+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 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.appletgui;\r
\r
-import jalview.jbappletgui.GFinder;\r
-import jalview.datamodel.*;\r
-import java.awt.event.*;\r
import java.util.*;\r
+\r
import java.awt.*;\r
+import java.awt.event.*;\r
+\r
+import jalview.datamodel.*;\r
+import java.awt.Rectangle;\r
\r
-public class Finder extends GFinder\r
+public class Finder extends Panel implements ActionListener\r
{\r
AlignViewport av;\r
AlignmentPanel ap;\r
Frame frame;\r
- SuperGroup searchGroup;\r
- Vector searchResults;\r
+\r
+ SearchResults searchResults;\r
\r
int seqIndex = 0;\r
int resIndex = 0;\r
public Finder(final AlignmentPanel ap)\r
{\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
this.av = ap.av;\r
this.ap = ap;\r
frame = new Frame();\r
frame.add(this);\r
- jalview.bin.JalviewLite.addFrame(frame, "Find", 340,120);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);\r
frame.repaint();\r
frame.addWindowListener(new WindowAdapter()\r
- {public void windowClosing(WindowEvent evt)\r
- { ap.highlightSearchResults( null ); }\r
- });\r
+ {\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ ap.highlightSearchResults(null);\r
+ }\r
+ });\r
}\r
\r
- public void textfield_actionPerformed(ActionEvent e)\r
+ public void actionPerformed(ActionEvent evt)\r
{\r
- doSearch(false);\r
- }\r
+ if (evt.getSource() == textfield)\r
+ doSearch(false);\r
\r
- public void findNext_actionPerformed(ActionEvent e)\r
- {\r
- doSearch(false);\r
- }\r
+ else if (evt.getSource() == findNext)\r
+ doSearch(false);\r
\r
- public void findAll_actionPerformed(ActionEvent e)\r
- {\r
- resIndex=0;\r
- seqIndex=0;\r
- doSearch(true);\r
+ else if (evt.getSource() == findAll)\r
+ {\r
+ resIndex = 0;\r
+ seqIndex = 0;\r
+ doSearch(true);\r
+ }\r
+ else if(evt.getSource() == createNewGroup)\r
+ createNewGroup_actionPerformed();\r
}\r
\r
- public void cancel_actionPerformed(ActionEvent e)\r
+\r
+ public void createNewGroup_actionPerformed()\r
{\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
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);\r
+ cap.ok.setLabel("Accept");\r
+ Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);\r
+ dialog.add(cap);\r
\r
- public void createNewGroup_actionPerformed(ActionEvent e)\r
- {\r
- Color [] newColors = new Color[24];\r
- for(int i=0; i<24; i++)\r
- newColors[i] = new Color(60,160,115);\r
+ cap.setText(textfield.getText());\r
\r
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);\r
- String searchString = textfield.getText();\r
+ dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,\r
+ frame.getLocation().y+20,300,100);\r
+ dialog.show();\r
\r
- searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
\r
+ String featureName = cap.getText().trim();\r
+ if(featureName.length()<1)\r
+ return;\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
+ for (int i = 0; i < searchResults.getSize(); i ++ )\r
+ {\r
+ SequenceI seq = searchResults.getResultSequence(i);\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
+ SequenceFeature sf = new SequenceFeature(featureName,\r
+ null, null,\r
+ searchResults.getResultStart(i),\r
+ searchResults.getResultEnd(i), "Search Results");\r
\r
+ ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
+ featureName, new Color(60,160,115));\r
+ seq.addSequenceFeature(sf);\r
}\r
\r
- ap.av.alignment.addSuperGroup(searchGroup);\r
- ap.highlightSearchResults( null );\r
+ ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();\r
+ ap.alignFrame.sequenceFeatures.setState(true);\r
+ av.showSequenceFeatures(true);\r
+ ap.highlightSearchResults(null);\r
}\r
\r
-\r
void doSearch(boolean findAll)\r
{\r
+ if(jalview.bin.JalviewLite.currentAlignFrame!=null)\r
+ {\r
+ ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;\r
+ av = ap.av;\r
+ }\r
createNewGroup.setEnabled(false);\r
\r
- String searchString = textfield.getText().toUpperCase();\r
+ String searchString = textfield.getText();\r
