Formatting

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

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 1a62fff..98579eb 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -1,6 +1,6 @@
 /*\r
  * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
  *\r
  * This program is free software; you can redistribute it and/or\r
  * modify it under the terms of the GNU General Public License\r
@@ -28,6 +28,12 @@ import jalview.datamodel.*;
 import jalview.jbgui.*;\r
 import jalview.schemes.*;\r
 \r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
 public class SliderPanel\r
     extends GSliderPanel\r
 {\r
@@ -37,6 +43,14 @@ public class SliderPanel
   boolean forConservation = true;\r
   ColourSchemeI cs;\r
 \r
+  /**\r
+   * Creates a new SliderPanel object.\r
+   *\r
+   * @param ap DOCUMENT ME!\r
+   * @param value DOCUMENT ME!\r
+   * @param forConserve DOCUMENT ME!\r
+   * @param cs DOCUMENT ME!\r
+   */\r
   public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,\r
                      ColourSchemeI cs)\r
   {\r
@@ -50,7 +64,7 @@ public class SliderPanel
     {\r
       label.setText("Enter value to increase conservation visibility");\r
       slider.setMinimum(0);\r
-      slider.setMaximum(50);\r
+      slider.setMaximum(100);\r
     }\r
     else\r
     {\r
@@ -72,15 +86,23 @@ public class SliderPanel
     valueField.setText(value + "");\r
   }\r
 \r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param ap DOCUMENT ME!\r
+   * @param cs DOCUMENT ME!\r
+   * @param source DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
   public static int setConservationSlider(AlignmentPanel ap,\r
                                           ColourSchemeI cs, String source)\r
   {\r
     SliderPanel sp = null;\r
-    ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
 \r
     if (conservationSlider == null)\r
     {\r
-      sp = new SliderPanel(ap, ccs.inc, true, cs);\r
+      sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);\r
       conservationSlider = new JInternalFrame();\r
       conservationSlider.setContentPane(sp);\r
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
@@ -106,6 +128,9 @@ public class SliderPanel
     return sp.getValue();\r
   }\r
 \r
+  /**\r
+   * DOCUMENT ME!\r
+   */\r
   public static void showConservationSlider()\r
   {\r
     try\r
@@ -134,21 +159,21 @@ public class SliderPanel
     }\r
   }\r
 \r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param ap DOCUMENT ME!\r
+   * @param cs DOCUMENT ME!\r
+   * @param source DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
   public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,\r
                                        String source)\r
   {\r
     SliderPanel pid = null;\r
 \r
-    int threshold = 50;\r
-\r
-    if (cs instanceof ResidueColourScheme)\r
-    {\r
-      threshold = ( ( (ResidueColourScheme) cs).getThreshold());\r
-    }\r
-    else if (cs instanceof ScoreColourScheme)\r
-    {\r
-      threshold = ( ( (ScoreColourScheme) cs).getThreshold());\r
-    }\r
+    int threshold = cs.getThreshold();\r
 \r
     if (PIDSlider == null)\r
     {\r
@@ -177,6 +202,9 @@ public class SliderPanel
     return pid.getValue();\r
   }\r
 \r
+  /**\r
+   * DOCUMENT ME!\r
+   */\r
   public static void showPIDSlider()\r
   {\r
     try\r
@@ -206,6 +234,11 @@ public class SliderPanel
     }\r
   }\r
 \r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param i DOCUMENT ME!\r
+   */\r
   public void valueChanged(int i)\r
   {\r
     if (cs == null)\r
@@ -232,23 +265,25 @@ public class SliderPanel
       if (allGroups != null)\r
       {\r
         toChange = ( (SequenceGroup) allGroups.get(groupIndex)).cs;\r
-        if(toChange==null)\r
+\r
+        if (toChange == null)\r
         {\r
           groupIndex--;\r
+\r
           continue;\r
         }\r
       }\r
 \r
       if (forConservation)\r
       {\r
-        if (toChange instanceof ConservationColourScheme)\r
+        if (toChange.conservationApplied())\r
         {\r
-          ( (ConservationColourScheme) toChange).inc = i;\r
+          toChange.setConservationInc(i);\r
         }\r
       }\r
       else\r
       {\r
-        ( (ResidueColourScheme) toChange).setThreshold(i);\r
+        toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());\r
       }\r
 \r
       groupIndex--;\r
@@ -257,11 +292,21 @@ public class SliderPanel
     ap.seqPanel.seqCanvas.repaint();\r
   }\r
 \r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param b DOCUMENT ME!\r
+   */\r
   public void setAllGroupsCheckEnabled(boolean b)\r
   {\r
     allGroupsCheck.setEnabled(b);\r
   }\r
 \r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param e DOCUMENT ME!\r
+   */\r
   public void valueField_actionPerformed(ActionEvent e)\r
   {\r
     try\r
@@ -269,19 +314,38 @@ public class SliderPanel
       int i = Integer.parseInt(valueField.getText());\r
       slider.setValue(i);\r
     }\r
-    catch (Exception ex)\r
+    catch (NumberFormatException ex)\r
     {\r
       valueField.setText(slider.getValue() + "");\r
     }\r
   }\r
 \r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param value DOCUMENT ME!\r
+   */\r
   public void setValue(int value)\r
   {\r
     slider.setValue(value);\r
   }\r
 \r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
   public int getValue()\r
   {\r
     return Integer.parseInt(valueField.getText());\r
   }\r
+\r
+  public void slider_mouseReleased(MouseEvent e)\r
+  {\r
+    if (ap.overviewPanel != null)\r
+    {\r
+      ap.overviewPanel.updateOverviewImage();\r
+    }\r
+  }\r
+\r
 }\r