-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
-\r
-\r
-public class Finder extends GFinder\r
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- JInternalFrame frame;\r
- String searchString;\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
- {\r
- textfield.requestFocus();\r
- }\r
- });\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
- frame.setClosed(true);\r
- }catch(Exception ex){ }\r
-\r
- }\r
-\r
- void doSearch(boolean findAll)\r
- {\r
- searchString = textfield.getText().toUpperCase();\r
-\r
- ArrayList searchResults = new ArrayList();\r
- int [] allResults = null;\r
-\r
- Sequence seq;\r
- String item;\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.getSelection().size()>0)\r
- seq = (Sequence)(av.getSelection().sequenceAt(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
-\r
- //av.getAlignment().getSequenceAt(seq).findPosition(res)\r
- }catch(NumberFormatException ex){}\r
-\r
-\r
- while( !found && seqIndex<av.getAlignment().getHeight())\r
- {\r
- seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);\r
-\r
- if(av.getSelection().size()>0 && !av.getSelection().contains(seq))\r
- {\r
- // if a selection has been made, only search within that selection\r
- seqIndex++;\r
- resIndex=0;\r
- continue;\r
- }\r
-\r
- item = seq.getSequence();\r
-\r
- for(int r = resIndex; r<item.length(); r++)\r
- {\r
- if(item.indexOf(searchString,r)>-1)\r
- {\r
- resIndex = item.indexOf(searchString,r);\r
- searchResults.add( Integer.toString(seqIndex) );\r
- searchResults.add( Integer.toString( resIndex) );\r
- searchResults.add( Integer.toString( (resIndex+searchString.length()-1) ) );\r
- if(!findAll)\r
- {\r
- // thats enough, break and display the result\r
- found = true;\r
- resIndex++;\r
- break;\r
- }\r
- }\r
- }\r
- if(!found)\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
- }\r
- }\r
-\r
- if(searchResults.size()>0)\r
- {\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
- }\r
- else\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Finished searching", null,\r
- 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
-\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Finder
+ extends GFinder
+{
+ AlignViewport av;
+ AlignmentPanel ap;
+ JInternalFrame frame;
+ int seqIndex = 0;
+ int resIndex = 0;
+
+ SearchResults searchResults;
+
+ /**
+ * Creates a new Finder object.
+ *
+ * @param av DOCUMENT ME!
+ * @param ap DOCUMENT ME!
+ * @param f DOCUMENT ME!
+ */
+ public Finder()
+ {
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame, "Find", 340, 110);
+
+ textfield.requestFocus();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void findNext_actionPerformed(ActionEvent e)
+ {
+ if (getFocusedViewport())
+ {
+ doSearch(false);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void findAll_actionPerformed(ActionEvent e)
+ {
+ if (getFocusedViewport())
+ {
+ resIndex = 0;
+ seqIndex = 0;
+ doSearch(true);
+ }
+ }
+
+ boolean getFocusedViewport()
+ {
+ JInternalFrame frame = Desktop.desktop.getAllFrames()[1];
+
+ if (frame != null && frame instanceof AlignFrame)
+ {
+ av = ( (AlignFrame) frame).viewport;
+ ap = ( (AlignFrame) frame).alignPanel;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void createNewGroup_actionPerformed(ActionEvent e)
+ {
+ JLabel label = new JLabel("Enter name of new sequence feature");
+ JTextField textinput = new JTextField(textfield.getText());
+ JPanel panel = new JPanel(new BorderLayout());
+ panel.add(label, BorderLayout.NORTH);
+ panel.add(textinput, BorderLayout.SOUTH);
+
+ SequenceI[] seqs = new SequenceI[searchResults.getSize()];
+ SequenceFeature[] features = new SequenceFeature[searchResults.getSize()];
+
+ for (int i = 0; i < searchResults.getSize(); i++)
+ {
+ seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
+
+ features[i] = new SequenceFeature(textinput.getText(),
+ "Search Results", null,
+ searchResults.getResultStart(i),
+ searchResults.getResultEnd(i),
+ "Search Results");
+ }
+
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .createNewFeatures(seqs, features))
+ {
+ ap.alignFrame.showSeqFeatures.setSelected(true);
+ av.setShowSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param findAll DOCUMENT ME!
+ */
+ void doSearch(boolean findAll)
+ {
+ createNewGroup.setEnabled(false);
+
+ String searchString = textfield.getText().trim();
+
+ if (searchString.length() < 1)
+ {
+ 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
+ jalview.analysis.Finder finder = new jalview.analysis.Finder(av.alignment,
+ av.getSelectionGroup(), seqIndex, resIndex);
+ finder.setCaseSensitive(caseSensitive.isSelected());
+ finder.setFindAll(findAll);
+
+ finder.find(searchString); // returns true if anything was actually found
+
+ seqIndex = finder.getSeqIndex();
+ resIndex = finder.getResIndex();
+
+ searchResults = finder.getSearchResults(); // find(regex, caseSensitive.isSelected(), )
+ Vector idMatch = finder.getIdMatch();
+ // set or reset the GUI
+ if ( (searchResults.getSize() == 0) && (idMatch.size() > 0))
+ {
+ ap.idPanel.highlightSearchResults(idMatch);
+ }
+
+ int resultSize = searchResults.getSize();
+
+ if (searchResults.getSize() > 0)
+ {
+ createNewGroup.setEnabled(true);
+ }
+ else
+ {
+ searchResults = null;
+ }
+
+ // 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 (!findAll && resultSize == 0)
+ {
+ JOptionPane.showInternalMessageDialog(this, "Finished searching",
+ null,
+ JOptionPane.INFORMATION_MESSAGE);
+ resIndex = 0;
+ seqIndex = 0;
+ }
+
+ if (findAll)
+ {
+ String message = resultSize + " matches found.";
+ JOptionPane.showInternalMessageDialog(this, message, null,
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff