+/*\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
package jalview.gui;\r
\r
-import jalview.jbgui.GFinder;\r
import jalview.datamodel.*;\r
+\r
+import jalview.jbgui.*;\r
+\r
+import java.awt.*;\r
import java.awt.event.*;\r
+\r
+import java.util.*;\r
+\r
import javax.swing.*;\r
import javax.swing.event.*;\r
-import java.util.*;\r
-import java.awt.*;\r
\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class Finder extends GFinder\r
{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- JInternalFrame frame;\r
- String searchString;\r
- SuperGroup searchGroup;\r
-\r
- int seqIndex = 0;\r
- int resIndex = 0;\r
- public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)\r
- {\r
- this.av = av;\r
- this.ap = ap;\r
- frame = f;\r
-\r
- // all a big pain, but we need to wait until the frame is visible before the textfield can\r
- // obtain the focus/////////////////////////\r
- frame.addInternalFrameListener(new InternalFrameAdapter()\r
+ AlignViewport av;\r
+ AlignmentPanel ap;\r
+ JInternalFrame frame;\r
+ int seqIndex = 0;\r
+ int resIndex = 0;\r
+\r
+ SearchResults searchResults;\r
+\r
+ /**\r
+ * Creates a new Finder object.\r
+ *\r
+ * @param av DOCUMENT ME!\r
+ * @param ap DOCUMENT ME!\r
+ * @param f DOCUMENT ME!\r
+ */\r
+ public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)\r
{\r
- public void internalFrameOpened(InternalFrameEvent evt)\r
- {\r
- SwingUtilities.invokeLater(new Runnable()\r
- {\r
- public void run()\r
- { textfield.requestFocus(); }\r
- });\r
- }\r
-\r
- public void internalFrameClosing(InternalFrameEvent evt)\r
- {\r
- cancel_actionPerformed(null);\r
- }\r
-});\r
-\r
- }\r
-\r
- public void textfield_actionPerformed(ActionEvent e)\r
- {\r
- doSearch(false);\r
- }\r
-\r
- public void findNext_actionPerformed(ActionEvent e)\r
- {\r
- doSearch(false);\r
- }\r
-\r
- public void findAll_actionPerformed(ActionEvent e)\r
- {\r
- resIndex=0;\r
- seqIndex=0;\r
- doSearch(true);\r
- }\r
-\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- try{\r
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults( null );\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
+ this.av = av;\r
+ this.ap = ap;\r
+ frame = f;\r
+\r
+ // all a big pain, but we need to wait until the frame is visible before the textfield can\r
+ // obtain the focus/////////////////////////\r
+ frame.addInternalFrameListener(new InternalFrameAdapter()\r
+ {\r
+ public void internalFrameOpened(InternalFrameEvent evt)\r
+ {\r
+ SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ textfield.requestFocus();\r
+ }\r
+ });\r
+ }\r
+ });\r
+ }\r
\r
\r
- void doSearch(boolean findAll)\r
- {\r
- createNewGroup.setEnabled(false);\r
- searchString = textfield.getText().toUpperCase();\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void findNext_actionPerformed(ActionEvent e)\r
+ {\r
+ doSearch(false);\r
+ }\r
\r
- ArrayList searchResults = new ArrayList();\r
- int [] allResults = null;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void findAll_actionPerformed(ActionEvent e)\r
+ {\r
+ resIndex = 0;\r
+ seqIndex = 0;\r
+ doSearch(true);\r
+ }\r
\r
- Sequence seq;\r
- String item=null;\r
- boolean found = false;\r
\r
- /// is the searchString a residue number?\r
- try{\r
- int res = Integer.parseInt(searchString);\r
- found = true;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createNewGroup_actionPerformed(ActionEvent e)\r
+ {\r
+ JLabel label = new JLabel("Enter name of new sequence feature");\r
+ JTextField textinput = new JTextField(textfield.getText());\r
