JAL-591 slider scale factor now derived from min-max range

diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 0d12347..fcb293c 100644 (file)
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -20,9 +20,6 @@
  */
 package jalview.gui;
 
-import static jalview.ws.params.simple.LogarithmicParameter.LOGSLIDERSCALE;
-
-import jalview.bin.Cache;
 import jalview.util.MessageManager;
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.OptionI;
@@ -33,6 +30,7 @@ import jalview.ws.params.simple.LogarithmicParameter;
 import jalview.ws.params.simple.StringParameter;
 
 import java.awt.BorderLayout;
+import java.awt.Color;
 import java.awt.Component;
 import java.awt.Dimension;
 import java.awt.FlowLayout;
@@ -304,7 +302,11 @@ public class OptsAndParamsPage
   public class ParamBox extends JPanel
           implements ChangeListener, ActionListener, MouseListener
   {
-    private static final float SLIDERSCALE = 1000f;
+    /*
+     * parameter values (or their logs) are multiplied by this
+     * scaling factor to ensure an integer range for the slider
+     */
+    private int sliderScaleFactor = 1;
 
     boolean isLogarithmicParameter;
 
@@ -349,17 +351,34 @@ public class OptsAndParamsPage
       finfo = parm.getFurtherDetails();
       validator = parm.getValidValue();
       parameter = parm;
+
+      isLogarithmicParameter = parm instanceof LogarithmicParameter;
+
       if (validator != null)
       {
-        isIntegerParameter = validator.getType() == ValueType.Integer;
-      }
-      else if (parameter.getPossibleValues() != null)
-      {
-        isChoiceParameter = true;
+        ValueType type = validator.getType();
+        isIntegerParameter = type == ValueType.Integer;
+
+        /*
+         * ensure slider has an integer range corresponding to
+         * the min-max range of the parameter
+         */
+        if (validator.getMin() != null && !isIntegerParameter)
+        {
+          double min = validator.getMin().doubleValue();
+          double max = validator.getMax().doubleValue();
+          if (isLogarithmicParameter)
+          {
+            min = Math.log(min);
+            max = Math.log(max);
+          }
+          sliderScaleFactor = (int) (1000000 / (max - min));
+          // todo scaleMin, scaleMax could also be final fields
+        }
       }
-      if (parm instanceof LogarithmicParameter)
+      else
       {
-        isLogarithmicParameter = true;
+        isChoiceParameter = parameter.getPossibleValues() != null;
       }
 
       if (compact)
@@ -582,15 +601,11 @@ public class OptsAndParamsPage
     @Override
     public void mouseEntered(MouseEvent e)
     {
-      // TODO Auto-generated method stub
-
     }
 
     @Override
     public void mouseExited(MouseEvent e)
     {
-      // TODO Auto-generated method stub
-
     }
 
     @Override
@@ -605,8 +620,6 @@ public class OptsAndParamsPage
     @Override
     public void mouseReleased(MouseEvent e)
     {
-      // TODO Auto-generated method stub
-
     }
 
     @Override
@@ -619,18 +632,19 @@ public class OptsAndParamsPage
           /*
            * set (int or float formatted) text field value
            */
-          valueField.setText(isIntegerParameter ? String.valueOf(slider.getValue())
-                  : String.valueOf(slider.getValue() / SLIDERSCALE));
+          valueField.setText(isIntegerParameter
+                  ? String.valueOf(slider.getValue())
+                  : formatDouble(
+                          slider.getValue() / (float) sliderScaleFactor));
         }
         else
         {
-          double base = ((LogarithmicParameter) parameter).getBase();
-          double value = Math.pow(base, slider.getValue() / LOGSLIDERSCALE);
+          double value = Math.pow(Math.E,
+                  slider.getValue() / (double) sliderScaleFactor);
           valueField.setText(formatDouble(value));
         }
         checkIfModified();
       }
-
     }
 
     /**
@@ -642,10 +656,22 @@ public class OptsAndParamsPage
      */
     String formatDouble(double value)
     {
-      String format = value < 0.001 ? "%3.3e" : "%3.3f";
+      String format = value < 0.001 ? "%3.1E" : "%3.3f";
       return String.format(format, value);
     }
 
