Return accurate RGB for transparent residues

[jalview.git] / src / jalview / appletgui / UserDefinedColours.java

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 80d91ef..36df306 100755 (executable)
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -19,7 +19,6 @@
 \r
 package jalview.appletgui;\r
 \r
-import java.io.*;\r
 import java.util.*;\r
 \r
 import java.awt.*;\r
@@ -83,6 +82,8 @@ public class UserDefinedColours
     makeButton("X", "X");\r
     makeButton("Gap", "'.','-',' '");\r
 \r
+    validate();\r
+\r
   }\r
 \r
   protected void rText_actionPerformed(ActionEvent e)\r
@@ -91,6 +92,7 @@ public class UserDefinedColours
     {\r
       int i = Integer.parseInt(rText.getText());\r
       rScroller.setValue(i);\r
+      rScroller_adjustmentValueChanged(null);\r
     }\r
     catch (NumberFormatException ex)\r
     {}\r
@@ -102,6 +104,7 @@ public class UserDefinedColours
     {\r
       int i = Integer.parseInt(gText.getText());\r
       gScroller.setValue(i);\r
+      gScroller_adjustmentValueChanged(null);\r
     }\r
     catch (NumberFormatException ex)\r
     {}\r
@@ -114,6 +117,7 @@ public class UserDefinedColours
     {\r
       int i = Integer.parseInt(bText.getText());\r
       bScroller.setValue(i);\r
+      bScroller_adjustmentValueChanged(null);\r
     }\r
     catch (NumberFormatException ex)\r
     {}\r
@@ -145,10 +149,12 @@ public class UserDefinedColours
   {\r
     Color col = new Color(R, G, B);\r
     target.setBackground(col);\r
+    target.repaint();\r
 \r
     if (selectedButton != null)\r
     {\r
       selectedButton.setBackground(col);\r
+      selectedButton.repaint();\r
     }\r
   }\r
 \r
@@ -188,7 +194,7 @@ public class UserDefinedColours
     button.setFont(new java.awt.Font("Verdana", 1, 10));\r
     button.addMouseListener(new java.awt.event.MouseAdapter()\r
     {\r
-      public void mouseClicked(MouseEvent e)\r
+      public void mousePressed(MouseEvent e)\r
       {\r
         colourButtonPressed(e);\r
       }\r
@@ -214,7 +220,7 @@ public class UserDefinedColours
     }\r
 \r
     UserColourScheme ucs = new UserColourScheme(newColours);\r
-    ucs.setThreshold(0);\r
+    ucs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
 \r
     if (seqGroup != null)\r
     {\r
@@ -225,30 +231,10 @@ public class UserDefinedColours
       ap.av.setGlobalColourScheme(ucs);\r
     }\r
 \r
+    ap.seqPanel.seqCanvas.img = null;\r
     ap.repaint();\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(newColours);\r
-      ucs.setThreshold(0);\r
-\r
-    }\r
-    catch (Exception ex)\r
-    {}\r
-\r
-    return ucs;\r
-  }\r
 \r
   protected void cancelButton_actionPerformed(ActionEvent e)\r
   {\r