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
AlignmentPanel ap;\r
JInternalFrame frame;\r
String searchString;\r
+ SuperGroup searchGroup;\r
\r
int seqIndex = 0;\r
int resIndex = 0;\r
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
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
+ ////// is the searchString a residue number?\r
try{\r
int res = Integer.parseInt(searchString);\r
found = true;\r
\r
- if(av.getSelection().size()>0)\r
- seq = (Sequence)(av.getSelection().sequenceAt(0));\r
+ if(av.getSelectionGroup().getSize()>0)\r
+ seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));\r
else\r
seq = (Sequence)av.getAlignment().getSequenceAt(0);\r
\r
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
+\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
- while( !found && seqIndex<av.getAlignment().getHeight())\r
+ searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+\r
+ int end = av.alignment.getHeight();\r
+\r
+ SequenceGroup selection = av.getSelectionGroup();\r
+ if(selection!=null)\r
+ if(selection.getSize()<1 || (selection.getEndRes()-selection.getStartRes()<2))\r
+ selection = null;\r
+\r
+ while( !found && seqIndex<end)\r
{\r
- seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);\r
- if(av.getSelection().size()>0 && !av.getSelection().contains(seq))\r
+ seq = (Sequence)av.alignment.getSequenceAt(seqIndex);\r
+\r
+\r
+ if(selection!=null && !selection.sequences.contains(seq))\r
{\r
- // if a selection has been made, only search within that selection\r
seqIndex++;\r
resIndex=0;\r
continue;\r
}\r
\r
- item = seq.getSequence();\r
+ item = seq.getSequence().toUpperCase();\r
+\r
+ if(selection!=null && selection.getEndRes()<av.alignment.getWidth())\r
+ item = item.substring(0, selection.getEndRes()+1);\r
\r
///Shall we ignore gaps????\r
StringBuffer noGaps = new StringBuffer();\r
}\r
\r
\r
- Pattern pattern = Pattern.compile(searchString);\r
- Matcher matcher = pattern.matcher(noGaps);\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( matcher.find( r ) )\r
+ if( regex.searchFrom( noGaps.toString(), r ) )\r
{\r
- resIndex = matcher.start();\r
+ resIndex = regex.matchedFrom();\r
+ if(selection!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<selection.getStartRes())\r
+ continue;\r
\r
searchResults.add( Integer.toString( seqIndex) );\r
searchResults.add( Integer.toString( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ) );\r
- searchResults.add( Integer.toString( matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).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
break;\r
}\r
\r
- r=resIndex+1;\r
+ r=resIndex;\r
}\r
}\r
if(!found)\r
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