X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=d2fe69c291198551a9b59dfc7ee04bf051de5103;hb=34d5dfb25731d7d797177cadfce954258ae90991;hp=ac7bc2c44caad2e74791750604563cf8dba9a1c1;hpb=df1c58f9669c477db082016aa919d6c6cc9da071;p=jalview.git
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
old mode 100755
new mode 100644
index ac7bc2c..d2fe69c
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,338 +1,298 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 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.appletgui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class Finder extends Panel implements ActionListener
-{
- AlignViewport av;
- AlignmentPanel ap;
- Frame frame;
- SuperGroup searchGroup;
-
- SearchResults searchResults;
-
- int seqIndex = 0;
- int resIndex = 0;
- public Finder(final AlignmentPanel ap)
- {
- try
- {
- jbInit();
- }
- catch (Exception e)
- {
- e.printStackTrace();
- }
-
- this.av = ap.av;
- this.ap = ap;
- frame = new Frame();
- frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);
- frame.repaint();
- frame.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent evt)
- {
- ap.highlightSearchResults(null);
- }
- });
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- if (evt.getSource() == textfield)
- doSearch(false);
-
- else if (evt.getSource() == findNext)
- doSearch(false);
-
- else if (evt.getSource() == findAll)
- {
- resIndex = 0;
- seqIndex = 0;
- doSearch(true);
- }
- else if(evt.getSource() == createNewGroup)
- createNewGroup_actionPerformed();
- }
-
-
- public void createNewGroup_actionPerformed()
- {
- Color[] newColors = new Color[24];
- for (int i = 0; i < 24; i++)
- {
- newColors[i] = new Color(60, 160, 115);
- }
-
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- newColors);
- String searchString = textfield.getText();
-
- searchGroup = new SuperGroup(searchString, ucs, true, true, false);
-
- for (int i = 0; i < searchResults.getSize(); i ++ )
- {
- // its possible edits may have occurred since search was performed
- // account for this here
-
- SequenceI seq = searchResults.getResultSequence(i);
- int startRes = seq.findIndex(searchResults.getResultStart(i)) - 1;
- int endRes = seq.findIndex(searchResults.getResultEnd(i)) - 1;
-
- SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
- startRes, endRes);
- sg.addSequence(seq, false);
- av.alignment.addGroup(sg);
- searchGroup.addGroup(sg);
-
- }
-
- ap.av.alignment.addSuperGroup(searchGroup);
- ap.highlightSearchResults(null);
- }
-
- void doSearch(boolean findAll)
- {
- createNewGroup.setEnabled(false);
-
- String searchString = textfield.getText().toUpperCase();
-
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
-
- searchResults = new SearchResults();
-
- Sequence seq;
- String item = null;
- boolean found = false;
-
- ////// is the searchString a residue number?
- try
- {
- int res = Integer.parseInt(searchString);
- found = true;
-
- if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
- {
- seq = (Sequence) av.getAlignment().getSequenceAt(0);
- }
- else
- {
- seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
- }
-
-
- searchResults.addResult(seq, res, res);
-
- }
- catch (NumberFormatException ex)
- {}
- ///////////////////////////////////////////////
-
-
- int end = av.alignment.getHeight();
-
- SequenceGroup selection = av.getSelectionGroup();
- if (selection != null)
- {
- if (selection.getSize() < 1 ||
- (selection.getEndRes() - selection.getStartRes() < 2))
- {
- selection = null;
- }
- }
-
- while (!found && seqIndex < end)
- {
- seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
-
- if (selection != null && !selection.sequences.contains(seq))
- {
- seqIndex++;
- resIndex = 0;
- continue;
- }
-
- item = seq.getSequence().toUpperCase();
-
- if (selection != null && selection.getEndRes() < av.alignment.getWidth())
- {
- item = item.substring(0, selection.getEndRes() + 1);
- }
-
- ///Shall we ignore gaps????
- StringBuffer noGaps = new StringBuffer();
- int insertCount = 0;
- Vector spaces = new Vector();
-
- for (int j = 0; j < item.length(); j++)
- {
-
- if (!jalview.util.Comparison.isGap(item.charAt(j)))
- {
- noGaps.append(item.charAt(j));
- spaces.addElement(new Integer(insertCount));
- }
- else
- {
- insertCount++;
- }
- }
-
- for (int r = resIndex; r < noGaps.length(); r++)
- {
-
- if (regex.searchFrom(noGaps.toString(), r))
- {
- resIndex = regex.matchedFrom();
- if (selection != null &&
- (resIndex + Integer.parseInt(spaces.elementAt(resIndex).toString())) <
- selection.getStartRes())
- {
- continue;
- }
-
-
- int sres = seq.findPosition(resIndex +
- Integer.parseInt(spaces.
