SequenceFeature sf = new SequenceFeature(textinput.getText(),\r
"Search Results", null,\r
searchResults.getResultStart(i),\r
- searchResults.getResultEnd(i));\r
+ searchResults.getResultEnd(i),\r
+ "Search Results");\r
\r
ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(\r
- textinput.getText(), new Color(60,160,115));\r
+ textinput.getText(), new Color(60,160,115),\r
+ "Search Results");\r
\r
seq.getDatasetSequence().addSequenceFeature(sf);\r
}\r
\r
- ap.alignFrame.sequenceFeatures.setSelected(true);\r
- ap.alignFrame.sequenceFeatures_actionPerformed(null);\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().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
int res = Integer.parseInt(searchString);\r
found = true;\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
}\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
- //SG 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()-1))\r