+ JPanel panel = new JPanel(new BorderLayout());\r
+ panel.add(label, BorderLayout.NORTH);\r
+ panel.add(textinput, BorderLayout.SOUTH);\r
\r
- if(av.getSelectionGroup().getSize()>0)\r
- seq = (Sequence)(av.getSelectionGroup().getSequenceAt(0));\r
- else\r
- seq = (Sequence)av.getAlignment().getSequenceAt(0);\r
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ panel, "New Sequence Feature Name",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
\r
- searchResults.add( Integer.toString( av.getAlignment().findIndex(seq) ) );\r
- searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
- searchResults.add( Integer.toString( seq.findIndex(res)-1 ) );\r
+ if(reply != JOptionPane.OK_OPTION)\r
+ return;\r
\r
- }catch(NumberFormatException ex){}\r
+ for (int i = 0; i < searchResults.getSize(); i ++ )\r
+ {\r
+ SequenceI seq = searchResults.getResultSequence(i);\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
+ SequenceFeature sf = new SequenceFeature(textinput.getText(),\r
+ "Search Results", null,\r
+ searchResults.getResultStart(i),\r
+ searchResults.getResultEnd(i),\r
+ "Search Results");\r
\r
- ucs.setColourScheme(newColors);\r
+ ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
+ textinput.getText(), new Color(60,160,115),\r
+ "Search Results");\r
\r
- searchGroup = new SuperGroup(searchString, ucs , true, true, false);\r
+ seq.getDatasetSequence().addSequenceFeature(sf);\r
+ }\r
\r
- int end = av.alignment.getHeight();\r
+ ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();\r
+ ap.alignFrame.showSeqFeatures.setSelected(true);\r
+ av.setShowSequenceFeatures(true);\r
+ ap.highlightSearchResults(null);\r
+ }\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param findAll DOCUMENT ME!\r
+ */\r
+ void doSearch(boolean findAll)\r
+ {\r
+ createNewGroup.setEnabled(false);\r
\r
- SequenceGroup rubberband = av.getSelectionGroup();\r
- if(rubberband!=null)\r
- end = rubberband.getEndRes();\r
+ String searchString = textfield.getText().trim();\r
+ if(!caseSensitive.isSelected())\r
+ searchString = searchString.toUpperCase();\r
\r
+ if(searchString.length()<1)\r
+ return;\r
\r
+ com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
\r
- while( !found && seqIndex<end)\r
- {\r
- seq = (Sequence)av.getAlignment().getSequenceAt(seqIndex);\r
-\r
- if( av.getSelectionGroup().getSize()>0 && !av.getSelectionGroup().sequences.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
- resIndex=0;\r
- continue;\r
- }\r
-\r
- item = seq.getSequence();\r
-\r
- if(rubberband!=null)\r
- item = item.substring(0, rubberband.getEndRes()+1);\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(!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
+ searchResults = new SearchResults();\r
\r
+ Sequence seq;\r
+ String item = null;\r
+ boolean found = false;\r
\r
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
+ ////// is the searchString a residue number?\r
+ try\r
+ {\r
+ int res = Integer.parseInt(searchString);\r
+ found = true;\r
+ if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
+ {\r
+ seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
+ }\r
+ else\r
+ {\r
+ seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
+ }\r
+\r
+ searchResults.addResult(seq, res, res);\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {\r
+ }\r
\r
- for(int r = resIndex; r<noGaps.length(); r++)\r
- {\r
+ ///////////////////////////////////////////////\r
\r
- if( regex.searchFrom( noGaps.toString(), r ) )\r
- {\r
- resIndex = regex.matchedFrom();\r
