-/*\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
-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
- SuperGroup searchGroup;\r
- Vector searchResults;\r
- int seqIndex = 0;\r
- int resIndex = 0;\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
- 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
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void internalFrameClosing(InternalFrameEvent evt)\r
- {\r
- cancel_actionPerformed(null);\r
- }\r
- });\r
- }\r
-\r
-\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
- /**\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- // if allResults is null, this effectively switches displaySearch flag in seqCanvas\r
- ap.highlightSearchResults(null);\r
- ap.idPanel.highlightSearchResults(null);\r
-\r
- // frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void createNewGroup_actionPerformed(ActionEvent e)\r
- {\r
- Color[] newColors = new Color[24];\r
-\r
- for (int i = 0; i < 24; i++)\r
- {\r
- newColors[i] = new Color(60, 160, 115);\r
- }\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
- 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
- SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(\r
- searchResults.elementAt(i).toString()));\r
- int startRes = seq.findIndex(Integer.parseInt(\r
- searchResults.elementAt(i + 1).toString())) - 1;\r
- int endRes = seq.findIndex(Integer.parseInt(\r
- searchResults.elementAt(i + 2).toString())) - 1;\r
-\r
- SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true,\r
- false, startRes, endRes);\r
- sg.addSequence(seq, false);\r
- av.alignment.addGroup(sg);\r
- searchGroup.addGroup(sg);\r
- }\r
-\r
- ap.av.alignment.addSuperGroup(searchGroup);\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
- String searchString = textfield.getText().toUpperCase().trim();\r
-\r
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
-\r
- searchResults = new Vector();\r
-\r
- int[] allResults = null;\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.add(Integer.toString(av.getAlignment().findIndex(seq)));\r
- searchResults.add(res+"");\r
- searchResults.add(res+"");\r
- }\r
- catch (NumberFormatException ex)\r
- {\r
- }\r
-\r
- ///////////////////////////////////////////////\r
- Color[] newColors = new Color[24];\r
-\r
- for (int i = 0; i < 24; i++)\r
- {\r
- newColors[i] = new Color(60, 160, 115);\r
- }\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
-\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.sequences.contains(seq))\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
-\r
- continue;\r
- }\r
-\r
- item = seq.getSequence().toUpperCase();\r
-\r
- if ((selection != null) &&\r
- (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
- 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
- noGaps.append(item.charAt(j));\r
- spaces.add(new Integer(insertCount));\r
- }\r
- else\r
- {\r
- insertCount++;\r
- }\r
- }\r
-\r
- for (int r = resIndex; r < noGaps.length(); r++)\r
- {\r
- if (regex.searchFrom(noGaps.toString(), 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
- searchResults.add(Integer.toString(seqIndex));\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.addElement(sres + "");\r
- searchResults.addElement(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
- }\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.size() == 0) && (idMatch.size() > 0))\r
- {\r
- ap.idPanel.highlightSearchResults(idMatch);\r
- }\r
-\r
- if (searchResults.size() > 0)\r
- {\r
- allResults = new int[searchResults.size()];\r
-\r
- for (int i = 0; i < searchResults.size(); i++)\r
- {\r
- allResults[i] = Integer.parseInt(searchResults.get(i).toString());\r
- }\r
-\r
- createNewGroup.setEnabled(true);\r
- }\r
- else\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
-\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
+/*
+ * 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(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
+ {
+ this.av = av;
+ this.ap = ap;
+ frame = f;
+
+ // all a big pain, but we need to wait until the frame is visible before the textfield can
+ // obtain the focus/////////////////////////
+ frame.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ public void internalFrameOpened(InternalFrameEvent evt)
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ textfield.requestFocus();
+ }
+ });
+ }
+ });
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void findNext_actionPerformed(ActionEvent e)
+ {
+ doSearch(false);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void findAll_actionPerformed(ActionEvent e)
+ {
+ resIndex = 0;
+ seqIndex = 0;
+ doSearch(true);
+ }
+
+
+ /**
+ * 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);
+
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ panel, "New Sequence Feature Name",
+ JOptionPane.OK_CANCEL_OPTION );
+
+ if(reply != JOptionPane.OK_OPTION)
+ return;
+
+ for (int i = 0; i < searchResults.getSize(); i ++ )
+ {
+ SequenceI seq = searchResults.getResultSequence(i);
+
+ SequenceFeature sf = new SequenceFeature(textinput.getText(),
+ "Search Results", null,
+ searchResults.getResultStart(i),
+ searchResults.getResultEnd(i),
+ "Search Results");
+
+ ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
+ textinput.getText(), new Color(60,160,115),
+ "Search Results");
+
+ seq.getDatasetSequence().addSequenceFeature(sf);
+ }
+
+ ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();
+ 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(!caseSensitive.isSelected())
+ searchString = searchString.toUpperCase();
+
+ if(searchString.length()<1)
+ return;
+
+ com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
+
+ searchResults = new SearchResults();
+
+ Sequence seq;
+ String item = null;
+ boolean found = false;
+
+ ////// is the searchString a residue number?