+    /**
+     * Formats a number as integer or float (3dp) or scientific notation (1dp)
+     * 
+     * @param n
+     * @return
+     */
+    String formatNumber(Number n)
+    {
+      return n instanceof Integer ? String.valueOf(n.intValue())
+              : formatDouble(n.doubleValue());
+    }
+
     void updateControls(ParameterI parm)
     {
       adjusting = true;
@@ -679,7 +705,7 @@ public class OptsAndParamsPage
               }
             }
           });
-          valueField.setPreferredSize(new Dimension(60, 25));
+          valueField.setPreferredSize(new Dimension(65, 25));
           controlsPanel.add(slider, BorderLayout.WEST);
           controlsPanel.add(valueField, BorderLayout.EAST);
         }
@@ -696,7 +722,6 @@ public class OptsAndParamsPage
               choicebox.addItem(val);
             }
           }
-
           if (parm.getValue() != null)
           {
             choicebox.setSelectedItem(parm.getValue());
@@ -704,18 +729,7 @@ public class OptsAndParamsPage
         }
         else
         {
-          if (parm instanceof LogarithmicParameter)
-          {
-            double base = ((LogarithmicParameter) parm).getBase();
-            // double value = Math.pow(base,
-            // Double.parseDouble(parm.getValue()) / LOGSLIDERSCALE);
-            double value = Double.parseDouble(parm.getValue());
-            valueField.setText(formatDouble(value));
-          }
-          else
-          {
-            valueField.setText(parm.getValue());
-          }
+          valueField.setText(parm.getValue());
         }
       }
       lastVal = updateSliderFromValueField();
@@ -740,43 +754,50 @@ public class OptsAndParamsPage
     {
       if (validator == null)
       {
-        if (!isChoiceParameter)
+        if (isChoiceParameter)
         {
-          slider.setVisible(false);
-          return valueField.getText().trim();
+          return choicebox.getSelectedItem();
         }
-        else
+        slider.setVisible(false);
+        return valueField.getText().trim();
+      }
+
+      valueField.setText(valueField.getText().trim());
+
+      /*
+       * ensure not outside min-max range
+       * TODO: provide some visual indicator if limit reached
+       */
+      try
+      {
+        valueField.setBackground(Color.WHITE);
+        double d = Double.parseDouble(valueField.getText());
+        if (validator.getMin() != null
+                && validator.getMin().doubleValue() > d)
         {
-          return choicebox.getSelectedItem();
+          valueField.setText(formatNumber(validator.getMin()));
         }
+        if (validator.getMax() != null
+                && validator.getMax().doubleValue() < d)
+        {
+          valueField.setText(formatNumber(validator.getMax()));
+        }
+      } catch (NumberFormatException e)
+      {
+        valueField.setBackground(Color.yellow);
+        return Float.NaN;
       }
+
       if (isIntegerParameter)
       {
         int iVal = 0;
         try
         {
-          valueField.setText(valueField.getText().trim());
           iVal = Integer.valueOf(valueField.getText());
-
-          /*
-           * ensure not outside min-max range
-           * TODO: provide some visual indicator if limit reached
-           */
-          if (validator.getMin() != null
-                  && validator.getMin().intValue() > iVal)
-          {
-            iVal = validator.getMin().intValue();
-            valueField.setText(String.valueOf(iVal));
-          }
-          if (validator.getMax() != null
-                  && validator.getMax().intValue() < iVal)
-          {
-            iVal = validator.getMax().intValue();
-            valueField.setText(String.valueOf(iVal));
-          }
         } catch (Exception e)
         {
-          Cache.log.error(e.getMessage());
+          valueField.setBackground(Color.yellow);
+          return Integer.valueOf(0);
         }
 
         if (validator.getMin() != null && validator.getMax() != null)
@@ -791,43 +812,28 @@ public class OptsAndParamsPage
         }
         return new Integer(iVal);
       }
-      else if (isLogarithmicParameter)
+
+      if (isLogarithmicParameter)
       {
         double dVal = 0d;
         try
         {
-          valueField.setText(valueField.getText().trim());
           double eValue = Double.valueOf(valueField.getText());
-
-          dVal = Math.log(eValue)
-                  / Math.log(((LogarithmicParameter) parameter).getBase())
-                  * LOGSLIDERSCALE;
-
-          /*
-           * ensure not outside min-max range
-           * TODO: provide some visual indicator if limit reached
-           */
-          if (validator.getMin() != null
-                  && validator.getMin().doubleValue() > dVal)
-          {
-            dVal = validator.getMin().doubleValue();
-            valueField.setText(formatDouble(eValue));
-          }
-          if (validator.getMax() != null
-                  && validator.getMax().doubleValue() < dVal)
-          {
-            dVal = validator.getMax().doubleValue();
-            valueField.setText(formatDouble(eValue));
-          }
+          dVal = Math.log(eValue) * sliderScaleFactor;
         } catch (Exception e)
         {
+          // shouldn't be possible here
+          valueField.setBackground(Color.yellow);
+          return Double.NaN;
         }
-
         if (validator.getMin() != null && validator.getMax() != null)
         {
+          double scaleMin = Math.log(validator.getMin().doubleValue())
+                  * sliderScaleFactor;
+          double scaleMax = Math.log(validator.getMax().doubleValue())
+                  * sliderScaleFactor;
           slider.getModel().setRangeProperties((int) (dVal), 1,
-                  (int) (validator.getMin().doubleValue()),
-                  1 + (int) (validator.getMax().doubleValue()), true);
+                  (int) scaleMin, 1 + (int) scaleMax, true);
         }
         else
         {
@@ -835,47 +841,30 @@ public class OptsAndParamsPage
         }
         return new Double(dVal);
       }
+
+      float fVal = 0f;
+      try
+      {
+        fVal = Float.valueOf(valueField.getText());
+      } catch (Exception e)
+      {
+        return Float.valueOf(0f); // shouldn't happen
+      }
+      if (validator.getMin() != null && validator.getMax() != null)
+      {
+        float scaleMin = validator.getMin().floatValue()
+                * sliderScaleFactor;
+        float scaleMax = validator.getMax().floatValue()
+                * sliderScaleFactor;
+        slider.getModel().setRangeProperties(
+                (int) (fVal * sliderScaleFactor), 1, (int) scaleMin,
+                1 + (int) scaleMax, true);
+      }
       else
       {
-        float fVal = 0f;
-        try
-        {
-          valueField.setText(valueField.getText().trim());
-          fVal = Float.valueOf(valueField.getText());
-
-          /*
-           * ensure not outside min-max range
-           * TODO: provide some visual indicator if limit reached
-           */
-          if (validator.getMin() != null
-                  && validator.getMin().floatValue() > fVal)
-          {
-            fVal = validator.getMin().floatValue();
-            valueField.setText(String.valueOf(fVal));
-          }
-          if (validator.getMax() != null
-                  && validator.getMax().floatValue() < fVal)
-          {
-            fVal = validator.getMax().floatValue();
-            valueField.setText(String.valueOf(fVal));
-          }
-        } catch (Exception e)
-        {
-        }
-
-        if (validator.getMin() != null && validator.getMax() != null)
-        {
-          slider.getModel().setRangeProperties((int) (fVal * SLIDERSCALE),
-                  1, (int) (validator.getMin().floatValue() * SLIDERSCALE),
-                  1 + (int) (validator.getMax().floatValue() * SLIDERSCALE),
-                  true);
-        }
-        else
-        {
-          slider.setVisible(false);
-        }
-        return new Float(fVal);
+        slider.setVisible(false);
       }
+      return new Float(fVal);
     }
   }
 

diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index 9c52f97..6f1f51f 100644 (file)
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -156,8 +156,6 @@ public final class HMMERParamStore implements ParamDatastoreI
        */
     args.add(new LogarithmicParameter(
             MessageManager.getString("label.dom_e_value"),
-            // MessageManager.getString("label.dom_e_value_desc"), false, -3d,
-            // -37.92977945, 1d, 10d));
             MessageManager.getString("label.dom_e_value_desc"), false, 1D,
             1E-38, 10D, 10D));
     /*

diff --git a/src/jalview/ws/params/simple/LogarithmicParameter.java b/src/jalview/ws/params/simple/LogarithmicParameter.java
index b127183..01744e7 100644 (file)
--- a/src/jalview/ws/params/simple/LogarithmicParameter.java
+++ b/src/jalview/ws/params/simple/LogarithmicParameter.java
@@ -8,19 +8,16 @@ import jalview.ws.params.ValueConstrainI;
  * logarithmic scale
  * 
  * @author TZVanaalten
- *
  */
 public class LogarithmicParameter extends Option implements ParameterI
 {
-  public static final double LOGSLIDERSCALE = 1000000D;
-
   final double defval;
 
   final double min;
 
   final double max;
 
-  final double base;
+  final double base; // todo is this even needed?
 
   @Override
   public ValueConstrainI getValidValue()
@@ -64,8 +61,8 @@ public class LogarithmicParameter extends Option implements ParameterI
     super(name, description, required, String.valueOf(defValue), null, null,
             null);
     defval = defValue;
-    this.min = min;// * LOGSLIDERSCALE;
-    this.max = max;// * LOGSLIDERSCALE;
+    this.min = min;
+    this.max = max;
     this.base = base;
   }
 
@@ -76,8 +73,8 @@ public class LogarithmicParameter extends Option implements ParameterI
     super(name, description, required, String.valueOf(defValue),
             String.valueOf(value), null, null);
     defval = defValue;
-    this.min = min;// * LOGSLIDERSCALE;
-    this.max = max;// * LOGSLIDERSCALE;
+    this.min = min;
+    this.max = max;
     this.base = base;
   }