-/*\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 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 Panel implements ActionListener\r
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- Frame frame;\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
- frame.repaint();\r
- frame.addWindowListener(new WindowAdapter()\r
- {\r
- public void windowClosing(WindowEvent evt)\r
- {\r
- ap.highlightSearchResults(null);\r
- }\r
- });\r
- }\r
-\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- if (evt.getSource() == textfield)\r
- doSearch(false);\r
-\r
- else if (evt.getSource() == findNext)\r
- doSearch(false);\r
-\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
-\r
- public void createNewGroup_actionPerformed()\r
- {\r
-\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);\r
- cap.accept.setLabel("Accept");\r
- Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);\r
- dialog.add(cap);\r
-\r
- cap.setText(textfield.getText());\r
-\r
- dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,\r
- frame.getLocation().y+20,300,100);\r
- dialog.show();\r
-\r
-\r
- String featureName = cap.getText().trim();\r
- if(featureName.length()<1)\r
- return;\r
-\r
-\r
- for (int i = 0; i < searchResults.getSize(); i ++ )\r
- {\r
- SequenceI seq = searchResults.getResultSequence(i);\r
-\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.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();\r
- ap.alignFrame.sequenceFeatures.setState(true);\r
- av.showSequenceFeatures(true);\r
- ap.highlightSearchResults(null);\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();\r
- if(!caseSensitive.getState())\r
- searchString = searchString.toUpperCase();\r
-\r
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
-\r
- searchResults = new SearchResults();\r
-\r
- Sequence seq;\r
- String item = null;\r
- boolean found = false;\r
-\r
- ////// is the searchString a residue number?\r
- try\r
- {\r
- int res = Integer.parseInt(searchString);\r
- found = true;\r
-\r
- if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)\r
- {\r
- seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
- }\r
- else\r
- {\r
- seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
- }\r
-\r
-\r
- searchResults.addResult(seq, res, res);\r
-\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
- {\r
- if (selection.getSize() < 1 ||\r
- (selection.getEndRes() - selection.getStartRes() < 2))\r
- {\r
- selection = null;\r
- }\r
- }\r
-\r
- while (!found && seqIndex < end)\r
- {\r
-\r
- seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
-\r
- if (selection != null && !selection.getSequences(null).contains(seq))\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
- continue;\r
- }\r
-\r
- item = seq.getSequenceAsString();\r
- if(!caseSensitive.getState())\r
- item = item.toUpperCase();\r
-\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 noGapsSB = 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
- noGapsSB.append(item.charAt(j));\r
- spaces.addElement(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
- 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
- {\r
- seqIndex++;\r
- resIndex = 0;\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
- {\r
- idMatch.addElement(av.alignment.getSequenceAt(id));\r
- }\r
- }\r
-\r
- if (searchResults.getSize() == 0 && idMatch.size() > 0)\r
- {\r
- ap.idPanel.highlightSearchResults(idMatch);\r
- }\r
-\r
- if (searchResults.getSize() > 0)\r
- {\r
- createNewGroup.setEnabled(true);\r
- }\r
- else\r
- {\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(searchResults);\r
-\r
- if (findAll)\r
- {\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import java.awt.Rectangle;
+
+public class Finder extends Panel implements ActionListener
+{
+ AlignViewport av;
+ AlignmentPanel ap;
+ Frame frame;
+
+ SearchResults searchResults;
+
+ int seqIndex = 0;
+ int resIndex = 0;
+ public Finder(final AlignmentPanel ap)
+ {
+ try
+ {
+ jbInit();
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+
+ this.av = ap.av;
+ this.ap = ap;
+ frame = new Frame();
+ frame.add(this);
+ jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);
