X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=167d8995453bb8a23d6c355001e23c1868242019;hb=refs%2Fheads%2Ffeatures%2Fr2_11_2_alphafold%2FJAL-2349_JAL-3855;hp=a3a61247feb71cd293c13077e6c85b13dea4ce3b;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
old mode 100755
new mode 100644
index a3a6124..167d899
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,298 +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.*;
-import jalview.jbappletgui.*;
-
-public class Finder
-    extends GFinder
-{
-  AlignViewport av;
-  AlignmentPanel ap;
-  Frame frame;
-  SuperGroup searchGroup;
-  Vector searchResults;
-
-  int seqIndex = 0;
-  int resIndex = 0;
-  public Finder(final AlignmentPanel ap)
-  {
-    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 textfield_actionPerformed(ActionEvent e)
-  {
-    doSearch(false);
-  }
-
-  public void findNext_actionPerformed(ActionEvent e)
-  {
-    doSearch(false);
-  }
-
-  public void findAll_actionPerformed(ActionEvent e)
-  {
-    resIndex = 0;
-    seqIndex = 0;
-    doSearch(true);
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-      ap.highlightSearchResults(null);
-      ap.idPanel.highlightSearchResults(null);
-      // frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {}
-  }
-
-  public void createNewGroup_actionPerformed(ActionEvent e)
-  {
-    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.size(); i += 3)
-    {
-      // its possible edits may have occurred since search was performed
-      // account for this here
-
-      SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(searchResults.
-          elementAt(i).toString()));
-      int startRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i +
-          1).toString())) - 1;
-      int endRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i + 2).
-                                                  toString())) - 1;
-
-      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
-                                           startRes, endRes);
-      sg.addSequence(seq);
-      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 Vector();
-    int[] allResults = null;
-
-    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().getSize() > 0)
-      {
-        seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
-      }
-      else
-      {
-        seq = (Sequence) av.getAlignment().getSequenceAt(0);
-      }
-
-      searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq)));
-      searchResults.addElement(Integer.toString(seq.findIndex(res) - 1));
-      searchResults.addElement(Integer.toString(seq.findIndex(res) - 1));
-
-    }
-    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;
-          }
-
-          searchResults.addElement(Integer.toString(seqIndex));
-          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.addElement(sres + "");
-          searchResults.addElement(eres + "");
-
-          if (!findAll)
-          {
-            // thats enough, break and display the result
-            found = true;
-            resIndex++;
-            break;
-          }
-
-          r = resIndex;
-        }
-      }
-      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.size() == 0 && idMatch.size() > 0)
-    {
-      ap.idPanel.highlightSearchResults(idMatch);
-    }
-
-    if (searchResults.size() > 0)
-    {
-      allResults = new int[searchResults.size()];
-      for (int i = 0; i < searchResults.size(); i++)
-      {
-        allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());
-      }
-
-      createNewGroup.setEnabled(true);
-    }
-    else
-    {
-      resIndex = 0;
-      seqIndex = 0;
-    }
-
-    // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-    ap.highlightSearchResults(allResults);
-
-    if (findAll)
-    {
-      String message = (searchResults.size() / 3) + " matches found.";
-      System.out.println(message);
-    }
-
-  }
-
-}
+/*
+ * 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 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;
+
+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;
+
+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<AlignViewportI, FinderI> 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<SequenceI> seqs = new ArrayList<>();
+    List<SequenceFeature> 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, false);
+    }
+    else
+    {
+      finder.findNext(searchString, isCaseSensitive, doSearchDescription,
+              false, false);
+    }
+
+    searchResults = finder.getSearchResults();
+
+    List<SequenceI> 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);
+  }
+
+}