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usercolours changed
author
amwaterhouse
<Andrew Waterhouse>
Wed, 25 May 2005 16:40:13 +0000
(16:40 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Wed, 25 May 2005 16:40:13 +0000
(16:40 +0000)
src/jalview/gui/AlignFrame.java
patch
|
blob
|
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src/jalview/gui/AlignViewport.java
patch
|
blob
|
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src/jalview/gui/Finder.java
patch
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src/jalview/gui/UserDefinedColours.java
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diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
de2d8ef
..
1f04fa3
100755
(executable)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-105,9
+105,8
@@
public class AlignFrame extends GAlignFrame
protected void outputText_actionPerformed(ActionEvent e)
{
protected void outputText_actionPerformed(ActionEvent e)
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();
JInternalFrame frame = new JInternalFrame();
JInternalFrame frame = new JInternalFrame();
- cap.formatForOutput();
frame.setContentPane(cap);
Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
frame.setContentPane(cap);
Desktop.addInternalFrame(frame, "Alignment output - "+e.getActionCommand(), 600, 500);
cap.setText( FormatAdapter.formatSequences(e.getActionCommand(), viewport.getAlignment().getSequences()));
@@
-115,8
+114,7
@@
public class AlignFrame extends GAlignFrame
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
protected void htmlMenuItem_actionPerformed(ActionEvent e)
{
- HTMLOutput htmlOutput = new HTMLOutput(viewport);
- htmlOutput = null;
+ new HTMLOutput(viewport);
}
protected void createPNG_actionPerformed(ActionEvent e)
}
protected void createPNG_actionPerformed(ActionEvent e)
@@
-737,7
+735,6
@@
public class AlignFrame extends GAlignFrame
public void clustalColour_actionPerformed(ActionEvent e)
{
public void clustalColour_actionPerformed(ActionEvent e)
{
- abovePIDThreshold.setSelected(false);
changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
}
changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth()));
}
@@
-834,7
+831,7
@@
public class AlignFrame extends GAlignFrame
ccs.setConsensus( viewport.vconsensus );
viewport.setGlobalColourScheme(ccs);
ccs.setConsensus( viewport.vconsensus );
viewport.setGlobalColourScheme(ccs);
- SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
+ ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs, "Background");
}
else
}
else
@@
-853,16
+850,16
@@
public class AlignFrame extends GAlignFrame
{
SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
{
SequenceGroup sg = (SequenceGroup)groups.elementAt(i);
- if (cs instanceof ClustalxColourScheme)
- {
+ if(cs==null)
+ sg.cs = null;
+ else if (cs instanceof ClustalxColourScheme)
sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());
- }
- else if(cs!=null)
- {
+ else if (cs instanceof UserColourScheme)
+ sg.cs = new UserColourScheme( ((UserColourScheme)cs).getColours());
+ else
try{
sg.cs = (ColourSchemeI) cs.getClass().newInstance();
try{
sg.cs = (ColourSchemeI) cs.getClass().newInstance();
- }catch(Exception ex){ex.printStackTrace();}
- }
+ }catch(Exception ex){}
if(viewport.getAbovePIDThreshold())
{
if(viewport.getAbovePIDThreshold())
{
@@
-959,7
+956,7
@@
public class AlignFrame extends GAlignFrame
public void userDefinedColour_actionPerformed(ActionEvent e)
{
public void userDefinedColour_actionPerformed(ActionEvent e)
{
- UserDefinedColours chooser = new UserDefinedColours( alignPanel, null);
+ new UserDefinedColours( alignPanel, null);
}
public void PIDColour_actionPerformed(ActionEvent e)
}
public void PIDColour_actionPerformed(ActionEvent e)
@@
-1063,7
+1060,7
@@
public class AlignFrame extends GAlignFrame
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)
{
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
}
void NewTreePanel(String type, String pwType, String title)
}
void NewTreePanel(String type, String pwType, String title)
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
82d2e3e
..
