X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFinder.java;h=db46177cedc6ff7b694ffcf3674655db184f855b;hb=b21920d2355ae42bdada6dfc0c42614aa0539137;hp=f59216fefc79d80fdfe9456583aca32bbea6329a;hpb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;p=jalview.git

diff --git a/src/jalview/appletgui/Finder.java b/src/jalview/appletgui/Finder.java
index f59216f..db46177 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
@@ -25,14 +25,15 @@ 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;
-  Vector searchResults;
+
+  SearchResults searchResults;
 
   int seqIndex = 0;
   int resIndex = 0;
@@ -83,52 +84,59 @@ 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);
+    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();
 
-    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
-    for (int i = 0; i < searchResults.size(); i += 3)
+    String featureName = cap.getText().trim();
+    if(featureName.length()<1)
+      return;
+
+
+    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(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);
 
-    searchResults = new Vector();
-    int[] allResults = null;
+    searchResults = new SearchResults();
 
     Sequence seq;
     String item = null;
@@ -140,7 +148,7 @@ 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);
       }
@@ -149,9 +157,8 @@ public class Finder extends Panel implements ActionListener
         seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
       }
 
-      searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq)));
-      searchResults.addElement(String.valueOf(res));
-      searchResults.addElement(String.valueOf(res));
+
+      searchResults.addResult(seq, res, res);
 
     }
     catch (NumberFormatException ex)
@@ -164,7 +171,7 @@ 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;
@@ -173,16 +180,19 @@ 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.getSequence();
+      if(!caseSensitive.getState())
+        item = item.toUpperCase();
 
       if (selection != null && selection.getEndRes() < av.alignment.getWidth())
       {
@@ -190,7 +200,7 @@ 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();
 
@@ -199,7 +209,7 @@ 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
@@ -208,10 +218,12 @@ 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 &&
@@ -221,7 +233,7 @@ public class Finder extends Panel implements ActionListener
             continue;
           }
 
-          searchResults.addElement(Integer.toString(seqIndex));
+
           int sres = seq.findPosition(resIndex +
                                       Integer.parseInt(spaces.
               elementAt(resIndex).toString()));
@@ -229,8 +241,8 @@ public class Finder extends Panel implements ActionListener
                                       Integer.parseInt(
                                       spaces.elementAt(regex.matchedTo() - 1).
                                       toString()));
-          searchResults.addElement(sres + "");
-          searchResults.addElement(eres + "");
+
+          searchResults.addResult(seq, sres, eres);
 
           if (!findAll)
           {
@@ -261,34 +273,29 @@ public class Finder extends Panel implements ActionListener
       }
     }
 
-    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.";
-      System.out.println(message);
+      String message = (searchResults==null?0 : searchResults.getSize()) + " matches found.";
+      ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message);
     }
 
   }
@@ -300,7 +307,7 @@ 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));
@@ -330,12 +337,15 @@ 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);
   }