X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=31c914ac53dcff78d7469ab34b6760306d2f1180;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=1201278d8fc45dc0d75924eed64c3de7a9ee5f93;hpb=d89379656a71c970b3eb44d22ae2d12ca588ed70;p=jalview.git
diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
old mode 100755
new mode 100644
index 1201278..31c914a
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,344 +1,296 @@
-/*
- * 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;
-
- 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()
- {
-
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);
- Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);
- dialog.add(cap);
-
- cap.setText(textfield.getText());
-
- dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,
- frame.getLocation().y+20,300,100);
- dialog.show();
-
-
- String featureName = cap.getText().trim();
- if(featureName.length()<1)
- return;
-
-
- for (int i = 0; i < searchResults.getSize(); i ++ )
- {
- SequenceI seq = searchResults.getResultSequence(i);
-
- SequenceFeature sf = new SequenceFeature(featureName,
- null, null,
- searchResults.getResultStart(i),
- searchResults.getResultEnd(i), "Search Results");
-
- ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
- featureName, new Color(60,160,115));
- seq.addSequenceFeature(sf);
- }
-
- ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
- ap.alignFrame.sequenceFeatures.setState(true);
- av.showSequenceFeatures(true);
- 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 noGapsSB = 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)))
- {
- noGapsSB.append(item.charAt(j));
- spaces.addElement(new Integer(insertCount));
- }
- else
- {
- insertCount++;
- }
- }
-
- String noGaps = noGapsSB.toString();
-
- for (int r = resIndex; r < noGaps.length(); r++)
- {
-
- if (regex.searchFrom(noGaps, 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==null?0 : searchResults.getSize()) + " matches found.";
- ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+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("New Feature");
- 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.api.AlignViewportI;
+import jalview.api.FinderI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
+
+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.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class Finder extends Panel implements ActionListener
+{
+ private AlignViewportI av;
+
+ private AlignmentPanel ap;
+
+ private TextField textfield = new TextField();
+
+ private Button findAll = new Button();
+
+ private Button findNext = new Button();
+
+ private Button createFeatures = new Button();
+
+ private Checkbox caseSensitive = new Checkbox();
+
+ private Checkbox searchDescription = new Checkbox();
+
+ private SearchResultsI searchResults;
+
+ /*
+ * Finder agent per viewport searched
+ */
+ Map finders;
+
+ public Finder(final AlignmentPanel ap)
+ {
+ finders = new HashMap<>();
+
+ try
+ {
+ jbInit();
+
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ this.av = ap.av;
+ this.ap = ap;
+ Frame 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)
+ {
+ doSearch(true);
+ }
+ else if (evt.getSource() == createFeatures)
+ {
+ createFeatures_actionPerformed();
+ }
+ }
+
+ public void createFeatures_actionPerformed()
+ {
+ List seqs = new ArrayList<>();
+ List features = new ArrayList<>();
+ String searchString = textfield.getText().trim();
+
+ for (SearchResultMatchI match : searchResults.getResults())
+ {
+ seqs.add(match.getSequence().getDatasetSequence());
+ features.add(new SequenceFeature(searchString, "Search Results",
+ match.getStart(), match.getEnd(), "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 doFindAll)
+ {
+ if (ap.av.applet.currentAlignFrame != null)
+ {
+ ap = ap.av.applet.currentAlignFrame.alignPanel;
+ av = ap.av;
+ }
+ createFeatures.setEnabled(false);
+ FinderI finder = finders.get(av);
+ if (finder == null)
+ {
+ /*
+ * first time we searched this viewport
+ */
+ finder = new jalview.analysis.Finder(av);
+ finders.put(av, finder);
+ }
+
+ String searchString = textfield.getText();
+ boolean isCaseSensitive = caseSensitive.getState();
+ boolean doSearchDescription = searchDescription.getState();
+ if (doFindAll)
+ {
+ finder.findAll(searchString, isCaseSensitive, doSearchDescription,
+ false);
+ }
+ else
+ {
+ finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+ false);
+ }
+
+ searchResults = finder.getSearchResults();
+
+ List idMatches = finder.getIdMatches();
+ ap.idPanel.highlightSearchResults(idMatches);
+
+ if (searchResults.isEmpty())
+ {
+ searchResults = null;
+ }
+ else
+ {
+ createFeatures.setEnabled(true);
+ }
+
+ // 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 (idMatches.isEmpty() && searchResults == null)
+ {
+ ap.alignFrame.statusBar.setText(
+ MessageManager.getString("label.finished_searching"));
+ }
+ else
+ {
+ if (doFindAll)
+ {
+ String message = (idMatches.size() > 0)
+ ? "" + idMatches.size() + " IDs"
+ : "";
+ if (idMatches.size() > 0 && searchResults != null
+ && searchResults.getCount() > 0)
+ {
+ message += " and ";
+ }
+ if (searchResults != null)
+ {
+ message += searchResults.getCount() + " 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 }));
+ }
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ Label jLabel1 = new Label(MessageManager.getString("action.find"));
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+ 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();
+ }
+ });
+ 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);
+
+ Panel actionsPanel = new Panel();
+ actionsPanel.setBounds(new Rectangle(195, 5, 141, 64));
+ GridLayout gridLayout1 = new GridLayout();
+ actionsPanel.setLayout(gridLayout1);
+ gridLayout1.setHgap(0);
+ gridLayout1.setRows(3);
+ gridLayout1.setVgap(2);
+ createFeatures.setEnabled(false);
+ createFeatures.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ createFeatures.setLabel(MessageManager.getString("label.new_feature"));
+ createFeatures.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(createFeatures, null);
+ this.add(caseSensitive);
+ this.add(textfield, null);
+ this.add(jLabel1, null);
+ this.add(actionsPanel, null);
+ this.add(searchDescription);
+ }
+
+ void textfield_keyTyped()
+ {
+ findNext.setEnabled(true);
+ }
+
+}