Merge branch 'patch/Release_2_11_1_Branch_patch_JAL-3490' into releases/Release_2_11_...

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

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 84b2c6f..d941107 100644 (file)
--- 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;
@@ -33,10 +34,11 @@ import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
+import java.awt.event.FocusAdapter;
+import java.awt.event.FocusEvent;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.KeyEvent;
-import java.util.ArrayList;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBox;
@@ -241,20 +243,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       {
         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null)
-        {
-          ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
-          for (int[] positions : regions)
-          {
-            av.hideColumns(positions[0], positions[1]);
-          }
-        }
-        // TODO not clear why we need to hide all the columns (above) if we are
-        // going to copy the hidden columns over wholesale anyway
         av.getAlignment().setHiddenColumns(oldHidden);
       }
       av.sendSelection();
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
   }
 
@@ -263,11 +255,11 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
   {
     if (slider.isEnabled())
     {
-      getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+      getCurrentAnnotation().threshold.value = getSliderValue();
       updateView();
       propagateSeqAssociatedThreshold(updateAllAnnotation,
               getCurrentAnnotation());
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -293,6 +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);
@@ -303,26 +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;
@@ -330,10 +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)
         {
@@ -389,9 +378,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     // adding them to the selection
     av.showAllHiddenColumns();
     av.getColumnSelection().filterAnnotations(
-            getCurrentAnnotation().annotations, filterParams);
+            currentAnnotation.annotations, filterParams);
 
-    if (getActionOption() == ACTION_OPTION_HIDE)
+    boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
+    if (hideCols)
     {
       av.hideSelectedColumns();
     }
@@ -399,7 +389,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
 
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);
-    ap.paintAlignment(true);
+    // only update overview and structures if columns were hidden
+    ap.paintAlignment(hideCols, hideCols);
   }
 
   public HiddenColumns getOldHiddenColumns()
@@ -727,7 +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)
     {
@@ -737,7 +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()
@@ -753,6 +743,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
                   }
                 }
               });
+      searchBox.getEditor().getEditorComponent()
+              .addFocusListener(new FocusAdapter()
+      {
+        @Override
+        public void focusLost(FocusEvent e)
+        {
+          searchStringAction();
+        }
+      });
 
       JvSwingUtils.jvInitComponent(displayName, "label.label");
       displayName.addActionListener(new ActionListener()
@@ -770,7 +769,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
         @Override
         public void actionPerformed(ActionEvent actionEvent)
         {
-          discriptionCheckboxAction();
+          descriptionCheckboxAction();
         }
       });
 
@@ -786,7 +785,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       aColChooser.updateView();
     }
 
-    public void discriptionCheckboxAction()
+    public void descriptionCheckboxAction()
     {
       aColChooser.setCurrentSearchPanel(this);
       aColChooser.updateView();