+ if(!caseSensitive.getState())\r
+ searchString = searchString.toUpperCase();\r
\r
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
+ com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
\r
- searchResults = new Vector();\r
- int [] allResults = null;\r
+ searchResults = new SearchResults();\r
\r
Sequence seq;\r
- String item=null;\r
+ String item = null;\r
boolean found = false;\r
\r
////// is the searchString a residue number?\r
- try{\r
+ try\r
+ {\r
int res = Integer.parseInt(searchString);\r
found = true;\r
\r
- if(av.getSelectionGroup().getSize()>0)\r
- seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));\r
+ if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
+ {\r
+ seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
+ }\r
else\r
- seq = (Sequence)av.getAlignment().getSequenceAt(0);\r
+ {\r
+ seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
+ }\r
+\r
\r
- searchResults.addElement( Integer.toString( av.getAlignment().findIndex(seq) ) );\r
- searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );\r
- searchResults.addElement( Integer.toString( seq.findIndex(res)-1 ) );\r
+ searchResults.addResult(seq, res, res);\r
\r
- }catch(NumberFormatException ex){}\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {}\r
///////////////////////////////////////////////\r
\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
+ if (selection != null)\r
+ {\r
+ if (selection.getSize(false) < 1 ||\r
+ (selection.getEndRes() - selection.getStartRes() < 2))\r
+ {\r
+ selection = null;\r
+ }\r
+ }\r
\r
- while( !found && seqIndex<end)\r
+ while (!found && seqIndex < end)\r
{\r
- seq = (Sequence)av.alignment.getSequenceAt(seqIndex);\r
\r
+ seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
\r
- if(selection!=null && !selection.sequences.contains(seq))\r
+ if (selection != null && !selection.getSequences(false).contains(seq))\r
{\r
seqIndex++;\r
- resIndex=0;\r
+ resIndex = 0;\r
continue;\r
}\r
\r
- item = seq.getSequence().toUpperCase();\r
+ item = seq.getSequenceAsString();\r
+ if(!caseSensitive.getState())\r
+ item = item.toUpperCase();\r
\r
- if(selection!=null && selection.getEndRes()<av.alignment.getWidth())\r
- item = item.substring(0, selection.getEndRes()+1);\r
+ if (selection != null && selection.getEndRes() < av.alignment.getWidth())\r
+ {\r
+ item = item.substring(0, selection.getEndRes() + 1);\r
+ }\r
\r
///Shall we ignore gaps????\r
- StringBuffer noGaps = new StringBuffer();\r
- int insertCount=0;\r
+ StringBuffer noGapsSB = new StringBuffer();\r
+ int insertCount = 0;\r
Vector spaces = new Vector();\r
\r
- for (int j=0; j < item.length(); j++)\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.addElement(new Integer(insertCount));\r
- }\r
+ if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
+ {\r
+ noGapsSB.append(item.charAt(j));\r
+ spaces.addElement(new Integer(insertCount));\r
+ }\r
else\r
- insertCount++;\r
+ {\r
+ insertCount++;\r
+ }\r
}\r
\r
+ String noGaps = noGapsSB.toString();\r
\r
-\r
- for(int r = resIndex; r<noGaps.length(); r++)\r
+ for (int r = resIndex; r < noGaps.length(); r++)\r
{\r
\r
- if( regex.searchFrom( noGaps.toString(), r ) )\r
- {\r
- resIndex = regex.matchedFrom();\r
- if(selection!=null && ( resIndex+ Integer.parseInt(spaces.elementAt(resIndex).toString()) )<selection.getStartRes())\r
- continue;\r
-\r
- searchResults.addElement( Integer.toString( seqIndex) );\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
- searchResults.addElement( sres+"" );\r
- searchResults.addElement( eres+"" );\r
-\r
-\r
- if(!findAll)\r
- {\r
- // thats enough, break and display the result\r
- found = true;\r
- resIndex++;\r
- break;\r
- }\r
-\r
- r=resIndex;\r
- }\r
+ if (regex.searchFrom(noGaps, r))\r
+ {\r
+ resIndex = regex.matchedFrom();\r
+ if (selection != null &&\r
+ (resIndex + Integer.parseInt(spaces.elementAt(resIndex).toString())) <\r
+ selection.getStartRes())\r
+ {\r
+ continue;\r
+ }\r
+\r
+\r
+ int sres = seq.findPosition(resIndex +\r