+ int end = av.alignment.getHeight();\r
\r
+ SequenceGroup selection = av.getSelectionGroup();\r
\r
- if(rubberband!=null && ( resIndex+ Integer.parseInt(spaces.get(resIndex).toString()) )<rubberband.getStartRes())\r
- continue;\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
+ {\r
+ seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
+\r
+ if ((selection != null) && !selection.getSequences(false).contains(seq))\r
+ {\r
+ seqIndex++;\r
+ resIndex = 0;\r
+\r
+ continue;\r
+ }\r
+\r
+ item = seq.getSequence();\r
+ if(!caseSensitive.isSelected())\r
+ item = item.toUpperCase();\r
+\r
+ if ((selection != null) &&\r
+ (selection.getEndRes() < av.alignment.getWidth()-1))\r
+ {\r
+ item = item.substring(0, selection.getEndRes() + 1);\r
+ }\r
+\r
+ ///Shall we ignore gaps????\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
+ {\r
+ if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
+ {\r
+ noGapsSB.append(item.charAt(j));\r
+ spaces.add(new Integer(insertCount));\r
+ }\r
+ else\r
+ {\r
+ insertCount++;\r
+ }\r
+ }\r
+\r
+ String noGaps = noGapsSB.toString();\r
+\r
+ for (int r = resIndex; r < noGaps.length(); r++)\r
+ {\r
+\r
+ if (regex.searchFrom(noGaps, r))\r
+ {\r
+ resIndex = regex.matchedFrom();\r
+\r
+ if ((selection != null) &&\r
+ ((resIndex +\r
+ Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))\r
+ {\r
+ continue;\r
+ }\r
+\r
+\r
+ int sres = seq.findPosition(resIndex +\r
+ Integer.parseInt(spaces.elementAt(resIndex)\r
+ .toString()));\r
+ int eres = seq.findPosition(regex.matchedTo() - 1 +\r
+ Integer.parseInt(spaces.elementAt(regex.matchedTo() -\r
+ 1).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
+\r
+ break;\r
+ }\r
+\r
+ r = resIndex;\r
+ }\r
+ else\r
+ {\r
+ break;\r
+ }\r
+ }\r
+\r
+ if (!found)\r
+ {\r
+ seqIndex++;\r
+ resIndex = 0;\r
+ }\r
+ }\r
+\r
+ Vector idMatch = new Vector();\r
+\r
+ for (int id = 0; id < av.alignment.getHeight(); id++)\r
+ {\r
+ if (regex.search(av.alignment.getSequenceAt(id).getName()))\r
+ {\r
+ idMatch.add(av.alignment.getSequenceAt(id));\r
+ }\r
+ }\r
\r
- searchResults.add( Integer.toString( seqIndex) );\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
+ if ((searchResults.getSize() == 0) && (idMatch.size() > 0))\r
+ {\r
+ ap.idPanel.highlightSearchResults(idMatch);\r
+ }\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
- found = true;\r
- resIndex++;\r
- break;\r
- }\r
+ int resultSize = searchResults.getSize();\r
\r
- r=resIndex;\r
- }\r
- }\r
- if(!found)\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
- }\r
- }\r
+ if (searchResults.getSize() > 0)\r
+ createNewGroup.setEnabled(true);\r
+ else\r
+ searchResults = null;\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
+ // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
+ ap.highlightSearchResults(searchResults);\r
\r
- createNewGroup.setEnabled(true);\r
- }\r
- else\r
- {\r
- JOptionPane.showInternalMessageDialog(this, "Finished searching", null, JOptionPane.INFORMATION_MESSAGE);\r
- resIndex=0;\r
- seqIndex=0;\r
- }\r
+ if(!findAll && resultSize==0)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(this, "Finished searching",\r
+ null, JOptionPane.INFORMATION_MESSAGE);\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
+ if (findAll)\r
+ {\r
+ String message = resultSize + " matches found.";\r
+ JOptionPane.showInternalMessageDialog(this, message, null,\r
+ JOptionPane.INFORMATION_MESSAGE);\r
+ }\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
}\r
git://source.jalview.org / jalview.git / blobdiff