+/*\r
+* Jalview - A Sequence Alignment Editor and Viewer\r
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+*\r
+* This program is free software; you can redistribute it and/or\r
+* modify it under the terms of the GNU General Public License\r
+* as published by the Free Software Foundation; either version 2\r
+* of the License, or (at your option) any later version.\r
+*\r
+* This program is distributed in the hope that it will be useful,\r
+* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+* GNU General Public License for more details.\r
+*\r
+* You should have received a copy of the GNU General Public License\r
+* along with this program; if not, write to the Free Software\r
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+*/\r
+\r
package jalview.gui;\r
\r
import jalview.jbgui.GFinder;\r
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
AlignViewport av;\r
AlignmentPanel ap;\r
JInternalFrame frame;\r
- String searchString;\r
SuperGroup searchGroup;\r
+ Vector searchResults;\r
\r
int seqIndex = 0;\r
int resIndex = 0;\r
try{\r
// if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
ap.highlightSearchResults( null );\r
+ ap.idPanel.highlightSearchResults( null );\r
// frame.setClosed(true);\r
}catch(Exception ex){ }\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
+ Color [] newColors = new Color[24];\r
+ for(int i=0; i<24; i++)\r
+ newColors[i] = new Color(60,160,115);\r
+\r
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);\r
+ String searchString = textfield.getText();\r
+\r
+ searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+\r
+\r
+ for(int i=0; i<searchResults.size(); i+=3)\r
+ {\r
+ // its possible edits may have occurred since search was performed\r
+ // account for this here\r
+\r
+ SequenceI seq = av.alignment.getSequenceAt( Integer.parseInt(searchResults.elementAt(i).toString()) );\r
+ int startRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+1).toString()) )-1;\r
+ int endRes = seq.findIndex( Integer.parseInt(searchResults.elementAt(i+2).toString()) )-1;\r
+\r
+ SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false, startRes , endRes );\r
+ sg.addSequence(seq);\r
+ av.alignment.addGroup(sg);\r
+ searchGroup.addGroup( sg );\r
+\r
+ }\r
\r
ap.av.alignment.addSuperGroup(searchGroup);\r
ap.highlightSearchResults( null );\r
void doSearch(boolean findAll)\r
{\r
createNewGroup.setEnabled(false);\r
- searchString = textfield.getText().toUpperCase();\r
\r
- ArrayList searchResults = new ArrayList();\r
+ String searchString = textfield.getText().toUpperCase();\r
+\r
+ com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
+\r
+ searchResults = new Vector();\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
\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
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);\r
\r
searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
\r
- while( !found && seqIndex<av.getAlignment().getHeight())\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
int insertCount=0;\r
- ArrayList spaces = new ArrayList();\r
+ Vector spaces = new Vector();\r
\r
for (int j=0; j < item.length(); j++)\r
{\r
}\r
\r
\r
- Pattern pattern = Pattern.compile(searchString);\r
- Matcher matcher = pattern.matcher(noGaps);\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
\r
- SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
- resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) ,\r
- matcher.end()-1 + Integer.parseInt(spaces.get(matcher.end()-1).toString())\r
- );\r
- sg.addSequence((Sequence)av.getAlignment().getSequenceAt(seqIndex));\r
- searchGroup.addGroup( sg );\r
+ int sres = seq.findPosition( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) );\r
+ int eres = seq.findPosition( regex.matchedTo()-1 + Integer.parseInt(spaces.elementAt(regex.matchedTo()-1).toString()) );\r
+\r
+ searchResults.addElement( sres+"" );\r
+ searchResults.addElement( eres+"" );\r
\r
if(!findAll)\r
{\r
break;\r
}\r
\r
- r=resIndex+1;\r
+ r=resIndex;\r
}\r
}\r
if(!found)\r
seqIndex++;\r
resIndex = 0;\r
}\r
- }\r
+ }\r
+\r
+\r
+ Vector idMatch = new Vector();\r
+ for(int id = 0; id<av.alignment.getHeight(); id++)\r
+ {\r
+ if( regex.search( av.alignment.getSequenceAt(id).getName() ) )\r
+ idMatch.add( av.alignment.getSequenceAt(id) );\r
+ }\r
+\r
+ if(searchResults.size()==0 && idMatch.size()>0)\r
+ ap.idPanel.highlightSearchResults( idMatch );\r
+\r
\r
if(searchResults.size()>0)\r
{\r
git://source.jalview.org / jalview.git / blobdiff