7256bed
100755
(executable)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-100,6
+100,8
@@
public class AlignViewport
if(Preferences.defaultColour!=null)
\r
{
\r
globalColourScheme = ColourSchemeProperty.getColour(alignment, Preferences.defaultColour);
\r
if(Preferences.defaultColour!=null)
\r
{
\r
globalColourScheme = ColourSchemeProperty.getColour(alignment, Preferences.defaultColour);
\r
+ if(globalColourScheme instanceof UserColourScheme)
\r
+ globalColourScheme = UserDefinedColours.loadDefaultColours();
\r
if(globalColourScheme!=null)
\r
globalColourScheme.setConsensus( vconsensus );
\r
}
\r
if(globalColourScheme!=null)
\r
globalColourScheme.setConsensus( vconsensus );
\r
}
\r
@@
-479,14
+481,10
@@
public class AlignViewport
}
\r
\r
public boolean getShowAnnotation()
\r
}
\r
\r
public boolean getShowAnnotation()
\r
- {
\r
- return showAnnotation;
\r
- }
\r
+ { return showAnnotation; }
\r
\r
public void setShowAnnotation(boolean b)
\r
\r
public void setShowAnnotation(boolean b)
\r
- {
\r
- showAnnotation = b;
\r
- }
\r
+ { showAnnotation = b; }
\r
\r
public boolean getScaleAboveWrapped()
\r
{ return scaleAboveWrapped;}
\r
\r
public boolean getScaleAboveWrapped()
\r
{ return scaleAboveWrapped;}
\r
diff --git
a/src/jalview/gui/Finder.java
b/src/jalview/gui/Finder.java
index
594baf8
..
ef28ebe
100755
(executable)
--- a/
src/jalview/gui/Finder.java
+++ b/
src/jalview/gui/Finder.java
@@
-75,12
+75,12
@@
public class Finder extends GFinder
\r
public void createNewGroup_actionPerformed(ActionEvent e)
\r
{
\r
\r
public void createNewGroup_actionPerformed(ActionEvent e)
\r
{
\r
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
\r
+
\r
Color [] newColors = new Color[24];
\r
for(int i=0; i<24; i++)
\r
newColors[i] = new Color(60,160,115);
\r
\r
Color [] newColors = new Color[24];
\r
for(int i=0; i<24; i++)
\r
newColors[i] = new Color(60,160,115);
\r
\r
- ucs.setColourScheme(newColors);
\r
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
\r
String searchString = textfield.getText();
\r
\r
searchGroup = new SuperGroup(searchString, ucs , true, true, false);
\r
String searchString = textfield.getText();
\r
\r
searchGroup = new SuperGroup(searchString, ucs , true, true, false);
\r
@@
-140,12
+140,12
@@
public class Finder extends GFinder
///////////////////////////////////////////////
\r
\r
\r
///////////////////////////////////////////////
\r
\r
\r
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
\r
+
\r
Color [] newColors = new Color[24];
\r
for(int i=0; i<24; i++)
\r
newColors[i] = new Color(60,160,115);
\r
\r
Color [] newColors = new Color[24];
\r
for(int i=0; i<24; i++)
\r
newColors[i] = new Color(60,160,115);
\r
\r
- ucs.setColourScheme(newColors);
\r
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
\r
\r
searchGroup = new SuperGroup(searchString, ucs , true, true, false);
\r
\r
\r
searchGroup = new SuperGroup(searchString, ucs , true, true, false);
\r
\r
diff --git
a/src/jalview/gui/UserDefinedColours.java
b/src/jalview/gui/UserDefinedColours.java
index
077a268
..
