+/*\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 javax.swing.*;\r
+import java.awt.*;\r
import java.awt.event.*;\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 copyGroup = new JMenuItem();\r
- JMenuItem moveGroup = new JMenuItem();\r
- JMenuItem deleteSequences = new JMenuItem();\r
- JMenuItem analyze = new JMenuItem();\r
- JMenu defineMenu = new JMenu();\r
JMenuItem groupName = new JMenuItem();\r
- JMenuItem groupAnnotation = 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
- JMenu residueMenu = new JMenu();\r
- JMenuItem annotateResidue = new JMenuItem();\r
-\r
- SequenceI sequence;\r
-\r
- public PopupMenu(AlignmentPanel ap, SequenceI seq)\r
+ Sequence sequence;\r
+ JMenuItem unGroupMenuItem = new JMenuItem();\r
+ JMenuItem pdbMenuItem = new JMenuItem();\r
+ JMenuItem outline = new JMenuItem();\r
+ JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
+ JMenu colourMenu = new JMenu();\r
+ JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
+ JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
+ JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
+\r
+ public PopupMenu(AlignmentPanel ap, Sequence seq)\r
{\r
///////////////////////////////////////////////////////////\r
// If this is activated from the sequence panel, the user may want to\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
\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
- if(sg!=null)\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(seq!=null)\r
+ if (!ap.av.alignment.getGroups().contains(sg))\r
{\r
- residueMenu.setVisible(false);\r
- sequenceName.setText( sequence.getName() );\r
+ unGroupMenuItem.setVisible(false);\r
}\r
else\r
- sequenceMenu.setVisible(false);\r
+ {\r
+ groupMenu.insertSeparator(3);\r
+ }\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
- copyGroup.setText("Copy region to new Alignment");\r
- copyGroup.addActionListener(new java.awt.event.ActionListener()\r
+ groupMenu.setText("Define");\r
+ groupName.setText("Name");\r
+ groupName.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ groupName_actionPerformed(e);\r
+ }\r
+ });\r
+ sequenceMenu.setText("Sequence");\r
+ sequenceName.setText("Edit name");\r
+ sequenceName.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- copyGroup_actionPerformed(e);\r
+ sequenceName_actionPerformed(e);\r
}\r
});\r
- moveGroup.setText("Move sequences to new Alignment");\r
- moveGroup.addActionListener(new java.awt.event.ActionListener()\r
+ PIDColour.setFocusPainted(false);\r
+ unGroupMenuItem.setText("Remove Group");\r
+ unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- moveGroup_actionPerformed(e);\r
+ unGroupMenuItem_actionPerformed(e);\r
}\r
});\r
- deleteSequences.setText("Delete sequences");\r
- deleteSequences.addActionListener(new java.awt.event.ActionListener()\r
+ pdbMenuItem.setText("View PDB structure");\r
+ pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- deleteSequences_actionPerformed(e);\r
+ pdbMenuItem_actionPerformed(e);\r
}\r
});\r
- analyze.setText("Analyze");\r
- analyze.addActionListener(new java.awt.event.ActionListener()\r
+ outline.setText("Border colour");\r
+ outline.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- analyze_actionPerformed(e);\r
+ outline_actionPerformed(e);\r
}\r
});\r
- defineMenu.setText("Define");\r
- groupName.setText("Name");\r
- groupName.addActionListener(new java.awt.event.ActionListener()\r
+ nucleotideMenuItem.setText("Nucleotide");\r
+ nucleotideMenuItem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupName_actionPerformed(e);\r
+ nucleotideMenuItem_actionPerformed(e);\r
}\r
});\r
- groupAnnotation.setText("Annotation");\r
- groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
+ colourMenu.setText("Group Colour");\r
+ showBoxes.setText("Boxes");\r
+ showBoxes.setState(true);\r
+ showBoxes.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupAnnotation_actionPerformed(e);\r
+ showBoxes_actionPerformed(e);\r
}\r
});\r
- sequenceMenu.setText("Sequence");\r
