/*\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
AlignViewport av;\r
AlignmentPanel ap;\r
JInternalFrame frame;\r
- SuperGroup searchGroup;\r
- Vector searchResults;\r
int seqIndex = 0;\r
int resIndex = 0;\r
\r
+ SearchResults searchResults;\r
+\r
/**\r
* Creates a new Finder object.\r
*\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
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void textfield_actionPerformed(ActionEvent e)\r
- {\r
- doSearch(false);\r
- }\r
\r
/**\r
* DOCUMENT ME!\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
public void createNewGroup_actionPerformed(ActionEvent e)\r
{\r
- Color[] newColors = new Color[24];\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
+ int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,\r
+ panel, "New Sequence Feature Name",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
\r
- for (int i = 0; i < 24; i++)\r
+ if(reply != JOptionPane.OK_OPTION)\r
+ return;\r
+\r
+ for (int i = 0; i < searchResults.getSize(); i ++ )\r
{\r
- newColors[i] = new Color(60, 160, 115);\r
- }\r
+ SequenceI seq = searchResults.getResultSequence(i);\r
\r
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);\r
- String searchString = textfield.getText();\r
+ SequenceFeature sf = new SequenceFeature(textinput.getText(),\r
+ "Search Results", null,\r
+ searchResults.getResultStart(i),\r
+ searchResults.getResultEnd(i),\r
+ "Search Results");\r
\r
- searchGroup = new SuperGroup(searchString, ucs, true, true, false);\r
+ ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
+ textinput.getText(), new Color(60,160,115),\r
+ "Search Results");\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
+ seq.getDatasetSequence().addSequenceFeature(sf);\r
}\r
\r
- ap.av.alignment.addSuperGroup(searchGroup);\r
+ ap.seqPanel.seqCanvas.getFeatureRenderer().findAllFeatures();\r
+ ap.alignFrame.showSeqFeatures.setSelected(true);\r
+ av.setShowSequenceFeatures(true);\r
ap.highlightSearchResults(null);\r
}\r
\r
{\r
createNewGroup.setEnabled(false);\r
\r
- String searchString = textfield.getText().toUpperCase();\r
+ String searchString = textfield.getText().trim();\r
+ if(!caseSensitive.isSelected())\r
+ searchString = searchString.toUpperCase();\r
\r
- com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
+ if(searchString.length()<1)\r
+ return;\r
\r
- searchResults = new Vector();\r
+ com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);\r
\r
- int[] allResults = null;\r
+ searchResults = new SearchResults();\r
\r
Sequence seq;\r
String item = null;\r
{\r
int res = Integer.parseInt(searchString);\r
found = true;\r
-\r
- if (av.getSelectionGroup().getSize() > 0)\r
+ if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize(false) < 1)\r
{\r
- seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
+ seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
}\r
else\r
{\r
- seq = (Sequence) av.getAlignment().getSequenceAt(0);\r
+ seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));\r
}\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
+ searchResults.addResult(seq, res, 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
\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
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.isSelected())\r
+ item = item.toUpperCase();\r
\r
if ((selection != null) &&\r
- (selection.getEndRes() < av.alignment.getWidth()))\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 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.add(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
- if (regex.searchFrom(noGaps.toString(), r))\r
+\r
+ if (regex.searchFrom(noGaps, r))\r
{\r
resIndex = regex.matchedFrom();\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
Integer.parseInt(spaces.elementAt(regex.matchedTo() -\r
1).toString()));\r
\r
- searchResults.addElement(sres + "");\r
- searchResults.addElement(eres + "");\r
+ searchResults.addResult(seq, sres, eres);\r
\r
if (!findAll)\r
{\r
\r
r = resIndex;\r
}\r
+ else\r
+ {\r
+ break;\r
+ }\r
}\r
\r
if (!found)\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
- {\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
+ int resultSize = searchResults.getSize();\r
\r
- createNewGroup.setEnabled(true);\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
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
+ String message = resultSize + " matches found.";\r
+ JOptionPane.showInternalMessageDialog(this, message, null,\r
+ JOptionPane.INFORMATION_MESSAGE);\r
}\r
+\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff