getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
fontNameMenuItem.setText(viewport.getFont().getName());\r
fontSizeMenuItem.setText(viewport.getFont().getSize()+"");\r
+\r
+ clustalColour.setSelected(true);\r
+ clustalColour_actionPerformed(null);\r
}\r
\r
protected void saveAs_actionPerformed(ActionEvent e)\r
\r
public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
- conservationMenuItem.setSelected(false);\r
+ viewport.setGlobalColourScheme(\r
+ new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
abovePIDThreshold.setSelected(false);\r
changeColour();\r
}\r
else if(conservationMenuItem.isSelected())\r
conservationMenuItem_actionPerformed(null);\r
\r
-\r
- alignPanel.RefreshPanels();\r
+ alignPanel.RefreshPanels();\r
}\r
\r
- void addConservationOrPIDColour()\r
+\r
+ protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
- int x=0, y=0, threshold = 70;\r
+ if(abovePIDThreshold.isSelected())\r
+ {\r
+ abovePIDThreshold.setSelected(false);\r
+ Desktop.hidePIDSlider();\r
+ }\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
+ viewport.setConservationSelected(conservationMenuItem.isSelected());\r
\r
- ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
+ ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
\r
- ConservationColourScheme ccs = null;\r
- if (oldCs instanceof ConservationColourScheme)\r
- ccs = (ConservationColourScheme) oldCs;\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
+ if (conservationMenuItem.isSelected())\r
+ {\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth());\r
\r
- c.calculate();\r
- c.verdict(false, 100);\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
+ 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
+ int threshold = Desktop.setConservationSliderSource(alignPanel, ccs, "Background");\r
\r
+ ccs.inc = threshold;\r
+\r
+ if (ccs.cs instanceof ResidueColourScheme)\r
+ ((ResidueColourScheme) ccs.cs).setThreshold(0);\r
+ else if (ccs.cs instanceof ScoreColourScheme)\r
+ ((ScoreColourScheme)ccs.cs).setThreshold(0);\r
+\r
+ viewport.setGlobalColourScheme(ccs);\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
+ else if (oldCs instanceof ConservationColourScheme)\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
+ /// ie, if we remove ConservationColourScheme from backgroundColour\r
+ oldCs = ccs.cs;\r
+ viewport.setGlobalColourScheme(oldCs);\r
+ Desktop.hideConservationSlider();\r
}\r
\r
- sliderFrame.setContentPane(sp);\r
- if(x!=0 && y!=0)\r
- sliderFrame.setLocation(x,y);\r
+ if(e!=null)\r
+ alignPanel.RefreshPanels();\r
+ }\r
\r
- }\r
- else\r
- threshold = 0;\r
\r
+ public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ {\r
+ if(conservationMenuItem.isSelected())\r
+ conservationMenuItem.setSelected(false);\r
\r
- if (oldCs instanceof ResidueColourScheme)\r
+ ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
+ int threshold = 0;\r
+ if (oldCs instanceof ConservationColourScheme)\r
{\r
- ResidueColourScheme rcs = (ResidueColourScheme) oldCs;\r
- rcs.setThreshold(threshold);\r
+ ConservationColourScheme ccs = (ConservationColourScheme) oldCs;\r
+ oldCs = ccs.cs;\r
}\r
- else if (oldCs instanceof ScoreColourScheme)\r
+\r
+ if(abovePIDThreshold.isSelected())\r
{\r
- ScoreColourScheme scs = (ScoreColourScheme) oldCs;\r
- scs.setThreshold(threshold);\r
+ threshold = Desktop.setPIDSliderSource(alignPanel, oldCs, "Background");\r
+ Desktop.hideConservationSlider();\r
}\r
+ else\r
+ Desktop.hidePIDSlider();\r
\r
+ if (oldCs instanceof ResidueColourScheme)\r
+ ((ResidueColourScheme) oldCs).setThreshold(threshold);\r
+ else if (oldCs instanceof ScoreColourScheme)\r
+ ((ScoreColourScheme)oldCs).setThreshold(threshold);\r
\r
- }\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(abovePIDThreshold.isSelected())\r
- abovePIDThreshold.setSelected(false);\r
-\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\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
-\r
- addConservationOrPIDColour();\r
+ viewport.setGlobalColourScheme(oldCs);\r
+ if(e!=null)\r
+ alignPanel.RefreshPanels();\r
}\r
\r
\r
public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );\r
- alignPanel.setColourScheme();\r
+ changeColour();\r
}\r
\r
\r