DEFAULT_FILE_FORMAT added

[jalview.git] / src / jalview / gui / SliderPanel.java

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 2fbe0cc..eba89e8 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -28,6 +28,7 @@ public class SliderPanel extends GSliderPanel
       sp = new SliderPanel(ap, value, true, cs);\r
       conservationSlider = new JInternalFrame();\r
       conservationSlider.setContentPane(sp);\r
+      conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
     }\r
     else\r
     {\r
@@ -72,9 +73,17 @@ public class SliderPanel extends GSliderPanel
   public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
    {\r
      SliderPanel pid = null;\r
+\r
+     int threshold = 50;\r
+     if (cs instanceof ResidueColourScheme)\r
+       threshold = ( ( (ResidueColourScheme) cs).getThreshold());\r
+     else if (cs instanceof ScoreColourScheme)\r
+       threshold = ( ( (ScoreColourScheme) cs).getThreshold());\r
+\r
+\r
      if(PIDSlider == null)\r
      {\r
-       pid = new SliderPanel(ap, 50, false, cs);\r
+       pid = new SliderPanel(ap, threshold, false, cs);\r
        PIDSlider = new JInternalFrame();\r
        PIDSlider.setContentPane(pid);\r
        PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
@@ -129,13 +138,13 @@ public class SliderPanel extends GSliderPanel
     applyButton.setVisible(false);\r
     if(forConservation)\r
     {\r
-      label.setText("Enter the value by which to decrease conservation colour intensity");\r
+      label.setText("Enter value to increase conservation visibility");\r
       slider.setMinimum(0);\r
       slider.setMaximum(50);\r
     }\r
     else\r
     {\r
-      label.setText("Enter the percent identity above which to colour residues");\r
+      label.setText("Enter % identity above which to colour residues");\r
       slider.setMinimum(0);\r
       slider.setMaximum(100);\r
     }\r
@@ -192,7 +201,7 @@ public class SliderPanel extends GSliderPanel
       groupIndex--;\r
     }\r
 \r
-    ap.seqPanel.repaint();\r
+    ap.seqPanel.seqCanvas.repaint();\r
 \r
   }\r
 \r