a35180b
100755
(executable)
--- a/
src/jalview/gui/UserDefinedColours.java
+++ b/
src/jalview/gui/UserDefinedColours.java
@@
-22,6
+22,7
@@
public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
ColourSchemeI oldColourScheme;
\r
JInternalFrame frame;
\r
\r
ColourSchemeI oldColourScheme;
\r
JInternalFrame frame;
\r
\r
+
\r
public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
\r
{
\r
super();
\r
public UserDefinedColours(AlignmentPanel ap, SequenceGroup sg)
\r
{
\r
super();
\r
@@
-56,7
+57,7
@@
public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
\r
if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
\r
{
\r
\r
if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
\r
{
\r
- loadColour(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
\r
+ loadColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
\r
}
\r
}
\r
\r
}
\r
}
\r
\r
@@
-109,7
+110,6
@@
public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
\r
protected void applyButton_actionPerformed(ActionEvent e)
\r
{
\r
\r
protected void applyButton_actionPerformed(ActionEvent e)
\r
{
\r
-
\r
Color [] newColours = new Color[24];
\r
for(int i=0; i<24; i++)
\r
{
\r
Color [] newColours = new Color[24];
\r
for(int i=0; i<24; i++)
\r
{
\r
@@
-117,16
+117,17
@@
public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
newColours[i] = button.getBackground();
\r
}
\r
\r
newColours[i] = button.getBackground();
\r
}
\r
\r
- UserColourScheme ucs = new UserColourScheme();
\r
+ UserColourScheme ucs = new UserColourScheme(newColours);
\r
ucs.setThreshold(0);
\r
ucs.setThreshold(0);
\r
- ucs.setColourScheme( newColours );
\r
\r
if(seqGroup!=null)
\r
\r
if(seqGroup!=null)
\r
+ {
\r
seqGroup.cs = ucs;
\r
seqGroup.cs = ucs;
\r
+ ap.repaint();
\r
+ }
\r
else
\r
else
\r
- ap.av.setGlobalColourScheme(ucs);
\r
+ ap.alignFrame.changeColour(ucs);
\r
\r
\r
- ap.repaint();
\r
}
\r
\r
protected void loadbutton_actionPerformed(ActionEvent e)
\r
}
\r
\r
protected void loadbutton_actionPerformed(ActionEvent e)
\r
@@
-144,51
+145,52
@@
public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
{
\r
File choice = chooser.getSelectedFile();
\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
\r
{
\r
File choice = chooser.getSelectedFile();
\r
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());
\r
- loadColour(choice.getAbsolutePath());
\r
+ Color[] colors = loadColours(choice.getAbsolutePath());
\r
+ for (int i = 0; i < colors.length; i++)
\r
+ {
\r
+ JButton button = (JButton) buttonPanel.getComponent(i);
\r
+ button.setBackground(colors[i]);
\r
+ }
\r
+
\r
}
\r
}
\r
+ }
\r
\r
\r
+ public static UserColourScheme loadDefaultColours()
\r
+ {
\r
+ if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
\r
+ return loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
\r
+ else
\r
+ return null;
\r
}
\r
\r
public static UserColourScheme loadDefaultColours(String file)
\r
{
\r
}
\r
\r
public static UserColourScheme loadDefaultColours(String file)
\r
{
\r
- UserColourScheme ucs = null;
\r
- try
\r
- {
\r
- BufferedReader in = new BufferedReader(new FileReader(file));
\r
- Color [] newColours = new Color[24];
\r
- for (int i = 0; i < 24; i++)
\r
- {
\r
- newColours[i] = new Color(Integer.parseInt(in.readLine()));
\r
- }
\r
-
\r
- ucs = new UserColourScheme();
\r
+ UserColourScheme ucs = null;
\r
+ ucs = new UserColourScheme(loadColours(file));
