/*\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
+ * 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
package jalview.gui;\r
\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.schemes.*;\r
import java.awt.*;\r
-import javax.swing.*;\r
import java.awt.event.*;\r
-import jalview.io.*;\r
+import javax.swing.*;\r
+\r
import MCview.*;\r
+import jalview.analysis.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.schemes.*;\r
\r
-public class PopupMenu extends JPopupMenu\r
+public class PopupMenu\r
+ extends JPopupMenu\r
{\r
JMenu groupMenu = new JMenu();\r
JMenuItem groupName = new JMenuItem();\r
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();\r
+ protected JRadioButtonMenuItem hydrophobicityColour = new\r
+ JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
-\r
-\r
AlignmentPanel ap;\r
JMenu sequenceMenu = new JMenu();\r
JMenuItem sequenceName = new JMenuItem();\r
//\r
// If from the IDPanel, we must display the sequence menu\r
//////////////////////////////////////////////////////////\r
-\r
this.ap = ap;\r
sequence = seq;\r
\r
colours.add(BLOSUM62Colour);\r
\r
try\r
- { jbInit(); }\r
- catch(Exception e)\r
- { e.printStackTrace(); }\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
+\r
+ if (sg != null)\r
{\r
groupName.setText(sg.getName());\r
- if(sg.cs instanceof ZappoColourScheme)\r
+\r
+ if (sg.cs instanceof ZappoColourScheme)\r
+ {\r
zappoColour.setSelected(true);\r
- else if(sg.cs instanceof TaylorColourScheme)\r
+ }\r
+ else if (sg.cs instanceof TaylorColourScheme)\r
+ {\r
taylorColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof PIDColourScheme)\r
+ {\r
PIDColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof Blosum62ColourScheme)\r
+ {\r
BLOSUM62Colour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof UserColourScheme)\r
+ {\r
userDefinedColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof HydrophobicColourScheme)\r
+ {\r
hydrophobicityColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof HelixColourScheme)\r
+ {\r
helixColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof StrandColourScheme)\r
+ {\r
strandColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof TurnColourScheme)\r
+ {\r
turnColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof BuriedColourScheme)\r
+ {\r
buriedColour.setSelected(true);\r
+ }\r
else if (sg.cs instanceof ClustalxColourScheme)\r
+ {\r
clustalColour.setSelected(true);\r
+ }\r
else\r
+ {\r
noColourmenuItem.setSelected(true);\r
+ }\r
\r
if (sg.cs instanceof ConservationColourScheme)\r
+ {\r
conservationMenuItem.setSelected(true);\r
+ }\r
\r
showText.setSelected(sg.getDisplayText());\r
showColourText.setSelected(sg.getColourText());\r
showBoxes.setSelected(sg.getDisplayBoxes());\r
}\r
\r
- if( !ap.av.alignment.getGroups().contains(sg))\r
+ if (!ap.av.alignment.getGroups().contains(sg))\r
+ {\r
unGroupMenuItem.setVisible(false);\r
+ }\r
else\r
+ {\r
groupMenu.insertSeparator(3);\r
+ }\r
\r
- if(seq==null)\r
- sequenceMenu.setVisible(false);\r
-\r
+ if (seq == null)\r
+ {\r
+ sequenceMenu.setVisible(false);\r
+ }\r
}\r
- private void jbInit() throws Exception\r
+\r
+ private void jbInit()\r
+ throws Exception\r
{\r
groupMenu.setText("Group");\r
groupMenu.setText("Define");\r
}\r
});\r
conservationMenuItem.setText("Conservation");\r
- conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationMenuItem_actionPerformed(e);\r
- }\r
- });\r
-\r
-\r
-\r
+ conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ conservationMenuItem_actionPerformed(e);\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
+\r
+ if (superG != null)\r
+ {\r
+ superG.setSuperGroupProperties(sg);\r
+ }\r
\r
ap.seqPanel.repaint();\r
}\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
- sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
+ sg.cs = new ClustalxColourScheme(sg.sequences,\r
+ ap.av.alignment.getWidth());\r
refresh();\r
}\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_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
+\r
if (abovePIDColour.isSelected())\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
+\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
+ getGroup().getName());\r
+\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
refresh();\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_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
\r
- if(conservationMenuItem.isSelected())\r
+ if (conservationMenuItem.isSelected())\r
{\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ ap.av.alignment.getWidth());\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
+ c.calculate();\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
\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 groupName_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
- String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
- if(reply==null)\r
+ String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Enter new group name", "Edit group name",\r
+ JOptionPane.QUESTION_MESSAGE);\r
+\r
+ if (reply == null)\r
+ {\r
return;\r
+ }\r
\r
sg.setName(reply);\r
groupName.setText(reply);\r
}\r
\r
-\r
protected void analyze_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(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.get(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();\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(cap);\r
+ Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
+\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.get(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
SequenceGroup getGroup()\r
void sequenceName_actionPerformed(ActionEvent e)\r
{\r
String id = sequence.getName();\r
- String s = (String)JOptionPane.showInternalInputDialog(\r
- ap,\r
- "Edit sequence name",\r
- "Edit sequence name ("+sequence.getName()+")",\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- null,\r
- id);\r
+ String s = (String) JOptionPane.showInternalInputDialog(ap,\r
+ "Edit sequence name",\r
+ "Edit sequence name (" + sequence.getName() + ")",\r
+ JOptionPane.PLAIN_MESSAGE, null, null, id);\r
\r
- if(s!=null)\r
+ if (s != null)\r
{\r
sequence.setName(s);\r
ap.repaint();\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
void pdbMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if(sequence.getPDBId()==null)\r
+ if (sequence.getPDBId() == null)\r
+ {\r
return;\r
+ }\r
\r
try\r
{\r
EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
+ String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,\r
+ null);\r
\r
PDBfile pdb = new PDBfile(result);\r
\r
rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
JInternalFrame frame = new JInternalFrame();\r
frame.setContentPane(rc);\r
- Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);\r
+ Desktop.addInternalFrame(frame,\r
+ sequence.getName() + " " + sequence.getPDBId(),\r
+ 400, 400);\r
}\r
catch (Exception ex)\r
{\r
protected void outline_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
- Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);\r
- if(col!=null)\r
+ Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
+ Color.BLUE);\r
+\r
+ if (col != null)\r
+ {\r
sg.setOutlineColour(col);\r
+ }\r
+\r
ap.repaint();\r
}\r
\r
getGroup().setColourText(showColourText.isSelected());\r
refresh();\r
}\r
-\r
}\r
git://source.jalview.org / jalview.git / blobdiff