+ frame.repaint();
+ frame.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosing(WindowEvent evt)
+ {
+ ap.highlightSearchResults(null);
+ }
+ });
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ if (evt.getSource() == textfield)
+ doSearch(false);
+
+ else if (evt.getSource() == findNext)
+ doSearch(false);
+
+ else if (evt.getSource() == findAll)
+ {
+ resIndex = 0;
+ seqIndex = 0;
+ doSearch(true);
+ }
+ else if(evt.getSource() == createNewGroup)
+ createNewGroup_actionPerformed();
+ }
+
+
+ public void createNewGroup_actionPerformed()
+ {
+
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);
+ cap.accept.setLabel("Accept");
+ Dialog dialog = new Dialog(ap.alignFrame, "Enter New Feature Name", true);
+ dialog.add(cap);
+
+ cap.setText(textfield.getText());
+
+ dialog.setBounds( frame.getLocation().x+frame.getSize().width+5,
+ frame.getLocation().y+20,300,100);
+ dialog.show();
+
+
+ String featureName = cap.getText().trim();
+ if(featureName.length()<1)
+ return;
+
+
+ for (int i = 0; i < searchResults.getSize(); i ++ )
+ {
+ SequenceI seq = searchResults.getResultSequence(i);
+
+ SequenceFeature sf = new SequenceFeature(featureName,
+ null, null,
+ searchResults.getResultStart(i),
+ searchResults.getResultEnd(i), "Search Results");
+
+ ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
+ featureName, new Color(60,160,115));
+ seq.addSequenceFeature(sf);
+ }
+
+ ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
+ ap.alignFrame.sequenceFeatures.setState(true);
+ av.showSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+
+ void doSearch(boolean findAll)
+ {
+ if(jalview.bin.JalviewLite.currentAlignFrame!=null)
+ {
+ ap = jalview.bin.JalviewLite.currentAlignFrame.alignPanel;
+ av = ap.av;
+ }
+ createNewGroup.setEnabled(false);
+ jalview.analysis.Finder finder=new jalview.analysis.Finder(av.getAlignment(), av.getSelectionGroup(), seqIndex, resIndex);
+ finder.setCaseSensitive(caseSensitive.getState());
+ finder.setFindAll(findAll);
+
+ String searchString = textfield.getText();
+
+ finder.find(searchString);
+ seqIndex=finder.getSeqIndex();
+ resIndex=finder.getResIndex();
+ searchResults = finder.getSearchResults();
+ Vector idMatch = finder.getIdMatch();
+
+ if (searchResults.getSize() == 0 && idMatch.size() > 0)
+ {
+ ap.idPanel.highlightSearchResults(idMatch);
+ }
+
+ if (searchResults.getSize() > 0)
+ {
+ createNewGroup.setEnabled(true);
+
+ }
+ else
+ {
+ searchResults = null;
+ resIndex = 0;
+ seqIndex = 0;
+ }
+
+ // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+ ap.highlightSearchResults(searchResults);
+
+ if (findAll)
+ {
+ String message = (searchResults==null?0 : searchResults.getSize()) + " matches found.";
+ ap.alignFrame.statusBar.setText("Search results: "+searchString+" : "+message);
+ }
+
+ }
+
+ Label jLabel1 = new Label();
+ protected TextField textfield = new TextField();
+ protected Button findAll = new Button();
+ protected Button findNext = new Button();
+ Panel jPanel1 = new Panel();
+ GridLayout gridLayout1 = new GridLayout();
+ protected Button createNewGroup = new Button();
+ Checkbox caseSensitive = new Checkbox();
+
+ private void jbInit() throws Exception {
+ jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));
+ jLabel1.setText("Find");
+ jLabel1.setBounds(new Rectangle(3, 30, 34, 15));
+ this.setLayout(null);
+ textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ textfield.setText("");
+ textfield.setBounds(new Rectangle(40, 27, 133, 21));
+ textfield.addKeyListener(new java.awt.event.KeyAdapter() {
+ public void keyTyped(KeyEvent e) {
+ textfield_keyTyped(e);
+ }
+ });
+ textfield.addActionListener(this);
+ findAll.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ findAll.setLabel("Find all");
+ findAll.addActionListener(this);
+ findNext.setEnabled(false);
+ findNext.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ findNext.setLabel("Find Next");
+ findNext.addActionListener(this);
+ jPanel1.setBounds(new Rectangle(180, 5, 141, 64));
+ jPanel1.setLayout(gridLayout1);
+ gridLayout1.setHgap(0);
+ gridLayout1.setRows(3);
+ gridLayout1.setVgap(2);