\r
ucs.setThreshold(0);
\r
ucs.setThreshold(0);
\r
- ucs.setColourScheme(newColours);
\r
-
\r
- }
\r
- catch (Exception ex)
\r
- {}
\r
-
\r
- return ucs;
\r
+ return ucs;
\r
}
\r
\r
}
\r
\r
- void loadColour(String file)
\r
+ static Color [] loadColours(String file)
\r
{
\r
{
\r
+ Color [] newColours=null;
\r
try
\r
{
\r
try
\r
{
\r
- BufferedReader in = new BufferedReader(new FileReader(file));
\r
+ InputStreamReader in = new InputStreamReader(
\r
+ new FileInputStream(file), "UTF-8");
\r
+
\r
+ jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
\r
+ ucs = (jalview.binding.JalviewUserColours)ucs.unmarshal(in);
\r
+
\r
+ newColours = new Color[ucs.getColourCount()];
\r
for (int i = 0; i < 24; i++)
\r
for (int i = 0; i < 24; i++)
\r
- {
\r
- JButton button = (JButton) buttonPanel.getComponent(i);
\r
- Color c = new Color(Integer.parseInt(in.readLine()));
\r
- button.setBackground(c);
\r
- }
\r
+ newColours[i] = new Color(Integer.parseInt(ucs.getColour(i).getRGB(), 16));
\r
\r
\r
- jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", file);
\r
}
\r
catch (Exception ex)
\r
}
\r
catch (Exception ex)
\r
- {}
\r
+ {ex.printStackTrace();}
\r
\r
\r
+ return newColours;
\r
}
\r
\r
protected void savebutton_actionPerformed(ActionEvent e)
\r
}
\r
\r
protected void savebutton_actionPerformed(ActionEvent e)
\r
@@
-207,15
+209,21
@@
public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
{
\r
String choice = chooser.getSelectedFile().getPath();
\r
jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);
\r
{
\r
String choice = chooser.getSelectedFile().getPath();
\r
jalview.bin.Cache.setProperty("USER_DEFINED_COLOUR", choice);
\r
+ jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
\r
\r
try{
\r
\r
try{
\r
- PrintWriter out = new PrintWriter(new FileWriter(choice));
\r
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(
\r
+ new FileOutputStream(choice), "UTF-8"));
\r
for(int i=0; i<24; i++)
\r
{
\r
for(int i=0; i<24; i++)
\r
{
\r
- JButton button = (JButton)buttonPanel.getComponent(i);
\r
- out.println(button.getBackground().getRGB() + "");
\r
+ JButton button = (JButton)buttonPanel.getComponent(i);
\r
+ jalview.binding.Colour col = new jalview.binding.Colour();
\r
+ col.setName(button.getText());
\r
+ col.setRGB( jalview.util.Format.getHexString( button.getBackground() ));
\r
+ ucs.addColour(col);
\r
}
\r
\r
}
\r
\r
+ ucs.marshal(out);
\r
out.close();
\r
}
\r
catch(Exception ex)
\r
out.close();
\r
}
\r
catch(Exception ex)
\r
@@
-226,7
+234,7
@@
public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
\r
protected void cancelButton_actionPerformed(ActionEvent e)
\r
{
\r
\r
protected void cancelButton_actionPerformed(ActionEvent e)
\r
{
\r
- UserColourScheme ucs = new UserColourScheme();
\r
+
\r
Color [] newColours = new Color[24];
\r
for(int i=0; i<24; i++)
\r
{
\r
Color [] newColours = new Color[24];
\r
for(int i=0; i<24; i++)
\r
{
\r
@@
-234,7
+242,8
@@
public class UserDefinedColours extends GUserDefinedColours implements ChangeLis
buttonPanel.getComponent(i).setBackground(newColours[i]);
\r
}
\r
\r
buttonPanel.getComponent(i).setBackground(newColours[i]);
\r
}
\r
\r
- ucs.setColourScheme( newColours );
\r
+ UserColourScheme ucs = new UserColourScheme( newColours );
\r
+
\r
if (seqGroup != null)
\r
seqGroup.cs = ucs;
\r
else
\r
if (seqGroup != null)
\r
seqGroup.cs = ucs;
\r
else
\r