- sequenceName.setText("sequenceName");\r
- sequenceName.addActionListener(new java.awt.event.ActionListener()\r
+ showText.setText("Text");\r
+ showText.setState(true);\r
+ showText.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- sequenceName_actionPerformed(e);\r
+ showText_actionPerformed(e);\r
+ }\r
+ });\r
+ showColourText.setText("Colour Text");\r
+ showColourText.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ showColourText_actionPerformed(e);\r
}\r
});\r
- residueMenu.setText("Residue");\r
- annotateResidue.setText("annotate residue???");\r
- PIDColour.setFocusPainted(false);\r
add(groupMenu);\r
- this.add(sequenceMenu);\r
- this.add(residueMenu);\r
- groupMenu.add(defineMenu);\r
+ add(sequenceMenu);\r
+ groupMenu.add(groupName);\r
groupMenu.addSeparator();\r
- groupMenu.add(copyGroup);\r
- groupMenu.add(moveGroup);\r
- groupMenu.add(deleteSequences);\r
+ groupMenu.add(unGroupMenuItem);\r
+ groupMenu.add(colourMenu);\r
groupMenu.addSeparator();\r
- groupMenu.add(analyze);\r
- defineMenu.add(groupName);\r
- defineMenu.add(groupAnnotation);\r
- defineMenu.addSeparator();\r
- defineMenu.add(noColourmenuItem);\r
- defineMenu.add(clustalColour);\r
- defineMenu.add(zappoColour);\r
- defineMenu.add(taylorColour);\r
- defineMenu.add(hydrophobicityColour);\r
- defineMenu.add(helixColour);\r
- defineMenu.add(strandColour);\r
- defineMenu.add(turnColour);\r
- defineMenu.add(buriedColour);\r
- defineMenu.add(userDefinedColour);\r
- defineMenu.add(PIDColour);\r
- defineMenu.add(BLOSUM62Colour);\r
- defineMenu.addSeparator();\r
- defineMenu.add(abovePIDColour);\r
- defineMenu.add(conservationMenuItem);\r
-\r
+ groupMenu.add(showBoxes);\r
+ groupMenu.add(showText);\r
+ groupMenu.add(showColourText);\r
+ groupMenu.addSeparator();\r
+ groupMenu.add(outline);\r
sequenceMenu.add(sequenceName);\r
- residueMenu.add(annotateResidue);\r
-\r
+ sequenceMenu.add(pdbMenuItem);\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideMenuItem);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(abovePIDColour);\r
+ colourMenu.add(conservationMenuItem);\r
noColourmenuItem.setText("None");\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
clustalColour_actionPerformed(e);\r
}\r
});\r
- zappoColour.setText("Zappo colour scheme");\r
+ zappoColour.setText("Zappo");\r
zappoColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
zappoColour_actionPerformed(e);\r
}\r
});\r
- taylorColour.setText("Taylor colour scheme");\r
+ taylorColour.setText("Taylor");\r
taylorColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
taylorColour_actionPerformed(e);\r
}\r
});\r
- hydrophobicityColour.setText("By hydrophobicity");\r
+ hydrophobicityColour.setText("Hydrophobicity");\r
hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
turnColour_actionPerformed(e);\r
}\r
});\r
- buriedColour.setText("Buried index");\r
+ buriedColour.setText("Buried Index");\r
buriedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
buriedColour_actionPerformed(e);\r
}\r
});\r
- abovePIDColour.setText("Above PID threshold only");\r
+ abovePIDColour.setText("Above % Identity");\r
abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
abovePIDColour_actionPerformed(e);\r
}\r
});\r
- userDefinedColour.setText("User defined colours");\r
+ userDefinedColour.setText("User Defined");\r
userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
PIDColour_actionPerformed(e);\r
}\r
});\r
- BLOSUM62Colour.setText("BLOSUM62 score");\r
+ BLOSUM62Colour.setText("BLOSUM62");\r
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
BLOSUM62Colour_actionPerformed(e);\r
}\r
});\r
- conservationMenuItem.setText("By 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.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
void refresh()\r
{\r
- ap.seqPanel.seqCanvas.paintFlag=true;\r
+ SequenceGroup sg = getGroup();\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
\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- getGroup().cs = new ClustalxColourScheme();\r
+ SequenceGroup sg = getGroup();\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
-public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
-{\r
-ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
-JInternalFrame frame = new JInternalFrame();\r
-frame.setContentPane(cip);\r
-Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
-frame.setMaximizable(false);\r
-\r
- }*/\r
-\r
+ public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ getGroup().cs = new NucleotideColourScheme();\r
+ refresh();\r
+ }\r
\r
protected void abovePIDColour_actionPerformed(ActionEvent e)\r
{\r
- SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(sp);\r
- Desktop.addInternalFrame(frame, "Percentage Identity Threshold ("+getGroup().getName()+")" , 400,90);\r
- frame.setMaximizable(false);\r
-\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
\r
- protected void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
- frame.setContentPane(chooser);\r
- Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );\r
- frame.setResizable(false);\r
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
+ getGroup().getName());\r
\r
- }\r
+ if (sg.cs instanceof ResidueColourScheme)\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
- protected void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
+ SliderPanel.showPIDSlider();\r
+ }\r
+ else // remove PIDColouring\r
+ {\r
+ ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
+ rcs.setThreshold(0);\r
+ sg.cs = rcs;\r
+ }\r
\r
+ refresh();\r
}\r
\r
- protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
+ protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- getGroup().cs = new Blosum62ColourScheme(ap.av);\r
- refresh();\r
+ new UserDefinedColours(ap, getGroup());\r
}\r
\r
-\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
+ protected void PIDColour_actionPerformed(ActionEvent e)\r
{\r
- getGroup().cs = null;\r
+ SequenceGroup sg = getGroup();\r
+ sg.cs = new PIDColourScheme();\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ ap.av.alignment.getWidth()));\r
refresh();\r
}\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = getGroup();\r
\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),\r
- sg.getEndRes() );\r
-\r
- c.calculate();\r
- c.verdict(false, 100);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
+ sg.cs = new Blosum62ColourScheme();\r
\r
- sg.cs = ccs;\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ ap.av.alignment.getWidth()));\r
\r
- refresh();\r
+ refresh();\r
}\r
\r
-/*\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme( null );\r
- changeColour();\r
- }\r
-\r
-\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
- conservationMenuItem.setSelected(false);\r
- abovePIDThreshold.setSelected(false);\r
- changeColour();\r
+ getGroup().cs = null;\r
+ refresh();\r
}\r
\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
- changeColour();\r
- }\r
+ SequenceGroup sg = getGroup();\r
\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
- changeColour();\r
- }\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
+ c.calculate();\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
- changeColour();\r
- }\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new HelixColourScheme() );\r
- changeColour();\r
- }\r
+ sg.cs = ccs;\r
\r
+ SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+ SliderPanel.showConservationSlider();\r
+ }\r
+ else // remove ConservationColouring\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
+ sg.cs = ccs.cs;\r
+ }\r
\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new StrandColourScheme() );\r
- changeColour();\r
+ refresh();\r
}\r
\r
-\r
- public void turnColour_actionPerformed(ActionEvent e)\r
+ protected void groupName_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(new TurnColourScheme() );\r
- changeColour();\r
- }\r
+ SequenceGroup sg = getGroup();\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
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
- changeColour();\r
