/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
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
- SuperGroup searchGroup;\r
- Vector searchResults;\r
+\r
+ SearchResults searchResults;\r
\r
int seqIndex = 0;\r
int resIndex = 0;\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
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, null);\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
- searchGroup = new SuperGroup(searchString, ucs, true, true, false);\r
\r
- for (int i = 0; i < searchResults.size(); i += 3)\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
- // 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.\r
- elementAt(i).toString()));\r
- int startRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i +\r
- 1).toString())) - 1;\r
- int endRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i + 2).\r
- toString())) - 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
+ 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.av.alignment.addSuperGroup(searchGroup);\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().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
\r
- searchResults = new Vector();\r
- int[] allResults = null;\r
+ searchResults = new SearchResults();\r
\r
Sequence seq;\r
String item = null;\r
int res = Integer.parseInt(searchString);\r
found = true;\r
\r
- if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)\r
+ if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
{\r
seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
}\r
seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
}\r
\r
- searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq)));\r
- searchResults.addElement(String.valueOf(res));\r
- searchResults.addElement(String.valueOf(res));\r
+\r
+ searchResults.addResult(seq, res, res);\r
\r
}\r
catch (NumberFormatException ex)\r
SequenceGroup selection = av.getSelectionGroup();\r
if (selection != null)\r
{\r
- if (selection.getSize() < 1 ||\r
+ if (selection.getSize(false) < 1 ||\r
(selection.getEndRes() - selection.getStartRes() < 2))\r
{\r
selection = null;\r
\r
while (!found && seqIndex < end)\r
{\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
continue;\r
}\r
\r
- item = seq.getSequence().toUpperCase();\r
+ item = seq.getSequence();\r
+ if(!caseSensitive.getState())\r
+ item = item.toUpperCase();\r
\r
if (selection != null && selection.getEndRes() < av.alignment.getWidth())\r
{\r
}\r
\r
///Shall we ignore gaps????\r
- StringBuffer noGaps = new StringBuffer();\r
+ StringBuffer noGapsSB = new StringBuffer();\r
int insertCount = 0;\r
Vector spaces = new Vector();\r
\r
\r
if (!jalview.util.Comparison.isGap(item.charAt(j)))\r
{\r
- noGaps.append(item.charAt(j));\r
+ noGapsSB.append(item.charAt(j));\r
spaces.addElement(new Integer(insertCount));\r
}\r
else\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.toString(), r))\r
+ if (regex.searchFrom(noGaps, r))\r
{\r
resIndex = regex.matchedFrom();\r
if (selection != null &&\r
continue;\r
}\r
\r
- searchResults.addElement(Integer.toString(seqIndex));\r
+\r
int sres = seq.findPosition(resIndex +\r
Integer.parseInt(spaces.\r
elementAt(resIndex).toString()));\r
Integer.parseInt(\r
spaces.elementAt(regex.matchedTo() - 1).\r
toString()));\r
- searchResults.addElement(sres + "");\r
- searchResults.addElement(eres + "");\r
+\r
+ searchResults.addResult(seq, sres, eres);\r
\r
if (!findAll)\r
{\r
}\r
}\r
\r
- if (searchResults.size() == 0 && idMatch.size() > 0)\r
+ if (searchResults.getSize() == 0 && idMatch.size() > 0)\r
{\r
ap.idPanel.highlightSearchResults(idMatch);\r
}\r
\r
- if (searchResults.size() > 0)\r
+ if (searchResults.getSize() > 0)\r
{\r
- allResults = new int[searchResults.size()];\r
- for (int i = 0; i < searchResults.size(); i++)\r
- {\r
- allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());\r
- }\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(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
Panel jPanel1 = new Panel();\r
GridLayout gridLayout1 = new GridLayout();\r
protected Button createNewGroup = new Button();\r
-\r
+ Checkbox caseSensitive = new Checkbox();\r
\r
private void jbInit() throws Exception {\r
jLabel1.setFont(new java.awt.Font("Verdana", 0, 12));\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.setLabel("New Feature");\r
createNewGroup.addActionListener(this);\r
- jPanel1.add(findNext, null);\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(textfield, null);\r
+ this.add(caseSensitive);\r
+ this.add(textfield, null);\r
this.add(jLabel1, null);\r
this.add(jPanel1, null);\r
}\r
git://source.jalview.org / jalview.git / blobdiff