-/*\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.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-public class Finder extends Panel implements ActionListener\r
-{\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- Frame frame;\r
- SuperGroup searchGroup;\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
- Color[] newColors = new Color[24];\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(\r
- newColors);\r
- String searchString = textfield.getText();\r
-\r
- searchGroup = new SuperGroup(searchString, ucs, true, true, false);\r
-\r
- for (int i = 0; i < searchResults.getSize(); i ++ )\r
- {\r
- // its possible edits may have occurred since search was performed\r
- // account for this here\r
-\r
- SequenceI seq = searchResults.getResultSequence(i);\r
- int startRes = seq.findIndex(searchResults.getResultStart(i)) - 1;\r
- int endRes = seq.findIndex(searchResults.getResultEnd(i)) - 1;\r
-\r
- SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,\r
- startRes, endRes);\r
- sg.addSequence(seq, false);\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
- void doSearch(boolean findAll)\r
- {\r
- createNewGroup.setEnabled(false);\r
-\r
- String searchString = textfield.getText().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
- seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
-\r
- if (selection != null && !selection.sequences.contains(seq))\r
- {\r
- seqIndex++;\r
- resIndex = 0;\r
- continue;\r
- }\r
-\r
- item = seq.getSequence().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 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.addElement(new Integer(insertCount));\r
- }\r
- else\r
- {\r
- insertCount++;\r
- }\r
- }\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 &&\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.getSize()) + " matches found.";\r
- System.out.println(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
-\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("Create new group");\r
- createNewGroup.addActionListener(this);\r
- jPanel1.add(findNext, null);\r
- jPanel1.add(findAll, null);\r
- jPanel1.add(createNewGroup, null);\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);
+ 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)
+ {
+ createNewGroup.setEnabled(false);
+
+ String searchString = textfield.getText();
+ if(!caseSensitive.getState())
+ searchString = searchString.toUpperCase();
+
+ 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.getState())
+ item = item.toUpperCase();
+
+ if (selection != null && selection.getEndRes() < av.alignment.getWidth())
+ {
+ 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.addElement(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.elementAt(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.addElement(av.alignment.getSequenceAt(id));
+ }
+ }
+
+ 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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff