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ThresholdIsMin available in applet
author
amwaterhouse
<Andrew Waterhouse>
Fri, 27 Apr 2007 09:54:58 +0000
(09:54 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Fri, 27 Apr 2007 09:54:58 +0000
(09:54 +0000)
src/jalview/appletgui/AnnotationColourChooser.java
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diff --git
a/src/jalview/appletgui/AnnotationColourChooser.java
b/src/jalview/appletgui/AnnotationColourChooser.java
index
430bf65
..
2853b6b
100755
(executable)
--- a/
src/jalview/appletgui/AnnotationColourChooser.java
+++ b/
src/jalview/appletgui/AnnotationColourChooser.java
@@
-25,6
+25,7
@@
import java.awt.event.*;
\r
import jalview.datamodel.*;
\r
import jalview.schemes.*;
\r
\r
import jalview.datamodel.*;
\r
import jalview.schemes.*;
\r
+import java.awt.Rectangle;
\r
\r
public class AnnotationColourChooser
\r
extends Panel implements ActionListener,
\r
\r
public class AnnotationColourChooser
\r
extends Panel implements ActionListener,
\r
@@
-83,12
+84,21
@@
public class AnnotationColourChooser
}
\r
\r
adjusting = true;
\r
}
\r
\r
adjusting = true;
\r
+
\r
+ Vector list = new Vector();
\r
+ int index = 1;
\r
for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
\r
{
\r
for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
\r
{
\r
- if (av.alignment.getAlignmentAnnotation()[i].graph > 0)
\r
- {
\r
- annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
\r
- }
\r
+ String label = av.alignment.getAlignmentAnnotation()[i].label;
\r
+ if (!list.contains(label))
\r
+ list.addElement(label);
\r
+ else
\r
+ list.addElement(label+"_"+(index++));
\r
+ }
\r
+
\r
+ for (int i = 0; i < list.size(); i++)
\r
+ {
\r
+ annotations.addItem(list.elementAt(i).toString());
\r
}
\r
\r
threshold.addItem("No Threshold");
\r
}
\r
\r
threshold.addItem("No Threshold");
\r
@@
-128,6
+138,7
@@
public class AnnotationColourChooser
maxColour.setLabel("Max Colour");
\r
maxColour.addActionListener(this);
\r
\r
maxColour.setLabel("Max Colour");
\r
maxColour.addActionListener(this);
\r
\r
+ thresholdIsMin.addItemListener(this);
\r
ok.setLabel("OK");
\r
ok.addActionListener(this);
\r
\r
ok.setLabel("OK");
\r
ok.addActionListener(this);
\r
\r
@@
-146,16
+157,19
@@
public class AnnotationColourChooser
\r
slider.setBackground(Color.white);
\r
slider.setEnabled(false);
\r
\r
slider.setBackground(Color.white);
\r
slider.setEnabled(false);
\r
- slider.setBounds(new Rectangle(172, 7, 120, 16));
\r
+ slider.setBounds(new Rectangle(125, 6, 82, 16));
\r
thresholdValue.setEnabled(false);
\r
thresholdValue.setEnabled(false);
\r
- thresholdValue.setBounds(new Rectangle(295, 4, 83, 22));
\r
- thresholdValue.setColumns(10);
\r
+ thresholdValue.setBounds(new Rectangle(211, 4, 56, 22));
\r
+ thresholdValue.setColumns(5);
\r
jPanel3.setBackground(Color.white);
\r
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
\r
currentColours.setLabel("Use Original Colours");
\r
currentColours.addItemListener(this);
\r
\r
jPanel3.setBackground(Color.white);
\r
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
\r
currentColours.setLabel("Use Original Colours");
\r
currentColours.addItemListener(this);
\r
\r
- threshold.setBounds(new Rectangle(19, 4, 141, 22));
\r
+ threshold.setBounds(new Rectangle(11, 3, 113, 22));
\r
+ thresholdIsMin.setBackground(Color.white);
\r
+ thresholdIsMin.setLabel("Threshold is min/max");
\r
+ thresholdIsMin.setBounds(new Rectangle(270, 3, 135, 23));
\r
jPanel1.add(ok);
\r
jPanel1.add(cancel);
\r
jPanel2.add(annotations);
\r
jPanel1.add(ok);
\r
jPanel1.add(cancel);
\r
jPanel2.add(annotations);
\r
@@
-165,6
+179,7
@@
public class AnnotationColourChooser
jPanel3.add(threshold);
\r
jPanel3.add(slider);
\r
jPanel3.add(thresholdValue);
\r
jPanel3.add(threshold);
\r
jPanel3.add(slider);
\r
jPanel3.add(thresholdValue);
\r
+ jPanel3.add(thresholdIsMin);
\r
this.add(jPanel2, java.awt.BorderLayout.NORTH);
\r
this.add(jPanel3, java.awt.BorderLayout.CENTER);
\r
this.add(jPanel1, java.awt.BorderLayout.SOUTH);
\r
this.add(jPanel2, java.awt.BorderLayout.NORTH);
\r
this.add(jPanel3, java.awt.BorderLayout.CENTER);
\r
this.add(jPanel1, java.awt.BorderLayout.SOUTH);
\r
@@
-184,6
+199,7
@@
public class AnnotationColourChooser
TextField thresholdValue = new TextField(20);
\r
Checkbox currentColours = new Checkbox();
\r
BorderLayout borderLayout1 = new BorderLayout();
\r
TextField thresholdValue = new TextField(20);
\r
Checkbox currentColours = new Checkbox();
\r
BorderLayout borderLayout1 = new BorderLayout();
\r
+ Checkbox thresholdIsMin = new Checkbox();
\r
\r
public void actionPerformed(ActionEvent evt)
\r
{
\r
\r
public void actionPerformed(ActionEvent evt)
\r
{
\r
@@
-297,27
+313,9
@@
public class AnnotationColourChooser
return;
\r
}
\r
\r
return;
\r
}
\r
\r
- // We removed the non-graph annotations when filling the combobox
\r
- // so allow for them again here
\r
- int nograph = 0, graph = -1;
\r
- for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
\r
- {
\r
- if (av.alignment.getAlignmentAnnotation()[i].graph == 0)
\r
- {
\r
- nograph++;
\r
- }
\r
- else
\r
- {
\r
- graph++;
\r
- }
\r
-
\r
- if (graph == annotations.getSelectedIndex())
\r
- {
\r
- break;
\r
- }
\r
- }
\r
\r
\r
- currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph];
\r
+ currentAnnotation = av.alignment.getAlignmentAnnotation()
\r
+ [annotations.getSelectedIndex()];
\r
\r
int aboveThreshold = -1;
\r
if (threshold.getSelectedItem().equals("Above Threshold"))
\r
\r
int aboveThreshold = -1;
\r
if (threshold.getSelectedItem().equals("Above Threshold"))
\r
@@
-378,6
+376,13
@@
public class AnnotationColourChooser
aboveThreshold);
\r
}
\r
\r
aboveThreshold);
\r
}
\r
\r
+ if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f)
\r
+ {
\r
+ acg.predefinedColours = true;
\r
+ }
\r
+
\r
+ acg.thresholdIsMinMax = thresholdIsMin.getState();
\r
+
\r
av.setGlobalColourScheme(acg);
\r
\r
if (av.alignment.getGroups() != null)
\r
av.setGlobalColourScheme(acg);
\r
\r
if (av.alignment.getGroups() != null)
\r