+/*\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
-\r
+import java.awt.*;\r
\r
public class Finder extends GFinder\r
{\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
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
+ ap.idPanel.highlightSearchResults( null );\r
+ // frame.setClosed(true);\r
}catch(Exception ex){ }\r
+ }\r
+\r
+\r
+ public void createNewGroup_actionPerformed(ActionEvent e)\r
+ {\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
}\r
\r
+\r
void doSearch(boolean findAll)\r
{\r
- searchString = textfield.getText().toUpperCase();\r
+ createNewGroup.setEnabled(false);\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
- while( !found && seqIndex<av.getAlignment().getHeight())\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
+\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
+ seq = (Sequence)av.alignment.getSequenceAt(seqIndex);\r
+\r
\r
- if(av.getSelection().size()>0 && !av.getSelection().contains(seq))\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
- for(int r = resIndex; r<item.length(); 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
+ Vector spaces = new Vector();\r
+\r
+ for (int j=0; j < item.length(); j++)\r
+ {\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
+\r
+ for(int r = resIndex; r<noGaps.length(); r++)\r
{\r
- if(item.indexOf(searchString,r)>-1)\r
+\r
+ if( regex.searchFrom( noGaps.toString(), r ) )\r
{\r
- resIndex = item.indexOf(searchString,r);\r
- searchResults.add( Integer.toString(seqIndex) );\r
- searchResults.add( Integer.toString( resIndex) );\r
- searchResults.add( Integer.toString( (resIndex+searchString.length()-1) ) );\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
+\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
// thats enough, break and display the result\r
resIndex++;\r
break;\r
}\r
+\r
+ r=resIndex;\r
}\r
}\r
if(!found)\r
}\r
}\r
\r
- if(searchResults.size()>0)\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
allResults = new int[searchResults.size()];\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
- JOptionPane.showInternalMessageDialog(this, "Finished searching", null,\r
- JOptionPane.INFORMATION_MESSAGE);\r
+ JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);\r
resIndex=0;\r
seqIndex=0;\r
}\r
// if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
ap.highlightSearchResults( allResults );\r
\r
+ if (findAll)\r
+ {\r
+ String message = (searchResults.size()/3) + " matches found.";\r
+ JOptionPane.showInternalMessageDialog(this, message, null,\r
+ JOptionPane.INFORMATION_MESSAGE);\r
+ }\r
\r
}\r
\r
git://source.jalview.org / jalview.git / blobdiff