+ sg.setName(reply);\r
+ groupName.setText(reply);\r
}\r
\r
- void changeColour()\r
+ protected void analyze_actionPerformed(ActionEvent e)\r
{\r
- if(abovePIDThreshold.isSelected())\r
- abovePIDThreshold_actionPerformed(null);\r
- else if(conservationMenuItem.isSelected())\r
- conservationMenuItem_actionPerformed(null);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(cap);\r
+ Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);\r
\r
- alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
- alignPanel.repaint();\r
- }\r
+ SequenceGroup sg = getGroup();\r
+ StringBuffer sb = new StringBuffer();\r
\r
- void addConservationOrPIDColour()\r
- {\r
- int x=0, y=0, threshold = 70;\r
-\r
- if(sliderFrame!=null)\r
- try\r
- {\r
- x = sliderFrame.getX();\r
- y = sliderFrame.getY();\r
- SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();\r
- threshold = sp.getValue();\r
- sliderFrame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- { ex.printStackTrace(); }\r
-\r
- ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
-\r
- ConservationColourScheme ccs = null;\r
- if (oldCs instanceof ConservationColourScheme)\r
- ccs = (ConservationColourScheme) oldCs;\r
-\r
- if(conservationMenuItem.isSelected())\r
- {\r
- Alignment al = (Alignment)viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, al.getSequences(), 0,\r
- al.getWidth() );\r
-\r
- c.calculate();\r
- c.verdict(false, 100);\r
-\r
- if(ccs!=null)\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
- else\r
- ccs = new ConservationColourScheme(c, oldCs);\r
-\r
- viewport.setGlobalColourScheme( ccs );\r
-\r
- }\r
- else if(oldCs instanceof ConservationColourScheme)\r
- {\r
- oldCs = ccs.cs;\r
- viewport.setGlobalColourScheme( oldCs );\r
- }\r
-\r
-\r
- if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )\r
- {\r
- sliderFrame = new JInternalFrame();\r
- sliderFrame.setMaximizable(false);\r
- sliderFrame.setResizable(false);\r
-\r
- SliderPanel sp = null;\r
- if (conservationMenuItem.isSelected())\r
- {\r
- if(threshold > 50)\r
- threshold = 30;\r
- sp = new SliderPanel(alignPanel, threshold, true,ccs);\r
- Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment (Global colour)", 400, 90);\r
- threshold = 0;\r
- }\r
- else if (abovePIDThreshold.isSelected())\r
- {\r
- sp = new SliderPanel(alignPanel, threshold, false, oldCs);\r
- sp.cs = oldCs;\r
- Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);\r
- }\r
-\r
- sliderFrame.setContentPane(sp);\r
- if(x!=0 && y!=0)\r
- sliderFrame.setLocation(x,y);\r
-\r
- }\r
- else\r
- threshold = 0;\r
-\r
-\r
- if (oldCs instanceof ResidueColourScheme)\r
- {\r
- ResidueColourScheme rcs = (ResidueColourScheme) oldCs;\r
- rcs.setThreshold(threshold);\r
- }\r
- else if (oldCs instanceof ScoreColourScheme)\r
- {\r
- ScoreColourScheme scs = (ScoreColourScheme) oldCs;\r
- scs.setThreshold(threshold);\r
- }\r
-\r
- alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
- alignPanel.repaint();\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
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ SequenceGroup getGroup()\r
{\r
- if(abovePIDThreshold.isSelected())\r
- abovePIDThreshold.setSelected(false);\r
-\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
- addConservationOrPIDColour();\r
- }\r
-\r
- JInternalFrame sliderFrame;\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
- {\r
- if(conservationMenuItem.isSelected())\r
- conservationMenuItem.setSelected(false);\r
+ // this method won't add a new group if it already exists\r
+ ap.av.alignment.addGroup(sg);\r
\r
- addConservationOrPIDColour();\r
+ return sg;\r
}\r
\r
-\r
-\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
+ void sequenceName_actionPerformed(ActionEvent e)\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
- frame.setContentPane(chooser);\r
- Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
- frame.setResizable(false);\r
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
- }\r
+ String id = sequence.getName();\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
- public void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new PIDColourScheme() );\r
- alignPanel.setColourScheme( );\r
+ if (s != null)\r
+ {\r
+ sequence.setName(s);\r
+ ap.repaint();\r
+ }\r
}\r
\r
-\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );\r
- alignPanel.setColourScheme();\r
- }\r
-*/\r
-//////////////////////////////////////\r
- protected void groupAnnotation_actionPerformed(ActionEvent e)\r
+ void unGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
-\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ap.av.alignment.deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ ap.repaint();\r
}\r
\r
- protected void groupName_actionPerformed(ActionEvent e)\r
+ void pdbMenuItem_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
+ if (sequence.getPDBId() == null)\r
+ {\r
return;\r
+ }\r
\r
- sg.setName(reply);\r
- groupName.setText(reply);\r
- }\r
-\r
- protected void copyGroup_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
-\r
- SequenceI[] s = new Sequence[sg.sequences.size()];\r
- for (int i=0; i < sg.sequences.size(); i++)\r
- {\r
- s[i] = new Sequence( sg.getSequenceAt(i));\r
- s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );\r
- }\r
- AlignFrame af = new AlignFrame(new Alignment(s));\r
- int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
- if (newHeight > 500)\r
- newHeight = 500;\r
- Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
- }\r
-\r
- protected void moveGroup_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
-\r
- SequenceI[] s = new Sequence[sg.sequences.size()];\r
-\r
- for (int i=0; i < sg.sequences.size(); i++)\r
- s[i] = new Sequence( sg.getSequenceAt(i));\r
-\r
- AlignFrame af = new AlignFrame(new Alignment(s));\r
- int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
- if(newHeight>500)\r
- newHeight=500;\r
- Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
-\r
-\r
- for (int i=0; i < sg.sequences.size(); i++)\r
- ap.av.alignment.deleteSequence(sg.getSequenceAt(i));\r
-\r
-\r
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
- ap.RefreshPanels();\r
-\r
-\r
+ try\r
+ {\r
+ EBIFetchClient ebi = new EBIFetchClient();\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,\r
+ sequence.getName() + " " + sequence.getPDBId(),\r
+ 400, 400);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
}\r
\r
- protected void deleteSequences_actionPerformed(ActionEvent e)\r
+ protected void outline_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
- for (int i=0;i < sg.sequences.size(); i++)\r
- ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
+ SequenceGroup sg = getGroup();\r
+ Color col = JColorChooser.showDialog(this, "Select Outline Colour",\r
+ Color.BLUE);\r
\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
- ap.seqPanel.parent.RefreshPanels();\r
+ if (col != null)\r
+ {\r
+ sg.setOutlineColour(col);\r
+ }\r
\r
+ ap.repaint();\r
}\r
\r
- protected void analyze_actionPerformed(ActionEvent e)\r
+ public void showBoxes_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- JInternalFrame frame = new JInternalFrame();\r
- cap.formatForOutput();\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
-\r
+ getGroup().setDisplayBoxes(showBoxes.isSelected());\r
+ refresh();\r
}\r
\r
- SequenceGroup getGroup()\r
+ public void showText_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
-\r
- // this method won't add a new group if it already exists\r
- ap.av.alignment.addGroup(sg);\r
- return sg;\r
+ getGroup().setDisplayText(showText.isSelected());\r
+ refresh();\r
}\r
\r
- void sequenceName_actionPerformed(ActionEvent e)\r
+ public void showColourText_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",\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- null,\r
- id);\r
-\r
- if(s!=null)\r
- {\r
- sequence.setName(s);\r
- ap.RefreshPanels();\r
- }\r
-\r
+ getGroup().setColourText(showColourText.isSelected());\r
+ refresh();\r
}\r
}\r
git://source.jalview.org / jalview.git / blobdiff