public void setGUINucleotide(boolean nucleotide)\r
{\r
showTranslation.setVisible( nucleotide );\r
- sequenceFeatures.setVisible(!nucleotide );\r
- featureSettings.setVisible( !nucleotide );\r
+ //sequenceFeatures.setVisible(!nucleotide );\r
+ //featureSettings.setVisible( !nucleotide );\r
conservationMenuItem.setVisible( !nucleotide );\r
modifyConservation.setVisible( !nucleotide );\r
\r
- //Deal with separators\r
//Remember AlignFrame always starts as protein\r
- if(nucleotide)\r
- {\r
- viewMenu.remove(viewMenu.getItemCount()-2);\r
- }\r
- else\r
+ if(!nucleotide)\r
{\r
calculateMenu.remove(calculateMenu.getItemCount()-2);\r
}\r
{\r
new SequenceFetcher(this);\r
}\r
-\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
if(str.length()<1)\r
return;\r
\r
- String format = IdentifyFile.Identify(str, "Paste");\r
+ String format = new IdentifyFile().Identify(str, "Paste");\r
SequenceI[] sequences;\r
\r
if(Desktop.jalviewClipboard!=null)\r
return;\r
}\r
\r
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
- HistoryItem.HIDE));\r
\r
SequenceGroup sg = viewport.getSelectionGroup();\r
- boolean allSequences = false;\r
- if (sg.sequences.size() == viewport.alignment.getHeight())\r
+\r
+\r
+\r
+ //Jalview no longer allows deletion of residues.\r
+ //Check here whether any residues are in selection area\r
+ if( sg.getEndRes()-sg.getStartRes() < viewport.alignment.getWidth()-1)\r
{\r
- allSequences = true;\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ SequenceI seq = sg.getSequenceAt(i);\r
+ int j = sg.getStartRes();\r
+ do\r
+ {\r
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(\r
+ Desktop.desktop, "Cannot delete residues from alignment!\n"\r
+ + "Try hiding columns instead.",\r
+ "Deletion of residues not permitted",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+ j++;\r
+ }while(j<=sg.getEndRes());\r
+ }\r
}\r
\r
+\r
+ addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
+ HistoryItem.HIDE));\r
+\r
+\r
for (int i = 0; i < sg.sequences.size(); i++)\r
{\r
SequenceI seq = sg.getSequenceAt(i);\r
int index = viewport.getAlignment().findIndex(seq);\r
+\r
seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
\r
// If the cut affects all sequences, remove highlighted columns\r
- if (allSequences)\r
+ if (sg.sequences.size() == viewport.alignment.getHeight())\r
{\r
viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
sg.getEndRes() + 1);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
- alignPanel.annotationPanel.activeRes = null;\r
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
JInternalFrame frame = new JInternalFrame();\r
Finder finder = new Finder(viewport, alignPanel, frame);\r
frame.setContentPane(finder);\r
- Desktop.addInternalFrame(frame, "Find", 340, 110);\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ Desktop.addInternalFrame(frame, "Find", 340, 110);\r
}\r
\r
/**\r
alignPanel.repaint();\r
}\r
\r
+ public void fetchSeqFeatures_actionPerformed(ActionEvent e)\r
+ {\r
+ if (!viewport.alignment.isNucleotide())\r
+ {\r
+ new SequenceFeatureFetcher(viewport.\r
+ alignment,\r
+ alignPanel);\r
+ viewport.setShowSequenceFeatures(true);\r
+ showSeqFeatures.setSelected(true);\r
+ }\r
+ }\r
+\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+ new FeatureSettings(viewport, alignPanel);\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @param evt DOCUMENT ME!\r
*/\r
- public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
+ public void showSeqFeatures_actionPerformed(ActionEvent evt)\r
{\r
- viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
-\r
- if (viewport.showSequenceFeatures)\r
+ viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());\r
+ alignPanel.repaint();\r
+ if (alignPanel.getOverviewPanel() != null)\r
{\r
- new SequenceFeatureFetcher(viewport.\r
- alignment,\r
- alignPanel);\r
+ alignPanel.getOverviewPanel().updateOverviewImage();\r
}\r
-\r
- featureSettings.setEnabled(true);\r
-\r
- alignPanel.repaint();\r
}\r
\r
/**\r
}\r
}*/\r
\r
- public void featureSettings_actionPerformed(ActionEvent e)\r
- {\r
- new FeatureSettings(viewport, alignPanel);\r
- }\r
+\r
\r
\r
\r
protein = new StringBuffer();\r
seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());\r
resSize = seq.length();\r
+ resSize -= resSize%3;\r
+\r
for(res = 0; res < resSize; res+=3)\r
{\r
String codon = seq.substring(res, res+3);\r
StringTokenizer st;\r
SequenceFeature sf;\r
int lineNo = 0;\r
+ String featureGroup = null;\r
while ( (line = in.readLine()) != null)\r
{\r
lineNo++;\r
if (st.countTokens() == 2)\r
{\r
type = st.nextToken();\r
- UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
- alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type, ucs.findColour("A"));\r
+ if (type.equalsIgnoreCase("startgroup"))\r
+ {\r
+ featureGroup = st.nextToken();\r
+ }\r
+ else if (type.equalsIgnoreCase("endgroup"))\r
+ {\r
+ //We should check whether this is the current group,\r
+ //but at present theres no way of showing more than 1 group\r
+ st.nextToken();\r
+ featureGroup = null;\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(type,\r
+ ucs.findColour("A"));\r
+ }\r
continue;\r
}\r
\r
end = Integer.parseInt(st.nextToken());\r
\r
seq = viewport.alignment.getSequenceAt(index);\r
- start = seq.findIndex(start) - 1;\r
- end = seq.findIndex(end) - 1;\r
\r
type = st.nextToken();\r
\r
}\r
\r
sf = new SequenceFeature(type, desc, "", start, end);\r
+ sf.setFeatureGroup(featureGroup);\r
\r
seq.getDatasetSequence().addSequenceFeature(sf);\r
}\r
}\r
catch (Exception ex)\r
{\r
+ ex.printStackTrace();\r
System.out.println("Error parsing groups file: " + ex);\r
return false;\r
}\r
\r
viewport.showSequenceFeatures = true;\r
+ showSeqFeatures.setSelected(true);\r
alignPanel.repaint();\r
return true;\r
}\r
if (!isGroupsFile)\r
{\r
String protocol = "File";\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
+ String format = new IdentifyFile().Identify(file, protocol);\r
SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format);\r
\r
FastaFile ff = new FastaFile();\r
git://source.jalview.org / jalview.git / blobdiff