+ Integer.parseInt(spaces.\r
+ elementAt(resIndex).toString()));\r
+ int eres = seq.findPosition(regex.matchedTo() - 1 +\r
+ Integer.parseInt(\r
+ spaces.elementAt(regex.matchedTo() - 1).\r
+ toString()));\r
+\r
+ searchResults.addResult(seq, sres, eres);\r
+\r
+ if (!findAll)\r
+ {\r
+ // thats enough, break and display the result\r
+ found = true;\r
+ resIndex++;\r
+ break;\r
+ }\r
+\r
+ r = resIndex;\r
+ }\r
+ else\r
+ break;\r
}\r
- if(!found)\r
+ if (!found)\r
{\r
seqIndex++;\r
resIndex = 0;\r
}\r
}\r
\r
-\r
Vector idMatch = new Vector();\r
- for(int id = 0; id<av.alignment.getHeight(); id++)\r
+ for (int id = 0; id < av.alignment.getHeight(); id++)\r
{\r
- if( regex.search( av.alignment.getSequenceAt(id).getName() ) )\r
- idMatch.addElement( av.alignment.getSequenceAt(id) );\r
+ if (regex.search(av.alignment.getSequenceAt(id).getName()))\r
+ {\r
+ idMatch.addElement(av.alignment.getSequenceAt(id));\r
+ }\r
}\r
\r
- if(searchResults.size()==0 && idMatch.size()>0)\r
- ap.idPanel.highlightSearchResults( idMatch );\r
-\r
-\r
- if(searchResults.size()>0)\r
+ if (searchResults.getSize() == 0 && idMatch.size() > 0)\r
{\r
- allResults = new int[searchResults.size()];\r
- for(int i=0; i<searchResults.size(); i++)\r
- allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());\r
+ ap.idPanel.highlightSearchResults(idMatch);\r
+ }\r
\r
+ if (searchResults.getSize() > 0)\r
+ {\r
createNewGroup.setEnabled(true);\r
}\r
else\r
{\r
- resIndex=0;\r
- seqIndex=0;\r
+ searchResults = null;\r
+ resIndex = 0;\r
+ seqIndex = 0;\r
}\r
\r
// if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults( allResults );\r
+ ap.highlightSearchResults(searchResults);\r
\r
if (findAll)\r
{\r
- String message = (searchResults.size()/3) + " matches found.";\r
- System.out.println(message);\r
+ String message = (searchResults==null?0 : searchResults.getSize()) + " matches found.";\r
+ ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message);\r
}\r
\r
}\r
\r
+ Label jLabel1 = new Label();\r
+ protected TextField textfield = new TextField();\r
+ protected Button findAll = new Button();\r
+ protected Button findNext = new Button();\r
+ Panel jPanel1 = new Panel();\r
+ GridLayout gridLayout1 = new GridLayout();\r
+ protected Button createNewGroup = new Button();\r
+ Checkbox caseSensitive = new Checkbox();\r
+\r
+ private void jbInit() throws Exception {\r
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\r
+ jLabel1.setText("Find");\r
+ jLabel1.setBounds(new Rectangle(3, 30, 34, 15));\r
+ this.setLayout(null);\r
+ textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ textfield.setText("");\r
+ textfield.setBounds(new Rectangle(40, 27, 133, 21));\r
+ textfield.addKeyListener(new java.awt.event.KeyAdapter() {\r
+ public void keyTyped(KeyEvent e) {\r
+ textfield_keyTyped(e);\r
+ }\r
+ });\r
+ textfield.addActionListener(this);\r
+ findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ findAll.setLabel("Find all");\r
+ findAll.addActionListener(this);\r
+ findNext.setEnabled(false);\r
+ findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ findNext.setLabel("Find Next");\r
+ findNext.addActionListener(this);\r
+ jPanel1.setBounds(new Rectangle(180, 5, 141, 64));\r
+ jPanel1.setLayout(gridLayout1);\r
+ gridLayout1.setHgap(0);\r
+ gridLayout1.setRows(3);\r
+ gridLayout1.setVgap(2);\r
+ createNewGroup.setEnabled(false);\r
+ createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));\r
+ createNewGroup.setLabel("New Feature");\r
+ createNewGroup.addActionListener(this);\r
+ caseSensitive.setLabel("Match Case");\r
+ caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));\r
+ jPanel1.add(findNext, null);\r
+ jPanel1.add(findAll, null);\r
+ jPanel1.add(createNewGroup, null);\r
+ this.add(caseSensitive);\r
+ this.add(textfield, null);\r
+ this.add(jLabel1, null);\r
+ this.add(jPanel1, null);\r
+ }\r
+\r
+ void textfield_keyTyped(KeyEvent e) {\r
+ findNext.setEnabled(true);\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff