-/*
- * 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.appletgui;
-
-import jalview.bin.JalviewLite;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-import jalview.viewmodel.AlignmentViewport;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import java.awt.Font;
-import javax.swing.JFrame;
-import java.awt.GridLayout;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import java.awt.Rectangle;
-import javax.swing.JTextField;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.util.Vector;
-
-public class Finder extends JPanel implements ActionListener
-{
- AlignmentViewport av;
-
- AlignmentPanel ap;
-
- JFrame frame;
-
- SearchResults searchResults;
-
- int seqIndex = 0;
-
- int resIndex = -1;
-
- public Finder(final AlignmentPanel ap)
- {
- try
- {
- jbInit();
-
- } catch (Exception e)
- {
- e.printStackTrace();
- }
-
- this.av = ap.av;
- this.ap = ap;
- frame = new JFrame();
- frame.add(this);
- JalviewLite.addFrame(frame,
- MessageManager.getString("action.find"), 340, 120);
- frame.repaint();
- frame.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- ap.highlightSearchResults(null);
- }
- });
- textfield.requestFocus();
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- if (evt.getSource() == textfield)
- {
- doSearch(false);
- }
-
- else if (evt.getSource() == findNext)
- {
- doSearch(false);
- }
-
- else if (evt.getSource() == findAll)
- {
- resIndex = -1;
- seqIndex = 0;
- doSearch(true);
- }
- else if (evt.getSource() == createNewGroup)
- {
- createNewGroup_actionPerformed();
- }
- }
-
- public void createNewGroup_actionPerformed()
- {
- 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);
-
- 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.sequenceFeatures.setState(true);
- av.setShowSequenceFeatures(true);
- ap.highlightSearchResults(null);
- }
- }
-
- void doSearch(boolean findAll)
- {
- if (ap.av.applet.currentAlignFrame != null)
- {
- ap = ap.av.applet.currentAlignFrame.alignPanel;
- av = ap.av;
- }
- createNewGroup.setEnabled(false);
- 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);
-
- String searchString = textfield.getText();
-
- finder.find(searchString);
- seqIndex = finder.getSeqIndex();
- resIndex = finder.getResIndex();
- searchResults = finder.getSearchResults();
- 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)
- {
- ap.alignFrame.statusBar.setText(MessageManager
- .getString("label.finished_searching"));
- resIndex = -1;
- seqIndex = 0;
- }
- else
- {
- if (findAll)
- {
- String message = (idMatch.size() > 0) ? "" + idMatch.size()
- + " IDs" : "";
- if (idMatch.size() > 0 && searchResults != null
- && searchResults.getSize() > 0)
- {
- message += " and ";
- }
- if (searchResults != null)
- {
- message += searchResults.getSize() + " subsequence matches.";
- }
- ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.search_results", new String[]
- { searchString, message }));
-
- }
- else
- {
- // TODO: indicate sequence and matching position in status bar
- ap.alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.found_match_for", new String[]
- { searchString }));
- }
- }
- }
-
- JLabel jLabel1 = new JLabel();
-
- protected JTextField textfield = new JTextField();
-
- protected JButton findAll = new JButton();
-
- protected JButton findNext = new JButton();
-
- JPanel actionsPanel = new JPanel();
-
- GridLayout gridLayout1 = new GridLayout();
-
- protected JButton createNewGroup = new JButton();
-
- JCheckBox caseSensitive = new JCheckBox();
-
- JCheckBox searchDescription = new JCheckBox();
-
- private void jbInit() throws Exception
- {
- jLabel1.setFont(new Font("Verdana", 0, 12));
- jLabel1.setText(MessageManager.getString("action.find"));
- jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
- this.setLayout(null);
- textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- textfield.setText("");
- textfield.setBounds(new Rectangle(40, 17, 133, 21));
- textfield.addKeyListener(new java.awt.event.KeyAdapter()
- {
- public void keyTyped(KeyEvent e)
- {
- textfield_keyTyped(e);
- }
- });
- textfield.addActionListener(this);
- findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- findAll.setLabel(MessageManager.getString("action.find_all"));
- findAll.addActionListener(this);
- findNext.setEnabled(false);
- findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- findNext.setLabel(MessageManager.getString("action.find_next"));
- findNext.addActionListener(this);
- actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));
- actionsPanel.setLayout(gridLayout1);
- gridLayout1.setHgap(0);
- gridLayout1.setRows(3);
- gridLayout1.setVgap(2);
- createNewGroup.setEnabled(false);
- createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- createNewGroup.setLabel(MessageManager.getString("label.new_feature"));
- createNewGroup.addActionListener(this);
- caseSensitive.setLabel(MessageManager.getString("label.match_case"));
- caseSensitive.setBounds(new Rectangle(30, 39, 126, 23));
-
- searchDescription.setLabel(MessageManager
- .getString("label.include_description"));
- searchDescription.setBounds(new Rectangle(30, 59, 170, 23));
- actionsPanel.add(findNext, null);
- actionsPanel.add(findAll, null);
- actionsPanel.add(createNewGroup, null);
- this.add(caseSensitive);
- this.add(textfield, null);
- this.add(jLabel1, null);
- this.add(actionsPanel, null);
- this.add(searchDescription);
- }
-
- void textfield_keyTyped(KeyEvent e)
- {
- findNext.setEnabled(true);
- }
-
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.bin.JalviewLite;\r
+import jalview.datamodel.SearchResults;\r
+import jalview.datamodel.SequenceFeature;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.util.MessageManager;\r
+import jalview.viewmodel.AlignmentViewport;\r
+\r
+import javax.swing.JButton;\r
+import javax.swing.JCheckBox;\r
+import java.awt.Font;\r
+import javax.swing.JFrame;\r
+import java.awt.GridLayout;\r
+import javax.swing.JLabel;\r
+import javax.swing.JPanel;\r
+import java.awt.Rectangle;\r
+import javax.swing.JTextField;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.KeyEvent;\r
+import java.awt.event.WindowAdapter;\r
+import java.awt.event.WindowEvent;\r
+import java.util.Vector;\r
+\r
+public class Finder extends JPanel implements ActionListener\r
+{\r
+ AlignmentViewport av;\r
+\r
+ AlignmentPanel ap;\r
+\r
+ JFrame frame;\r
+\r
+ SearchResults searchResults;\r
+\r
+ int seqIndex = 0;\r
+\r
+ int resIndex = -1;\r
+\r
+ public Finder(final AlignmentPanel ap)\r
+ {\r
+ try\r
+ {\r
+ jbInit();\r
+\r
+ } catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ this.av = ap.av;\r
+ this.ap = ap;\r
+ frame = new JFrame();\r
+ frame.add(this);\r
+ JalviewLite.addFrame(frame,\r
+ MessageManager.getString("action.find"), 340, 120);\r
+ frame.repaint();\r
+ frame.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ ap.highlightSearchResults(null);\r
+ }\r
+ });\r
+ textfield.requestFocus();\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ if (evt.getSource() == textfield)\r
+ {\r
+ doSearch(false);\r
+ }\r
+\r
+ else if (evt.getSource() == findNext)\r
+ {\r
+ doSearch(false);\r
+ }\r
+\r
+ else if (evt.getSource() == findAll)\r
+ {\r
+ resIndex = -1;\r
+ seqIndex = 0;\r
+ doSearch(true);\r
+ }\r
+ else if (evt.getSource() == createNewGroup)\r
+ {\r
+ createNewGroup_actionPerformed();\r
+ }\r
+ }\r
+\r
+ public void createNewGroup_actionPerformed()\r
+ {\r
+ SequenceI[] seqs = new SequenceI[searchResults.getSize()];\r
+ SequenceFeature[] features = new SequenceFeature[searchResults\r
+ .getSize()];\r
+\r
+ for (int i = 0; i < searchResults.getSize(); i++)\r
+ {\r
+ seqs[i] = searchResults.getResultSequence(i);\r
+\r
+ features[i] = new SequenceFeature(textfield.getText().trim(),\r
+ "Search Results", null, searchResults.getResultStart(i),\r
+ searchResults.getResultEnd(i), "Search Results");\r
+ }\r
+\r
+ if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,\r
+ features, true, ap))\r
+ {\r
+ ap.alignFrame.sequenceFeatures.setState(true);\r
+ av.setShowSequenceFeatures(true);\r
+ ap.highlightSearchResults(null);\r
+ }\r
+ }\r
+\r
+ void doSearch(boolean findAll)\r
+ {\r
+ if (ap.av.applet.currentAlignFrame != null)\r
+ {\r
+ ap = ap.av.applet.currentAlignFrame.alignPanel;\r
+ av = ap.av;\r
+ }\r
+ createNewGroup.setEnabled(false);\r
+ jalview.analysis.Finder finder = new jalview.analysis.Finder(\r
+ av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);\r
+ finder.setCaseSensitive(caseSensitive.isSelected());\r
+ finder.setIncludeDescription(searchDescription.isSelected());\r
+ finder.setFindAll(findAll);\r
+\r
+ String searchString = textfield.getText();\r