+ createNewGroup.setEnabled(false);
+ createNewGroup.setFont(new java.awt.Font("Verdana", Font.PLAIN, 10));
+ createNewGroup.setLabel("New Feature");
+ createNewGroup.addActionListener(this);
+ caseSensitive.setLabel("Match Case");
+ caseSensitive.setBounds(new Rectangle(40, 49, 126, 23));
+ jPanel1.add(findNext, null);
+ jPanel1.add(findAll, null);
+ jPanel1.add(createNewGroup, null);
+ this.add(caseSensitive);
+ this.add(textfield, null);
+ this.add(jLabel1, null);
+ this.add(jPanel1, null);
+ }
+
+ void textfield_keyTyped(KeyEvent e) {
+ findNext.setEnabled(true);
+ }
+
+}
-/*\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.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
-\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
- 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()\r
- {\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- Desktop.addInternalFrame(frame, "Find", 340, 110);\r
-\r
- textfield.requestFocus();\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void findNext_actionPerformed(ActionEvent e)\r
- {\r
- if (getFocusedViewport())\r
- doSearch(false);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void findAll_actionPerformed(ActionEvent e)\r
- {\r
- if(getFocusedViewport())\r
- {\r
- resIndex = 0;\r
- seqIndex = 0;\r
- doSearch(true);\r
- }\r
- }\r
-\r
- boolean getFocusedViewport()\r
- {\r
- JInternalFrame frame = Desktop.desktop.getAllFrames()[1];\r
-\r
- if(frame!=null && frame instanceof AlignFrame)\r
- {\r
- av = ((AlignFrame)frame).viewport;\r
- ap = ((AlignFrame)frame).alignPanel;\r
- return true;\r
- }\r
- return false;\r
- }\r
-\r
-\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
-\r
- SequenceI [] seqs = new SequenceI[searchResults.getSize()];\r
- SequenceFeature [] features = new SequenceFeature[searchResults.getSize()];\r
-\r
-\r
- for (int i = 0; i < searchResults.getSize(); i ++ )\r
- {\r
- seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();\r
-\r
- features[i] = new SequenceFeature(textinput.getText(),\r
- "Search Results", null,\r
- searchResults.getResultStart(i),\r
- searchResults.getResultEnd(i),\r
- "Search Results");\r
- }\r
-\r
- if( ap.seqPanel.seqCanvas.getFeatureRenderer()\r
- .createNewFeatures(seqs, features))\r
- {\r
- ap.alignFrame.showSeqFeatures.setSelected(true);\r
- av.setShowSequenceFeatures(true);\r
- ap.highlightSearchResults(null);\r
- }\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
- 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
- searchResults = new SearchResults();\r
-\r
- Sequence seq;\r
- String item = null;\r
- boolean found = false;\r
-\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() < 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
- ///////////////////////////////////////////////\r
-\r
- int end = av.alignment.getHeight();\r
-\r
- SequenceGroup selection = av.getSelectionGroup();\r
-\r
- if (selection != null)\r
- {\r
- if ((selection.getSize() < 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(null).contains(seq))\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
-\r
- continue;\r
- }\r
-\r
- item = seq.getSequenceAsString();\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
- if ((searchResults.getSize() == 0) && (idMatch.size() > 0))\r
- {\r
- ap.idPanel.highlightSearchResults(idMatch);\r
- }\r
-\r
-\r
- int resultSize = searchResults.getSize();\r
-\r
- if (searchResults.getSize() > 0)\r
- createNewGroup.setEnabled(true);\r
- else\r
- searchResults = null;\r
-\r
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults(searchResults);\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 (findAll)\r
- {\r
- String message = resultSize + " matches found.";\r
- JOptionPane.showInternalMessageDialog(this, message, null,\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import java.util.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Finder extends GFinder
+{
+ AlignViewport av;
+ AlignmentPanel ap;
+ JInternalFrame frame;
+ int seqIndex = 0;
+ int resIndex = 0;
+
+ SearchResults searchResults;
+
+ /**
+ * Creates a new Finder object.
+ *
+ * @param av DOCUMENT ME!
+ * @param ap DOCUMENT ME!
