-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Finder extends GFinder\r
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- JInternalFrame frame;\r
- int seqIndex = 0;\r
- int resIndex = 0;\r
-\r
- SearchResults searchResults;\r
-\r
- /**\r
- * Creates a new Finder object.\r
- *\r
- * @param av DOCUMENT ME!\r
- * @param ap DOCUMENT ME!\r
- * @param f DOCUMENT ME!\r
- */\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void findNext_actionPerformed(ActionEvent e)\r
- {\r
- doSearch(false);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void findAll_actionPerformed(ActionEvent e)\r
- {\r
- resIndex = 0;\r
- seqIndex = 0;\r
- doSearch(true);\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void createNewGroup_actionPerformed(ActionEvent e)\r
- {\r
- JLabel label = new JLabel("Enter name of new sequence feature");\r
- JTextField textinput = new JTextField(textfield.getText());\r
- JPanel panel = new JPanel(new BorderLayout());\r
- panel.add(label, BorderLayout.NORTH);\r
- panel.add(textinput, BorderLayout.SOUTH);\r
-\r
- int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
- panel, "New Sequence Feature Name",\r
- JOptionPane.OK_CANCEL_OPTION );\r
-\r
- if(reply != JOptionPane.OK_OPTION)\r
- return;\r
-\r
- for (int i = 0; i < searchResults.getSize(); i ++ )\r
- {\r
- SequenceI seq = searchResults.getResultSequence(i);\r
-\r
- SequenceFeature sf = new SequenceFeature(textinput.getText(),\r
- "Search Results", null,\r
- searchResults.getResultStart(i),\r
- searchResults.getResultEnd(i));\r
-\r
- ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
- textinput.getText(), new Color(60,160,115));\r
-\r
- seq.getDatasetSequence().addSequenceFeature(sf);\r
- }\r
-\r
- ap.alignFrame.showSeqFeatures.setSelected(true);\r
- av.setShowSequenceFeatures(true);\r
- ap.highlightSearchResults(null);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param findAll DOCUMENT ME!\r
- */\r
- void doSearch(boolean findAll)\r
- {\r
- createNewGroup.setEnabled(false);\r
-\r
- String searchString = textfield.getText().toUpperCase().trim();\r
- if(searchString.length()<1)\r
- return;\r
-\r
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
-\r
- searchResults = new SearchResults();\r
-\r
- Sequence seq;\r
- String item = null;\r
- boolean found = false;\r
-\r
- ////// is the searchString a residue number?\r
- try\r
- {\r
- int res = Integer.parseInt(searchString);\r
- found = true;\r
- if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)\r
- {\r
- seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
- }\r
- else\r
- {\r
- seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
- }\r
-\r
- searchResults.addResult(seq, res, res);\r
- }\r
- catch (NumberFormatException ex)\r
- {\r
- }\r
-\r
- ///////////////////////////////////////////////\r
-\r
- int end = av.alignment.getHeight();\r
-\r
- SequenceGroup selection = av.getSelectionGroup();\r
-\r
- if (selection != null)\r
- {\r
- if ((selection.getSize() < 1) ||\r
- ((selection.getEndRes() - selection.getStartRes()) < 2))\r
- {\r
- selection = null;\r
- }\r
- }\r
-\r
- while (!found && (seqIndex < end))\r
- {\r
- seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
-\r
- if ((selection != null) && !selection.sequences.contains(seq))\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
-\r
- continue;\r
- }\r
-\r
- item = seq.getSequence().toUpperCase();\r
-\r
- if ((selection != null) &&\r
- (selection.getEndRes() < av.alignment.getWidth()-1))\r
- {\r
- item = item.substring(0, selection.getEndRes() + 1);\r
- }\r
-\r
- ///Shall we ignore gaps????\r
- StringBuffer noGapsSB = new StringBuffer();\r
- int insertCount = 0;\r
- Vector spaces = new Vector();\r
-\r
- for (int j = 0; j < item.length(); j++)\r
- {\r
- if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
- {\r
- noGapsSB.append(item.charAt(j));\r
- spaces.add(new Integer(insertCount));\r
- }\r
- else\r
- {\r
- insertCount++;\r
- }\r
- }\r
-\r
- String noGaps = noGapsSB.toString();\r
-\r
- for (int r = resIndex; r < noGaps.length(); r++)\r
- {\r
-\r
- if (regex.searchFrom(noGaps, r))\r
- {\r
- resIndex = regex.matchedFrom();\r
-\r
- if ((selection != null) &&\r
- ((resIndex +\r
- Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))\r
- {\r
- continue;\r
- }\r
-\r
-\r
- int sres = seq.findPosition(resIndex +\r
- Integer.parseInt(spaces.elementAt(resIndex)\r
- .toString()));\r
- int eres = seq.findPosition(regex.matchedTo() - 1 +\r
- Integer.parseInt(spaces.elementAt(regex.matchedTo() -\r
- 1).toString()));\r
-\r
- searchResults.addResult(seq, sres, eres);\r
-\r
- if (!findAll)\r
- {\r
- // thats enough, break and display the result\r
- found = true;\r
- resIndex++;\r
-\r
- break;\r
- }\r
-\r
- r = resIndex;\r
- }\r
- else\r
- {\r
- break;\r
- }\r
- }\r
-\r
- if (!found)\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
- }\r
- }\r
-\r
- Vector idMatch = new Vector();\r
-\r
- for (int id = 0; id < av.alignment.getHeight(); id++)\r
- {\r
- if (regex.search(av.alignment.getSequenceAt(id).getName()))\r
- {\r
- idMatch.add(av.alignment.getSequenceAt(id));\r
- }\r
- }\r
-\r
- if ((searchResults.getSize() == 0) && (idMatch.size() > 0))\r
- {\r
- ap.idPanel.highlightSearchResults(idMatch);\r
- }\r
-\r
-\r
- int resultSize = searchResults.getSize();\r
-\r
- if (searchResults.getSize() > 0)\r
- createNewGroup.setEnabled(true);\r
- else\r
- searchResults = null;\r
-\r
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults(searchResults);\r
-\r
- if(!findAll && resultSize==0)\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Finished searching",\r
- null, JOptionPane.INFORMATION_MESSAGE);\r
- resIndex = 0;\r
- seqIndex = 0;\r
- }\r
-\r
- if (findAll)\r
- {\r
- String message = resultSize + " matches found.";\r
- JOptionPane.showInternalMessageDialog(this, message, null,\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+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 = -1;
+
+ SearchResults searchResults;
+
+ /**
+ * Creates a new Finder object.
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param ap
+ * DOCUMENT ME!
+ * @param f
+ * DOCUMENT ME!
+ */
+ public Finder()
+ {
+ this(null, null);
+ focusfixed = false;
+ }
+
+ public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
+ {
+ av = viewport;
+ ap = alignPanel;
+ focusfixed = true;
+ 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 = -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
+ *
+ * @return false if no alignment window was found
+ */
+ boolean getFocusedViewport()
+ {
+ if (focusfixed || 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 frame = frames[f];
+ 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)
+ {
+ 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(textfield.getText().trim(),
+ "Search Results", null, searchResults.getResultStart(i),
+ searchResults.getResultEnd(i), "Search Results");
+ }
+
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
+ features, true, ap))
+ {
+ ap.alignFrame.showSeqFeatures.setSelected(true);
+ av.setShowSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+ }
+
+ /**
+ * incrementally search the alignment
+ *
+ * @param findAll
+ * true means find all results and raise a dialog box
+ */
+ 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();
+ boolean haveResults = false;
+ // set or reset the GUI
+ if ((idMatch.size() > 0))
+ {
+ haveResults = true;
+ ap.idPanel.highlightSearchResults(idMatch);
+ }
+ else
+ {
+ ap.idPanel.highlightSearchResults(null);
+ }
+
+ if (searchResults.getSize() > 0)
+ {
+ haveResults = true;
+ 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 (!haveResults)
+ {
+ JOptionPane.showInternalMessageDialog(this, "Finished searching",
+ null, JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
+ }
+
+ if (findAll)
+ {
+ String message = (idMatch.size() > 0) ? "" + idMatch.size() + " IDs"
+ : "";
+ if (searchResults != null)
+ {
+ if (idMatch.size() > 0 && searchResults.getSize() > 0)
+ {
+ message += " and ";
+ }
+ message += searchResults.getSize() + " subsequence matches found.";
+ }
+ JOptionPane.showInternalMessageDialog(this, message, null,
+ JOptionPane.INFORMATION_MESSAGE);
+ resIndex = -1;
+ seqIndex = 0;
+ }
+
+ }
+}
git://source.jalview.org / jalview.git / blobdiff