+\r
+ finder.find(searchString);\r
+ seqIndex = finder.getSeqIndex();\r
+ resIndex = finder.getResIndex();\r
+ searchResults = finder.getSearchResults();\r
+ Vector idMatch = finder.getIdMatch();\r
+ boolean haveResults = false;\r
+ // set or reset the GUI\r
+ if ((idMatch.size() > 0))\r
+ {\r
+ haveResults = true;\r
+ ap.idPanel.highlightSearchResults(idMatch);\r
+ }\r
+ else\r
+ {\r
+ ap.idPanel.highlightSearchResults(null);\r
+ }\r
+\r
+ if (searchResults.getSize() > 0)\r
+ {\r
+ haveResults = true;\r
+ createNewGroup.setEnabled(true);\r
+\r
+ }\r
+ else\r
+ {\r
+ searchResults = null;\r
+ }\r
+\r
+ // if allResults is null, this effectively switches displaySearch flag in\r
+ // seqCanvas\r
+ ap.highlightSearchResults(searchResults);\r
+ // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or\r
+ // 'SelectRegion' selection\r
+ if (!haveResults)\r
+ {\r
+ ap.alignFrame.statusBar.setText(MessageManager\r
+ .getString("label.finished_searching"));\r
+ resIndex = -1;\r
+ seqIndex = 0;\r
+ }\r
+ else\r
+ {\r
+ if (findAll)\r
+ {\r
+ String message = (idMatch.size() > 0) ? "" + idMatch.size()\r
+ + " IDs" : "";\r
+ if (idMatch.size() > 0 && searchResults != null\r
+ && searchResults.getSize() > 0)\r
+ {\r
+ message += " and ";\r
+ }\r
+ if (searchResults != null)\r
+ {\r
+ message += searchResults.getSize() + " subsequence matches.";\r
+ }\r
+ ap.alignFrame.statusBar.setText(MessageManager.formatMessage(\r
+ "label.search_results", new String[]\r
+ { searchString, message }));\r
+\r
+ }\r
+ else\r
+ {\r
+ // TODO: indicate sequence and matching position in status bar\r
+ ap.alignFrame.statusBar.setText(MessageManager.formatMessage(\r
+ "label.found_match_for", new String[]\r
+ { searchString }));\r
+ }\r
+ }\r
+ }\r
+\r
+ JLabel jLabel1 = new JLabel();\r
+\r
+ protected JTextField textfield = new JTextField();\r
+\r
+ protected JButton findAll = new JButton();\r
+\r
+ protected JButton findNext = new JButton();\r
+\r
+ JPanel actionsPanel = new JPanel();\r
+\r
+ GridLayout gridLayout1 = new GridLayout();\r
+\r
+ protected JButton createNewGroup = new JButton();\r
+\r
+ JCheckBox caseSensitive = new JCheckBox();\r
+\r
+ JCheckBox searchDescription = new JCheckBox();\r
+\r
+ private void jbInit() throws Exception\r
+ {\r
+ jLabel1.setFont(new Font("Verdana", 0, 12));\r
+ jLabel1.setText(MessageManager.getString("action.find"));\r
+ jLabel1.setBounds(new Rectangle(3, 30, 34, 15));\r
+ this.setLayout(null);\r
+ textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ textfield.setText("");\r
+ textfield.setBounds(new Rectangle(40, 17, 133, 21));\r
+ textfield.addKeyListener(new java.awt.event.KeyAdapter()\r
+ {\r
+ public void keyTyped(KeyEvent e)\r
+ {\r
+ textfield_keyTyped(e);\r
+ }\r
+ });\r
+ textfield.addActionListener(this);\r
+ findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ findAll.setLabel(MessageManager.getString("action.find_all"));\r
+ findAll.addActionListener(this);\r
+ findNext.setEnabled(false);\r
+ findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ findNext.setLabel(MessageManager.getString("action.find_next"));\r
+ findNext.addActionListener(this);\r
+ actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));\r
+ actionsPanel.setLayout(gridLayout1);\r
+ gridLayout1.setHgap(0);\r
+ gridLayout1.setRows(3);\r
+ gridLayout1.setVgap(2);\r
+ createNewGroup.setEnabled(false);\r
+ createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ createNewGroup.setLabel(MessageManager.getString("label.new_feature"));\r
+ createNewGroup.addActionListener(this);\r
+ caseSensitive.setLabel(MessageManager.getString("label.match_case"));\r
+ caseSensitive.setBounds(new Rectangle(30, 39, 126, 23));\r
+\r
+ searchDescription.setLabel(MessageManager\r
+ .getString("label.include_description"));\r
+ searchDescription.setBounds(new Rectangle(30, 59, 170, 23));\r
+ actionsPanel.add(findNext, null);\r
+ actionsPanel.add(findAll, null);\r
+ actionsPanel.add(createNewGroup, null);\r
+ this.add(caseSensitive);\r
+ this.add(textfield, null);\r
+ this.add(jLabel1, null);\r
+ this.add(actionsPanel, null);\r
+ this.add(searchDescription);\r
+ }\r
+\r
+ void textfield_keyTyped(KeyEvent e)\r
+ {\r
+ findNext.setEnabled(true);\r
+ }\r
+\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff