Merge branch 'develop' into releases/Release_2_10_2_Branch

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

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 6fc5fad..84b2c6f 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -50,8 +50,8 @@ import javax.swing.border.TitledBorder;
 import net.miginfocom.swing.MigLayout;
 
 @SuppressWarnings("serial")
-public class AnnotationColumnChooser extends AnnotationRowFilter implements
-        ItemListener
+public class AnnotationColumnChooser extends AnnotationRowFilter
+        implements ItemListener
 {
   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
 
@@ -119,18 +119,16 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     // restore Object state from the previous session if one exists
     if (lastChooser != null)
     {
-      currentSearchPanel = lastChooser
-              .getCurrentSearchPanel();
+      currentSearchPanel = lastChooser.getCurrentSearchPanel();
       currentStructureFilterPanel = lastChooser
               .getCurrentStructureFilterPanel();
-      annotations.setSelectedIndex(lastChooser
-              .getAnnotations().getSelectedIndex());
-      threshold.setSelectedIndex(lastChooser
-              .getThreshold().getSelectedIndex());
-      actionOption = lastChooser
-              .getActionOption();
-      percentThreshold.setSelected(lastChooser.percentThreshold
-              .isSelected());
+      annotations.setSelectedIndex(
+              lastChooser.getAnnotations().getSelectedIndex());
+      threshold.setSelectedIndex(
+              lastChooser.getThreshold().getSelectedIndex());
+      actionOption = lastChooser.getActionOption();
+      percentThreshold
+              .setSelected(lastChooser.percentThreshold.isSelected());
     }
 
     try
@@ -152,8 +150,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     super.jbInit();
 
     JPanel thresholdPanel = new JPanel();
-    thresholdPanel.setBorder(new TitledBorder(MessageManager
-            .getString("label.threshold_filter")));
+    thresholdPanel.setBorder(new TitledBorder(
+            MessageManager.getString("label.threshold_filter")));
     thresholdPanel.setBackground(Color.white);
     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
@@ -241,8 +239,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
       if (av.getAnnotationColumnSelectionState() != null)
       {
-        HiddenColumns oldHidden = av
-                .getAnnotationColumnSelectionState()
+        HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
         if (oldHidden != null)
         {
@@ -285,11 +282,12 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 
-    setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
-            .getSelectedIndex()]]);
+    setCurrentAnnotation(av.getAlignment()
+            .getAlignmentAnnotation()[annmap[getAnnotations()
+                    .getSelectedIndex()]]);
 
-    int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
-            .getSelectedIndex());
+    int selectedThresholdItem = getSelectedThresholdItem(
+            getThreshold().getSelectedIndex());
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
@@ -307,11 +305,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       if (getCurrentAnnotation().threshold == null)
       {
-        getCurrentAnnotation()
-                .setThreshold(
-                        new jalview.datamodel.GraphLine(
-                                (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
-                                "Threshold", Color.black));
+        getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
+                (getCurrentAnnotation().graphMax
+                        - getCurrentAnnotation().graphMin) / 2f,
+                "Threshold", Color.black));
       }
 
       adjusting = true;
@@ -320,8 +317,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
-      slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
-      
+      slider.setValue(
+              (int) (getCurrentAnnotation().threshold.value * 1000));
+
       setThresholdValueText();
 
       slider.setMajorTickSpacing((int) (range / 10f));
@@ -330,8 +328,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       adjusting = false;
 
       // build filter params
-      filterParams
-              .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
+      filterParams.setThresholdType(
+              AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
       if (getCurrentAnnotation().isQuantitative())
       {
         filterParams
@@ -339,13 +337,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
         {
-          filterParams
-                  .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
+          filterParams.setThresholdType(
+                  AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
         }
         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
         {
-          filterParams
-                  .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
+          filterParams.setThresholdType(
+                  AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
         }
       }
     }
@@ -371,17 +369,17 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
       {
-        filterParams.setRegexString(currentSearchPanel.searchBox
-                .getUserInput());
+        filterParams.setRegexString(
+                currentSearchPanel.searchBox.getUserInput());
         if (currentSearchPanel.displayName.isSelected())
         {
-          filterParams
-                  .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
+          filterParams.addRegexSearchField(
+                  AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
         }
         if (currentSearchPanel.description.isSelected())
         {
-          filterParams
-                  .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
+          filterParams.addRegexSearchField(
+                  AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
         }
       }
     }
@@ -489,8 +487,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
   public void selectedAnnotationChanged()
   {
     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
-    if (av.getAlignment()
-            .getAlignmentAnnotation()[annmap[getAnnotations()
+    if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
             .getSelectedIndex()]].isQuantitative())
     {
       currentView = AnnotationColumnChooser.GRAPH_VIEW;
@@ -568,7 +565,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     public void syncState()
     {
-      if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
+      if (aColChooser
+              .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
       {
         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
       }
@@ -635,8 +633,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      this.setBorder(new TitledBorder(MessageManager
-              .getString("label.structures_filter")));
+      this.setBorder(new TitledBorder(
+              MessageManager.getString("label.structures_filter")));
       JvSwingUtils.jvInitComponent(this);
 
       this.add(all);
@@ -736,12 +734,12 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
       this.aColChooser = aColChooser;
       JvSwingUtils.jvInitComponent(this);
-      this.setBorder(new TitledBorder(MessageManager
-              .getString("label.search_filter")));
+      this.setBorder(new TitledBorder(
+              MessageManager.getString("label.search_filter")));
 
       searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
-      searchBox.setToolTipText(MessageManager
-              .getString("info.enter_search_text_here"));
+      searchBox.setToolTipText(
+              MessageManager.getString("info.enter_search_text_here"));
       searchBox.getEditor().getEditorComponent()
               .addKeyListener(new java.awt.event.KeyAdapter()
               {
@@ -756,8 +754,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
                 }
               });
 
-
-
       JvSwingUtils.jvInitComponent(displayName, "label.label");
       displayName.addActionListener(new ActionListener()
       {
@@ -825,15 +821,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       String defaultTtip = MessageManager
               .getString("info.enter_search_text_to_enable");
       String labelTtip = MessageManager.formatMessage(
-              "info.search_in_annotation_label", annotations
-                      .getSelectedItem().toString());
+              "info.search_in_annotation_label",
+              annotations.getSelectedItem().toString());
       String descTtip = MessageManager.formatMessage(
-              "info.search_in_annotation_description", annotations
-                      .getSelectedItem().toString());
-      displayName.setToolTipText(displayName.isEnabled() ? labelTtip
-              : defaultTtip);
-      description.setToolTipText(description.isEnabled() ? descTtip
-              : defaultTtip);
+              "info.search_in_annotation_description",
+              annotations.getSelectedItem().toString());
+      displayName.setToolTipText(
+              displayName.isEnabled() ? labelTtip : defaultTtip);
+      description.setToolTipText(
+              description.isEnabled() ? descTtip : defaultTtip);
     }
   }