/*\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
int seqIndex = 0;\r
int resIndex = 0;\r
\r
* @param ap DOCUMENT ME!\r
* @param f DOCUMENT ME!\r
*/\r
- public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)\r
+ public Finder()\r
{\r
- this.av = av;\r
- this.ap = ap;\r
- frame = f;\r
+ frame = new JInternalFrame();\r
+ frame.setContentPane(this);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ Desktop.addInternalFrame(frame, "Find", 340, 110);\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
+ textfield.requestFocus();\r
}\r
\r
\r
*/\r
public void findNext_actionPerformed(ActionEvent e)\r
{\r
+ if (getFocusedViewport())\r
doSearch(false);\r
}\r
\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
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
- 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
+ SequenceI [] seqs = new SequenceI[searchResults.getSize()];\r
+ SequenceFeature [] features = new SequenceFeature[searchResults.getSize()];\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
- 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,\r
- false, startRes, endRes);\r
- sg.addSequence(seq, false);\r
- av.alignment.addGroup(sg);\r
- searchGroup.addGroup(sg);\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
- ap.av.alignment.addSuperGroup(searchGroup);\r
- ap.highlightSearchResults(null);\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
{\r
createNewGroup.setEnabled(false);\r
\r
- String searchString = textfield.getText().toUpperCase().trim();\r
+ String searchString = textfield.getText().trim();\r
+ if(!caseSensitive.isSelected())\r
+ searchString = searchString.toUpperCase();\r
+\r
if(searchString.length()<1)\r
return;\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
seq = (Sequence) av.alignment.getSequenceAt(seqIndex);\r
\r
- if ((selection != null) && !selection.sequences.contains(seq))\r
+ if ((selection != null) && !selection.getSequences(null).contains(seq))\r
{\r
seqIndex++;\r
resIndex = 0;\r
continue;\r
}\r
\r
- item = seq.getSequence().toUpperCase();\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
git://source.jalview.org / jalview.git / blobdiff