchResults;
+
+ /**
+ * Constructor given an associated alignment panel. Constructs and displays an
+ * internal frame where the user can enter a search string.
+ *
+ * @param alignPanel
+ */
+ public Finder(AlignmentPanel alignPanel)
+ {
+ av = alignPanel.getAlignViewport();
+ ap = alignPanel;
+ finders = new HashMap<>();
+ 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"),
+ MY_WIDTH, MY_HEIGHT);
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ searchBox.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();
+ }
+ });
+ }
+
+ /**
+ * Performs the 'Find Next' action on the alignment panel with focus
+ */
+ @Override
+ public void findNext_actionPerformed()
+ {
+ if (getFocusedViewport())
+ {
+ doSearch(false);
+ }
+ }
+
+ /**
+ * Performs the 'Find All' action on the alignment panel with focus
+ */
+ @Override
+ public void findAll_actionPerformed()
+ {
+ if (getFocusedViewport())
+ {
+ doSearch(true);
+ }
+ }
+
+ /**
+ * 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. Also sets the 'ignore hidden' checkbox disabled if the viewport
+ * has no hidden columns.
+ *
+ * @return false if no alignment window was found
+ */
+ boolean getFocusedViewport()
+ {
+ if (Desktop.desktop == null)
+ {
+ if (ap != null && av != null)
+ {
+ return true;
+ }
+ // we aren't in a desktop environment, so give up now.
+ return false;
+ }
+ // now checks further down the window stack to fix bug
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36008
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ for (int f = 0; f < frames.length; f++)
+ {
+ JInternalFrame alignFrame = frames[f];
+ if (alignFrame != null && alignFrame instanceof AlignFrame
+ && !alignFrame.isIcon())
+ {
+ av = ((AlignFrame) alignFrame).viewport;
+ ap = ((AlignFrame) alignFrame).alignPanel;
+ ignoreHidden.setEnabled(av.hasHiddenColumns());
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Opens a dialog that allows the user to create sequence features for the
+ * find match results.
+ */
+ @Override
+ public void createFeatures_actionPerformed()
+ {
+ List<SequenceI> seqs = new ArrayList<>();
+ List<SequenceFeature> features = new ArrayList<>();
+
+ String searchString = searchBox.getEditor().getItem().toString().trim();
+ String desc = "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);
+ }
+ }
+
+ /**
+ * 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 doFindAll
+ */
+ void doSearch(boolean doFindAll)
+ {
+ createFeatures.setEnabled(false);
+
+ String searchString = searchBox.getUserInput().trim();
+
+ if (isInvalidSearchString(searchString))
+ {
+ return;
+ }
+ // TODO: extend finder to match descriptions, features and annotation, and
+ // other stuff
+ // TODO: add switches to control what is searched - sequences, IDS,
+ // descriptions, features
+ 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);
+ }
+
+ boolean isCaseSensitive = caseSensitive.isSelected();
+ boolean doSearchDescription = searchDescription.isSelected();
+ boolean skipHidden = ignoreHidden.isSelected();
+ if (doFindAll)
+ {
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+ skipHidden);
+ }
+ else
+ {
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+ skipHidden);
+ }
+
+ searchResults = finder.getSearchResults();
+ List<SequenceI> idMatch = finder.getIdMatches();
+ ap.getIdPanel().highlightSearchResults(idMatch);
+
+ if (searchResults.isEmpty())
+ {
+ searchResults = null;
+ }
+ else
+ {
+ createFeatures.setEnabled(true);
+ }
+
+ ap.highlightSearchResults(searchResults);
+ // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or
+ // 'SelectRegion' selection
+ if (idMatch.isEmpty() && searchResults == null)
+ {
+ JvOptionPane.showInternalMessageDialog(this,
+ MessageManager.getString("label.finished_searching"), null,
+ JvOptionPane.INFORMATION_MESSAGE);
+ }
+ else
+ {
+ if (doFindAll)
+ {
+ // then we report the matches that were found
+ String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+ : "";
+ if (searchResults != null)
+ {
+ if (idMatch.size() > 0 && searchResults.getCount() > 0)
+ {
+ message += " and ";
+ }
+ message += searchResults.getCount()
+ + " subsequence matches found.";
+ }
+ JvOptionPane.showInternalMessageDialog(this, message, null,
+ JvOptionPane.INFORMATION_MESSAGE);
+ }
+ }
+ searchBox.updateCache();
+ }
+
+ /**
+ * Displays an error dialog, and answers false, if the search string is
+ * invalid, else answers true.
+ *
+ * @param searchString
+ * @return
+ */
+ protected boolean isInvalidSearchString(String searchString)
+ {
+ String error = getSearchValidationError(searchString);
+ if (error == null)
+ {
+ return false;
+ }
+ JvOptionPane.showInternalMessageDialog(this, error,
+ MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
+ JvOptionPane.ERROR_MESSAGE);
+ return true;
+ }
+
+ /**
+ * Returns an error message string if the search string is invalid, else
+ * returns null.
+ *
+ * Currently validation is limited to checking the string is not empty, and is
+ * a valid regular expression (simple searches for base sub-sequences will
+ * pass this test). Additional validations may be added in future if the
+ * search syntax is expanded.
+ *
+ * @param searchString
+ * @return
+ */
+ protected String getSearchValidationError(String searchString)
+ {
+ String error = null;
+ if (searchString == null || searchString.length() == 0)
+ {
+ error = MessageManager.getString("label.invalid_search");
+ }
+ try
+ {
+ Pattern.compile(searchString);
+ } catch (PatternSyntaxException e)
+ {
+ error = MessageManager.getString("error.invalid_regex") + ": "
+ + e.getDescription();
+ }
+ return error;
+ }
+
+ protected void closeAction()
+ {
+ frame.setVisible(false);
+ frame.dispose();
+ searchBox.persistCache();
+ if (getFocusedViewport())
+ {
+ ap.alignFrame.requestFocus();
+ }
+ }
+
+ @Override
+ protected void paintComponent(Graphics g)
+ {
+ /*
+ * enable 'hidden regions' option only if
+ * 'top' viewport has hidden columns
+ */
+ getFocusedViewport();
+ super.paintComponent(g);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff