/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
\r
package jalview.appletgui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.schemes.*;\r
import java.awt.*;\r
import java.awt.event.*;\r
\r
-public class APopupMenu extends java.awt.PopupMenu\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
+\r
+public class APopupMenu\r
+ extends java.awt.PopupMenu\r
{\r
Menu groupMenu = new Menu();\r
protected MenuItem clustalColour = new MenuItem();\r
MenuItem noColourmenuItem = new MenuItem();\r
protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
\r
-\r
AlignmentPanel ap;\r
Menu sequenceMenu = new Menu();\r
MenuItem sequenceName = new MenuItem();\r
sequence = seq;\r
\r
try\r
- { jbInit(); }\r
- catch(Exception e)\r
- { e.printStackTrace(); }\r
-\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
- if(sg!=null)\r
+ if (sg != null)\r
{\r
showText.setState(sg.getDisplayText());\r
showColourText.setState(sg.getColourText());\r
showBoxes.setState(sg.getDisplayBoxes());\r
}\r
\r
- if( !ap.av.alignment.getGroups().contains(sg))\r
- groupMenu.remove(unGroupMenuItem);\r
-\r
- if(seq==null)\r
- remove(sequenceMenu);\r
+ if (!ap.av.alignment.getGroups().contains(sg))\r
+ {\r
+ groupMenu.remove(unGroupMenuItem);\r
+ }\r
\r
+ if (seq == null)\r
+ {\r
+ remove(sequenceMenu);\r
+ }\r
\r
}\r
- private void jbInit() throws Exception\r
+\r
+ private void jbInit()\r
+ throws Exception\r
{\r
groupMenu.setLabel("Group");\r
groupMenu.setLabel("Define");\r
}\r
});\r
\r
-\r
nucleotideMenuItem.setLabel("Nucleotide");\r
nucleotideMenuItem.addActionListener(new ActionListener()\r
{\r
});\r
conservationMenuItem.setLabel("Conservation");\r
\r
-\r
}\r
\r
void refresh()\r
{\r
SequenceGroup sg = getGroup();\r
- SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
- if( superG !=null)\r
- superG.setSuperGroupProperties( sg );\r
+ SuperGroup superG = ap.av.alignment.getSuperGroup(sg);\r
+ if (superG != null)\r
+ {\r
+ superG.setSuperGroupProperties(sg);\r
+ }\r
\r
ap.seqPanel.seqCanvas.repaint();\r
}\r
refresh();\r
}\r
\r
-\r
protected void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
getGroup().cs = new HydrophobicColourScheme();\r
refresh();\r
}\r
\r
-\r
-\r
protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
{\r
SequenceGroup sg = getGroup();\r
{\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
ap.av.alignment.getWidth()));\r
- int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
+ getGroup().getName());\r
if (sg.cs instanceof ResidueColourScheme)\r
- ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
+ {\r
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
else if (sg.cs instanceof ScoreColourScheme)\r
+ {\r
( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+ }\r
\r
SliderPanel.showPIDSlider();\r
\r
-\r
}\r
else // remove PIDColouring\r
{\r
\r
}\r
\r
-\r
protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- new UserDefinedColours( ap, getGroup());\r
+ new UserDefinedColours(ap, getGroup());\r
}\r
\r
protected void PIDColour_actionPerformed(ActionEvent e)\r
SequenceGroup sg = getGroup();\r
sg.cs = new PIDColourScheme();\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ ap.av.alignment.getWidth()));\r
refresh();\r
}\r
\r
sg.cs = new Blosum62ColourScheme();\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
- ap.av.alignment.getWidth()));\r
+ ap.av.alignment.getWidth()));\r
\r
refresh();\r
}\r
\r
-\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
getGroup().cs = null;\r
refresh();\r
}\r
\r
- protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
+ protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
{\r
SequenceGroup sg = getGroup();\r
\r
- if(conservationMenuItem.getState())\r
+ if (conservationMenuItem.getState())\r
{\r
\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
- ap.av.alignment.getWidth());\r
-\r
- c.calculate();\r
- c.verdict(false, ap.av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ ap.av.alignment.getWidth());\r
\r
+ c.calculate();\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
sg.cs = ccs;\r
\r
}\r
else // remove ConservationColouring\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
- sg.cs = ccs.cs;\r
+ ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
+ sg.cs = ccs.cs;\r
}\r
\r
- refresh();\r
+ refresh();\r
}\r
\r
-\r
protected void analyze_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for(int i=0; i<sg.sequences.size(); i++)\r
- {\r
- Sequence tmp = (Sequence)sg.sequences.elementAt(i);\r
- sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));\r
- sb.append("\n");\r
- }\r
-\r
- sb.append("Something amazing will happen soon");\r
- cap.setText( sb.toString() );\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
+ SequenceGroup sg = getGroup();\r
+ StringBuffer sb = new StringBuffer();\r
+\r
+ for (int i = 0; i < sg.sequences.size(); i++)\r
+ {\r
+ Sequence tmp = (Sequence) sg.sequences.elementAt(i);\r
+ sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
+ sb.append("\n");\r
+ }\r
+\r
+ sb.append("Something amazing will happen soon");\r
+ cap.setText(sb.toString());\r
\r
}\r
\r
\r
void unGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.setSelectionGroup(null);\r
- ap.repaint();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ap.av.alignment.deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ ap.repaint();\r
}\r
\r
-\r
public void showColourText_itemStateChanged(ItemEvent itemEvent)\r
{\r
getGroup().setColourText(showColourText.getState());\r
git://source.jalview.org / jalview.git / blobdiff