+ try
+ {
+ int res = Integer.parseInt(searchString);
+ found = true;
+ if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)
+ {
+ seq = (Sequence) av.getAlignment().getSequenceAt(0);
+ }
+ else
+ {
+ seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
+ }
+
+ searchResults.addResult(seq, res, res);
+ }
+ catch (NumberFormatException ex)
+ {
+ }
+
+ ///////////////////////////////////////////////
+
+ int end = av.alignment.getHeight();
+
+ SequenceGroup selection = av.getSelectionGroup();
+
+ if (selection != null)
+ {
+ if ((selection.getSize(false) < 1) ||
+ ((selection.getEndRes() - selection.getStartRes()) < 2))
+ {
+ selection = null;
+ }
+ }
+
+ while (!found && (seqIndex < end))
+ {
+ seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
+
+ if ((selection != null) && !selection.getSequences(false).contains(seq))
+ {
+ seqIndex++;
+ resIndex = 0;
+
+ continue;
+ }
+
+ item = seq.getSequence();
+ if(!caseSensitive.isSelected())
+ item = item.toUpperCase();
+
+ if ((selection != null) &&
+ (selection.getEndRes() < av.alignment.getWidth()-1))
+ {
+ item = item.substring(0, selection.getEndRes() + 1);
+ }
+
+ ///Shall we ignore gaps????
+ StringBuffer noGapsSB = new StringBuffer();
+ int insertCount = 0;
+ Vector spaces = new Vector();
+
+ for (int j = 0; j < item.length(); j++)
+ {
+ if (!jalview.util.Comparison.isGap(item.charAt(j)))
+ {
+ noGapsSB.append(item.charAt(j));
+ spaces.add(new Integer(insertCount));
+ }
+ else
+ {
+ insertCount++;
+ }
+ }
+
+ String noGaps = noGapsSB.toString();
+
+ for (int r = resIndex; r < noGaps.length(); r++)
+ {
+
+ if (regex.searchFrom(noGaps, r))
+ {
+ resIndex = regex.matchedFrom();
+
+ if ((selection != null) &&
+ ((resIndex +
+ Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))
+ {
+ continue;
+ }
+
+
+ int sres = seq.findPosition(resIndex +
+ Integer.parseInt(spaces.elementAt(resIndex)
+ .toString()));
+ int eres = seq.findPosition(regex.matchedTo() - 1 +
+ Integer.parseInt(spaces.elementAt(regex.matchedTo() -
+ 1).toString()));
+
+ searchResults.addResult(seq, sres, eres);
+
+ if (!findAll)
+ {
+ // thats enough, break and display the result
+ found = true;
+ resIndex++;
+
+ break;
+ }
+
+ r = resIndex;
+ }
+ else
+ {
+ break;
+ }
+ }
+
+ if (!found)
+ {
+ seqIndex++;
+ resIndex = 0;
+ }
+ }
+
+ Vector idMatch = new Vector();
+
+ for (int id = 0; id < av.alignment.getHeight(); id++)
+ {
+ if (regex.search(av.alignment.getSequenceAt(id).getName()))
+ {
+ idMatch.add(av.alignment.getSequenceAt(id));
+ }
+ }
+
+ 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);
+
+ 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 / blobdiff