X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=fb8c28012dd936001df121f204e7edbe1d1a3585;hb=42ae188a9819c341cd345baeab442cd0606ff157;hp=e152506f5e55f15c4e21188320822b7b15421a28;hpb=4ebc6d5b362bc093c39312aa1a69836e3dd6ae84;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index e152506..fb8c280 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -25,21 +25,28 @@ import java.awt.*;
 import java.awt.event.*;
 
 import jalview.datamodel.*;
-import jalview.jbappletgui.*;
 
-public class Finder
-    extends GFinder
+public class Finder extends Panel implements ActionListener
 {
   AlignViewport av;
   AlignmentPanel ap;
   Frame frame;
-  SuperGroup searchGroup;
-  Vector searchResults;
+
+  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();
@@ -55,71 +62,44 @@ public class Finder
     });
   }
 
-  public void textfield_actionPerformed(ActionEvent e)
-  {
-    doSearch(false);
-  }
-
-  public void findNext_actionPerformed(ActionEvent e)
+  public void actionPerformed(ActionEvent evt)
   {
-    doSearch(false);
-  }
+    if (evt.getSource() == textfield)
+      doSearch(false);
 
-  public void findAll_actionPerformed(ActionEvent e)
-  {
-    resIndex = 0;
-    seqIndex = 0;
-    doSearch(true);
-  }
+    else if (evt.getSource() == findNext)
+      doSearch(false);
 
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try
+    else if (evt.getSource() == findAll)
     {
-      // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-      ap.highlightSearchResults(null);
-      ap.idPanel.highlightSearchResults(null);
-      // frame.setClosed(true);
+      resIndex = 0;
+      seqIndex = 0;
+      doSearch(true);
     }
-    catch (Exception ex)
-    {}
+    else if(evt.getSource() == createNewGroup)
+      createNewGroup_actionPerformed();
   }
 
-  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);
+  public void createNewGroup_actionPerformed()
+  {
 
-    for (int i = 0; i < searchResults.size(); i += 3)
+    for (int i = 0; i < searchResults.getSize(); i ++ )
     {
-      // 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, false);
-      av.alignment.addGroup(sg);
-      searchGroup.addGroup(sg);
+        SequenceI seq = searchResults.getResultSequence(i);
 
+        SequenceFeature sf = new SequenceFeature(textfield.getText(),
+            "Search Results", null,
+            searchResults.getResultStart(i),
+           searchResults.getResultEnd(i));
+
+        ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
+            textfield.getText(), new Color(60,160,115));
+        seq.addSequenceFeature(sf);
     }
 
-    ap.av.alignment.addSuperGroup(searchGroup);
+    ap.alignFrame.sequenceFeatures.setState(true);
+    av.showSequenceFeatures(true);
     ap.highlightSearchResults(null);
   }
 
@@ -131,8 +111,7 @@ public class Finder
 
     com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
-    searchResults = new Vector();
-    int[] allResults = null;
+    searchResults = new SearchResults();
 
     Sequence seq;
     String item = null;
@@ -144,18 +123,17 @@ public class Finder
       int res = Integer.parseInt(searchString);
       found = true;
 
-      if (av.getSelectionGroup().getSize() > 0)
+      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
       {
-        seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
+        seq = (Sequence) av.getAlignment().getSequenceAt(0);
       }
       else
       {
-        seq = (Sequence) av.getAlignment().getSequenceAt(0);
+        seq = (Sequence) (av.getSelectionGroup().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));
+
+      searchResults.addResult(seq, res, res);
 
     }
     catch (NumberFormatException ex)
@@ -225,7 +203,7 @@ public class Finder
             continue;
           }
 
-          searchResults.addElement(Integer.toString(seqIndex));
+
           int sres = seq.findPosition(resIndex +
                                       Integer.parseInt(spaces.
               elementAt(resIndex).toString()));
@@ -233,8 +211,8 @@ public class Finder
                                       Integer.parseInt(
                                       spaces.elementAt(regex.matchedTo() - 1).
                                       toString()));
-          searchResults.addElement(sres + "");
-          searchResults.addElement(eres + "");
+
+          searchResults.addResult(seq, sres, eres);
 
           if (!findAll)
           {
@@ -246,6 +224,8 @@ public class Finder
 
           r = resIndex;
         }
+        else
+          break;
       }
       if (!found)
       {
@@ -263,36 +243,82 @@ public class Finder
       }
     }
 
-    if (searchResults.size() == 0 && idMatch.size() > 0)
+    if (searchResults.getSize() == 0 && idMatch.size() > 0)
     {
       ap.idPanel.highlightSearchResults(idMatch);
     }
 
-    if (searchResults.size() > 0)
+    if (searchResults.getSize() > 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
     {
+      searchResults = null;
       resIndex = 0;
       seqIndex = 0;
     }
 
     // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-    ap.highlightSearchResults(allResults);
+    ap.highlightSearchResults(searchResults);
 
     if (findAll)
     {
-      String message = (searchResults.size() / 3) + " matches found.";
+      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("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);
+  }
+
 }