Tree fits to window by default

[jalview.git] / src / jalview / gui / Finder.java

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index e1a3082..2311a9f 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -6,7 +6,7 @@ import java.awt.event.*;
 import javax.swing.*;\r
 import javax.swing.event.*;\r
 import java.util.*;\r
-import java.util.regex.*;\r
+import java.awt.*;\r
 \r
 public class Finder extends GFinder\r
 {\r
@@ -14,6 +14,7 @@ public class Finder extends GFinder
   AlignmentPanel ap;\r
   JInternalFrame frame;\r
   String searchString;\r
+  SuperGroup searchGroup;\r
 \r
   int seqIndex = 0;\r
   int resIndex = 0;\r
@@ -32,11 +33,14 @@ public class Finder extends GFinder
         SwingUtilities.invokeLater(new Runnable()\r
         {\r
           public void run()\r
-          {\r
-            textfield.requestFocus();\r
-          }\r
+          {   textfield.requestFocus();      }\r
        });\r
-   }\r
+     }\r
+\r
+     public void internalFrameClosing(InternalFrameEvent evt)\r
+     {\r
+       cancel_actionPerformed(null);\r
+     }\r
 });\r
 \r
   }\r
@@ -63,20 +67,31 @@ public class Finder extends GFinder
     try{\r
       // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
       ap.highlightSearchResults( null );\r
-      frame.setClosed(true);\r
+     // frame.setClosed(true);\r
     }catch(Exception ex){ }\r
+  }\r
 \r
+\r
+  public void createNewGroup_actionPerformed(ActionEvent e)\r
+  {\r
+    for(int i=0; i<searchGroup.getSize(); i++)\r
+      av.alignment.addGroup( searchGroup.getGroupeAt(i));\r
+\r
+    ap.av.alignment.addSuperGroup(searchGroup);\r
+    ap.highlightSearchResults( null );\r
   }\r
 \r
+\r
   void doSearch(boolean findAll)\r
   {\r
+    createNewGroup.setEnabled(false);\r
     searchString = textfield.getText().toUpperCase();\r
 \r
     ArrayList searchResults = new ArrayList();\r
     int [] allResults = null;\r
 \r
     Sequence seq;\r
-    String item;\r
+    String item=null;\r
     boolean found = false;\r
 \r
     /// is the searchString a residue number?\r
@@ -93,16 +108,32 @@ public class Finder extends GFinder
       searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
       searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
 \r
-\r
-      //av.getAlignment().getSequenceAt(seq).findPosition(res)\r
     }catch(NumberFormatException ex){}\r
 \r
+    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();\r
+    Color [] newColors = new Color[24];\r
+    for(int i=0; i<24; i++)\r
+      newColors[i] = new Color(60,160,115);\r
+\r
+    ucs.setColourScheme(newColors);\r
+\r
+    searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+\r
+    int end = av.alignment.getHeight();\r
+\r
+\r
+    SequenceGroup rubberband = av.getRubberbandGroup();\r
+    if(rubberband!=null)\r
+      end = rubberband.getEndRes();\r
+\r
+\r
 \r
-    while( !found && seqIndex<av.getAlignment().getHeight())\r
+    while( !found && seqIndex<end)\r
     {\r
       seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);\r
 \r
-      if(av.getSelection().size()>0 && !av.getSelection().contains(seq))\r
+      if(   av.getSelection().size()>0 && !av.getSelection().contains(seq)\r
+            || (rubberband!=null && !rubberband.sequences.contains(seq))  )\r
       {\r
         // if a selection has been made, only search within that selection\r
         seqIndex++;\r
@@ -112,19 +143,51 @@ public class Finder extends GFinder
 \r
       item = seq.getSequence();\r
 \r
-      Pattern pattern = Pattern.compile(searchString);\r
-      Matcher matcher = pattern.matcher(item);\r
+      if(rubberband!=null)\r
+        item = item.substring(0, rubberband.getEndRes()+1);\r
 \r
-      for(int r = resIndex; r<item.length(); r++)\r
+      ///Shall we ignore gaps????\r
+      StringBuffer noGaps = new StringBuffer();\r
+      int insertCount=0;\r
+      ArrayList spaces = new ArrayList();\r
+\r
+      for (int j=0; j < item.length(); j++)\r
       {\r
 \r
-       if( matcher.find( r ) )\r
+        if(!jalview.util.Comparison.isGap(item.charAt(j)))\r
+         {\r
+           noGaps.append(item.charAt(j));\r
+           spaces.add(new Integer(insertCount));\r
+         }\r
+        else\r
+           insertCount++;\r
+      }\r
+\r
+\r
+      com.stevesoft.pat.Regex regex = new  com.stevesoft.pat.Regex(searchString);\r
+\r
+      for(int r = resIndex; r<noGaps.length(); r++)\r
+      {\r
+\r
+       if( regex.searchFrom( noGaps.toString(), r ) )\r
        {\r
-         resIndex = matcher.start();\r
+         resIndex = regex.matchedFrom();\r
+\r
+\r
+         if(rubberband!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<rubberband.getStartRes())\r
+           continue;\r
 \r
          searchResults.add( Integer.toString( seqIndex) );\r
-         searchResults.add( Integer.toString( resIndex) );\r
-         searchResults.add( Integer.toString( matcher.end()-1 ) );\r
+         searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );\r
+         searchResults.add( Integer.toString( regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString()) ) );\r
+\r
+         SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
+                                             resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,\r
+                                      regex.matchedTo()-1 + Integer.parseInt(spaces.get(regex.matchedTo()-1).toString())\r
+            );\r
+         sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));\r
+         searchGroup.addGroup( sg );\r
+\r
          if(!findAll)\r
          {\r
            // thats enough, break and display the result\r
@@ -133,7 +196,7 @@ public class Finder extends GFinder
            break;\r
          }\r
 \r
-         r=resIndex+1;\r
+         r=resIndex;\r
        }\r
       }\r
       if(!found)\r
@@ -149,6 +212,7 @@ public class Finder extends GFinder
       for(int i=0; i<searchResults.size(); i++)\r
         allResults[i] = Integer.parseInt(searchResults.get(i).toString());\r
 \r
+      createNewGroup.setEnabled(true);\r
     }\r
     else\r
     {\r