X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=4c195e819766edd3d3ed781a2c00bb68c9b3a21b;hb=2e699d341f8e64868e3c279f9c02af617c4e9b44;hp=ac7bc2c44caad2e74791750604563cf8dba9a1c1;hpb=df1c58f9669c477db082016aa919d6c6cc9da071;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index ac7bc2c..4c195e8 100755
--- a/src/jalview/appletgui/Finder.java
+++ b/src/jalview/appletgui/Finder.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -25,13 +25,13 @@ import java.awt.*;
 import java.awt.event.*;
 
 import jalview.datamodel.*;
+import java.awt.Rectangle;
 
 public class Finder extends Panel implements ActionListener
 {
   AlignViewport av;
   AlignmentPanel ap;
   Frame frame;
-  SuperGroup searchGroup;
 
   SearchResults searchResults;
 
@@ -84,44 +84,56 @@ public class Finder extends Panel implements ActionListener
 
   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();
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);
+    cap.ok.setLabel("Accept");
+    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;
 
-    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);
 
-      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);
+        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.av.alignment.addSuperGroup(searchGroup);
+    ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
+    ap.alignFrame.sequenceFeatures.setState(true);
+    av.showSequenceFeatures(true);
     ap.highlightSearchResults(null);
   }
 
   void doSearch(boolean findAll)
   {
+    if(jalview.bin.JalviewLite.currentAlignFrame!=null)
+    {
+      ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;
+      av = ap.av;
+    }
     createNewGroup.setEnabled(false);
 
-    String searchString = textfield.getText().toUpperCase();
+    String searchString = textfield.getText();
+    if(!caseSensitive.getState())
+      searchString = searchString.toUpperCase();
 
     com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
@@ -137,7 +149,7 @@ public class Finder extends Panel implements ActionListener
       int res = Integer.parseInt(searchString);
       found = true;
 
-      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
+      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)
       {
         seq = (Sequence) av.getAlignment().getSequenceAt(0);
       }
@@ -160,7 +172,7 @@ public class Finder extends Panel implements ActionListener
     SequenceGroup selection = av.getSelectionGroup();
     if (selection != null)
     {
-      if (selection.getSize() < 1 ||
+      if (selection.getSize(false) < 1 ||
           (selection.getEndRes() - selection.getStartRes() < 2))
       {
         selection = null;
@@ -169,16 +181,19 @@ public class Finder extends Panel implements ActionListener
 
     while (!found && seqIndex < end)
     {
+
       seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
 
-      if (selection != null && !selection.sequences.contains(seq))
+      if (selection != null && !selection.getSequences(false).contains(seq))
       {
         seqIndex++;
         resIndex = 0;
         continue;
       }
 
-      item = seq.getSequence().toUpperCase();
+      item = seq.getSequenceAsString();
+      if(!caseSensitive.getState())
+        item = item.toUpperCase();
 
       if (selection != null && selection.getEndRes() < av.alignment.getWidth())
       {
@@ -186,7 +201,7 @@ public class Finder extends Panel implements ActionListener
       }
 
       ///Shall we ignore gaps????
-      StringBuffer noGaps = new StringBuffer();
+      StringBuffer noGapsSB = new StringBuffer();
       int insertCount = 0;
       Vector spaces = new Vector();
 
@@ -195,7 +210,7 @@ public class Finder extends Panel implements ActionListener
 
         if (!jalview.util.Comparison.isGap(item.charAt(j)))
         {
-          noGaps.append(item.charAt(j));
+          noGapsSB.append(item.charAt(j));
           spaces.addElement(new Integer(insertCount));
         }
         else
@@ -204,10 +219,12 @@ public class Finder extends Panel implements ActionListener
         }
       }
 
+      String noGaps = noGapsSB.toString();
+
       for (int r = resIndex; r < noGaps.length(); r++)
       {
 
-        if (regex.searchFrom(noGaps.toString(), r))
+        if (regex.searchFrom(noGaps, r))
         {
           resIndex = regex.matchedFrom();
           if (selection != null &&
@@ -278,8 +295,8 @@ public class Finder extends Panel implements ActionListener
 
     if (findAll)
     {
-      String message = (searchResults.getSize()) + " matches found.";
-      System.out.println(message);
+      String message = (searchResults==null?0 : searchResults.getSize()) + " matches found.";
+      ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message);
     }
 
   }
@@ -291,7 +308,7 @@ public class Finder extends Panel implements ActionListener
   Panel jPanel1 = new Panel();
   GridLayout gridLayout1 = new GridLayout();
   protected Button createNewGroup = new Button();
-
+  Checkbox caseSensitive = new Checkbox();
 
   private void jbInit() throws Exception {
       jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
@@ -321,12 +338,15 @@ public class Finder extends Panel implements ActionListener
       gridLayout1.setVgap(2);
       createNewGroup.setEnabled(false);
       createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
-      createNewGroup.setLabel("Create new group");
+      createNewGroup.setLabel("New Feature");
       createNewGroup.addActionListener(this);
-      jPanel1.add(findNext, null);
+    caseSensitive.setLabel("Match Case");
+    caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));
+    jPanel1.add(findNext, null);
       jPanel1.add(findAll, null);
       jPanel1.add(createNewGroup, null);
-      this.add(textfield, null);
+    this.add(caseSensitive);
+    this.add(textfield, null);
       this.add(jLabel1, null);
       this.add(jPanel1, null);
   }