+ * @param f DOCUMENT ME!
+ */
+ public Finder()
+ {
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame, "Find", 340, 110);
+
+ textfield.requestFocus();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void findNext_actionPerformed(ActionEvent e)
+ {
+ if (getFocusedViewport())
+ doSearch(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void findAll_actionPerformed(ActionEvent e)
+ {
+ if(getFocusedViewport())
+ {
+ resIndex = 0;
+ seqIndex = 0;
+ doSearch(true);
+ }
+ }
+
+ boolean getFocusedViewport()
+ {
+ JInternalFrame frame = Desktop.desktop.getAllFrames()[1];
+
+ if(frame!=null && frame instanceof AlignFrame)
+ {
+ av = ((AlignFrame)frame).viewport;
+ ap = ((AlignFrame)frame).alignPanel;
+ return true;
+ }
+ return false;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void createNewGroup_actionPerformed(ActionEvent e)
+ {
+ JLabel label = new JLabel("Enter name of new sequence feature");
+ JTextField textinput = new JTextField(textfield.getText());
+ JPanel panel = new JPanel(new BorderLayout());
+ panel.add(label, BorderLayout.NORTH);
+ panel.add(textinput, BorderLayout.SOUTH);
+
+
+ SequenceI [] seqs = new SequenceI[searchResults.getSize()];
+ SequenceFeature [] features = new SequenceFeature[searchResults.getSize()];
+
+
+ for (int i = 0; i < searchResults.getSize(); i ++ )
+ {
+ seqs[i] = searchResults.getResultSequence(i).getDatasetSequence();
+
+ features[i] = new SequenceFeature(textinput.getText(),
+ "Search Results", null,
+ searchResults.getResultStart(i),
+ searchResults.getResultEnd(i),
+ "Search Results");
+ }
+
+ if( ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .createNewFeatures(seqs, features))
+ {
+ ap.alignFrame.showSeqFeatures.setSelected(true);
+ av.setShowSequenceFeatures(true);
+ ap.highlightSearchResults(null);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param findAll DOCUMENT ME!
+ */
+ void doSearch(boolean findAll)
+ {
+ createNewGroup.setEnabled(false);
+
+ String searchString = textfield.getText().trim();
+
+ if(searchString.length()<1)
+ return;
+ // TODO: extend finder to match descriptions, features and annotation, and other stuff
+ // TODO: add switches to control what is searched - sequences, IDS, descriptions, features
+ jalview.analysis.Finder finder=new jalview.analysis.Finder(av.alignment, av.getSelectionGroup(), seqIndex, resIndex);
+ finder.setCaseSensitive(caseSensitive.isSelected());
+ finder.setFindAll(findAll);
+
+ finder.find(searchString); // returns true if anything was actually found
+
+ seqIndex=finder.getSeqIndex();
+ resIndex=finder.getResIndex();
+
+ searchResults = finder.getSearchResults(); // find(regex, caseSensitive.isSelected(), )
+ Vector idMatch = finder.getIdMatch();
+ // set or reset the GUI
+ if ((searchResults.getSize() == 0) && (idMatch.size() > 0))
+ {
+ ap.idPanel.highlightSearchResults(idMatch);
+ }
+
+
+ int resultSize = searchResults.getSize();
+
+ if (searchResults.getSize() > 0)
+ createNewGroup.setEnabled(true);
+ else
+ searchResults = null;
+
+ // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+ ap.highlightSearchResults(searchResults);
+ // TODO: add enablers for 'SelectSequences' or 'SelectColumns' or 'SelectRegion' selection
+ if(!findAll && resultSize==0)
+ {
+ JOptionPane.showInternalMessageDialog(this, "Finished searching",
+ null, JOptionPane.INFORMATION_MESSAGE);
+ resIndex = 0;
+ seqIndex = 0;
+ }
+
+ if (findAll)
+ {
+ String message = resultSize + " matches found.";
+ JOptionPane.showInternalMessageDialog(this, message, null,
+ JOptionPane.INFORMATION_MESSAGE);
+ }
+
+ }
+}
git://source.jalview.org / jalview.git / commitdiff