- elementAt(resIndex).toString()));
- int eres = seq.findPosition(regex.matchedTo() - 1 +
- Integer.parseInt(
- spaces.elementAt(regex.matchedTo() - 1).
- toString()));
-
- searchResults.addResult(seq, sres, eres);
-
- if (!findAll)
- {
- // thats enough, break and display the result
- found = true;
- resIndex++;
- break;
- }
-
- r = resIndex;
- }
- else
- break;
- }
- if (!found)
- {
- seqIndex++;
- resIndex = 0;
- }
- }
-
- Vector idMatch = new Vector();
- for (int id = 0; id < av.alignment.getHeight(); id++)
- {
- if (regex.search(av.alignment.getSequenceAt(id).getName()))
- {
- idMatch.addElement(av.alignment.getSequenceAt(id));
- }
- }
-
- if (searchResults.getSize() == 0 && idMatch.size() > 0)
- {
- ap.idPanel.highlightSearchResults(idMatch);
- }
-
- if (searchResults.getSize() > 0)
- {
- createNewGroup.setEnabled(true);
- }
- else
- {
- searchResults = null;
- resIndex = 0;
- seqIndex = 0;
- }
-
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas
- ap.highlightSearchResults(searchResults);
-
- if (findAll)
- {
- String message = (searchResults.getSize()) + " matches found.";
- System.out.println(message);
- }
-
- }
-
- Label jLabel1 = new Label();
- protected TextField textfield = new TextField();
- protected Button findAll = new Button();
- protected Button findNext = new Button();
- Panel jPanel1 = new Panel();
- GridLayout gridLayout1 = new GridLayout();
- protected Button createNewGroup = new Button();
-
-
- private void jbInit() throws Exception {
- jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
- jLabel1.setText("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, 27, 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("Find all");
- findAll.addActionListener(this);
- findNext.setEnabled(false);
- findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
- findNext.setLabel("Find Next");
- findNext.addActionListener(this);
- jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
- jPanel1.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("Create new group");
- createNewGroup.addActionListener(this);
- jPanel1.add(findNext, null);
- jPanel1.add(findAll, null);
- jPanel1.add(createNewGroup, null);
- this.add(textfield, null);
- this.add(jLabel1, null);
- this.add(jPanel1, null);
- }
-
- void textfield_keyTyped(KeyEvent e) {
- findNext.setEnabled(true);
- }
-
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.appletgui;
+
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.TextField;
+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 Panel implements ActionListener
+{
+ AlignmentViewport av;
+
+ AlignmentPanel ap;
+
+ Frame frame;
+
+ SearchResultsI 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 Frame();
+ frame.add(this);
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("action.find"), 340, 120);
+ frame.repaint();
+ frame.addWindowListener(new WindowAdapter()
+ {
+ @Override
+ public void windowClosing(WindowEvent evt)
+ {
+ ap.highlightSearchResults(null);
+ }
+ });
+ textfield.requestFocus();
+ }
+
+ @Override
+ 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()];
+
+ int i = 0;
+ for (SearchResultMatchI match : searchResults.getResults())
+ {
+ seqs[i] = match.getSequence().getDatasetSequence();
+
+ features[i] = new SequenceFeature(textfield.getText().trim(),
+ "Search Results", null, match.getStart(), match.getEnd(),
+ "Search Results");
+ i++;
+ }
+
+ 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.getState());
+ finder.setIncludeDescription(searchDescription.getState());
+ 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 }));
+ }
+ }
+ }
+
+ Label jLabel1 = new Label();
+
+ protected TextField textfield = new TextField();
+
+ protected Button findAll = new Button();
+
+ protected Button findNext = new Button();
+
+ Panel actionsPanel = new Panel();
+
+ GridLayout gridLayout1 = new GridLayout();
+
+ protected Button createNewGroup = new Button();
+
+ Checkbox caseSensitive = new Checkbox();
+
+ Checkbox searchDescription = new Checkbox();
+
+ private void jbInit() throws Exception
+ {
+ jLabel1.setFont(new java.awt.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()
+ {
+ @Override
+ 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);
+ }
+
+}