X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColumnChooser.java;h=d941107898529ce2f5505b0cce17f5eec5456c66;hb=refs%2Fheads%2Fbug%2FJAL-3700_JAL-3748_reconstructCDSafterProteinMSA_for2_11_1_2;hp=5adecad0a226dbe24e45a7c72c9ee25177844a18;hpb=6f04e0a80f3c3ba8087a1ad316debd395d0a4db0;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 5adecad..d941107 100644
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -21,6 +21,7 @@
 
 package jalview.gui;
 
+import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.HiddenColumns;
 import jalview.io.cache.JvCacheableInputBox;
 import jalview.schemes.AnnotationColourGradient;
@@ -254,7 +255,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
   {
     if (slider.isEnabled())
     {
-      getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+      getCurrentAnnotation().threshold.value = getSliderValue();
       updateView();
       propagateSeqAssociatedThreshold(updateAllAnnotation,
               getCurrentAnnotation());
@@ -284,6 +285,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     thresholdValue.setEnabled(true);
     percentThreshold.setEnabled(true);
 
+    final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
@@ -294,26 +296,22 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     }
     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
     {
-      if (getCurrentAnnotation().threshold == null)
+      if (currentAnnotation.threshold == null)
       {
-        getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
-                (getCurrentAnnotation().graphMax
-                        - getCurrentAnnotation().graphMin) / 2f,
+        currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
+                (currentAnnotation.graphMax
+                        - currentAnnotation.graphMin) / 2f,
                 "Threshold", Color.black));
       }
 
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * 1000
-              - getCurrentAnnotation().graphMin * 1000;
 
-      slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
-      slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
-      slider.setValue(
-              (int) (getCurrentAnnotation().threshold.value * 1000));
+      setSliderModel(currentAnnotation.graphMin,
+              currentAnnotation.graphMax,
+              currentAnnotation.threshold.value);
 
       setThresholdValueText();
 
-      slider.setMajorTickSpacing((int) (range / 10f));
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
       adjusting = false;
@@ -321,10 +319,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       // build filter params
       filterParams.setThresholdType(
               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
-      if (getCurrentAnnotation().isQuantitative())
+      if (currentAnnotation.isQuantitative())
       {
         filterParams
-                .setThresholdValue(getCurrentAnnotation().threshold.value);
+                .setThresholdValue(currentAnnotation.threshold.value);
 
         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
         {
@@ -380,7 +378,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     // adding them to the selection
     av.showAllHiddenColumns();
     av.getColumnSelection().filterAnnotations(
-            getCurrentAnnotation().annotations, filterParams);
+            currentAnnotation.annotations, filterParams);
 
     boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
     if (hideCols)
@@ -720,7 +718,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 
     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
-            FILTER_BY_ANN_CACHE_KEY);
+            FILTER_BY_ANN_CACHE_KEY, 23);
 
     public SearchPanel(AnnotationColumnChooser aColChooser)
     {
@@ -730,7 +728,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       this.setBorder(new TitledBorder(
               MessageManager.getString("label.search_filter")));
 
-      searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
       searchBox.setToolTipText(
               MessageManager.getString("info.enter_search_text_here"));
       searchBox.getEditor().getEditorComponent()