Further abstractions and clean up

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 57bcd5f..5c1de0b 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1178,3 +1178,14 @@ label.no_colour_selection_in_scheme = Please, make a colour selection before to
 label.no_colour_selection_warn = Error saving colour scheme
 label.select_by_annotation = Select By Annotation
 action.select_by_annotation = Select by annotation...
+label.threshold_filter =  Threshold Filter
+action.hide = Hide
+action.select = Select
+label.alpha_helix = Alpha Helix
+label.beta_strand = Beta Strand
+label.turn = Turn
+label.select_all = Select All
+label.structures_filter = Structures Filter
+label.search_filter = Search Filter
+label.display_name = Display Label
+label.description = Description

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 21cf630..7b42a30 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -20,11 +20,6 @@
  */
 package jalview.controller;
 
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.List;
-
 import jalview.analysis.AlignmentSorter;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
@@ -33,12 +28,20 @@ import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.List;
 
 public class AlignViewController implements AlignViewControllerI
 {
@@ -100,7 +103,9 @@ public class AlignViewController implements AlignViewControllerI
                 (int) (Math.random() * 255), (int) (Math.random() * 255));
         col = col.brighter();
         for (SequenceI sq : gps[g].getSequences(null))
+        {
           viewport.setSequenceColour(sq, col);
+        }
       }
       return true;
     }
@@ -300,6 +305,91 @@ public class AlignViewController implements AlignViewControllerI
     }
   }
 
+  public static boolean filterAnnotations(Annotation[] annotations,
+          AnnotationFilterParameter filterParams, ColumnSelection cs)
+  {
+    cs.revealAllHiddenColumns();
+    cs.clear();
+    int count = 0;
+    do
+    {
+      if (annotations[count] != null)
+      {
+
+        boolean itemMatched = false;
+
+        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+                && annotations[count].value > filterParams
+                        .getThresholdValue())
+        {
+          itemMatched = true;
+        }
+        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
+                && annotations[count].value < filterParams
+                        .getThresholdValue())
+        {
+          itemMatched = true;
+        }
+
+        if (filterParams.isFilterAlphaHelix()
+                && annotations[count].secondaryStructure == 'H')
+        {
+          itemMatched = true;
+        }
+
+        if (filterParams.isFilterBetaSheet()
+                && annotations[count].secondaryStructure == 'E')
+        {
+          itemMatched = true;
+        }
+
+        if (filterParams.isFilterTurn()
+                && annotations[count].secondaryStructure == 'S')
+        {
+          itemMatched = true;
+        }
+
+        String regexSearchString = filterParams.getRegexString();
+        if (regexSearchString != null
+                && !filterParams.getRegexSearchFields().isEmpty())
+        {
+          List<SearchableAnnotationField> fields = filterParams
+                  .getRegexSearchFields();
+          try
+          {
+            if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
+                    && annotations[count].displayCharacter
+                            .matches(regexSearchString))
+            {
+              itemMatched = true;
+            }
+          } catch (java.util.regex.PatternSyntaxException pse)
+          {
+            if (annotations[count].displayCharacter
+                    .equals(regexSearchString))
+            {
+              itemMatched = true;
+            }
+          }
+          if (fields.contains(SearchableAnnotationField.DESCRIPTION)
+                  && annotations[count].description != null
+                  && annotations[count].description
+                          .matches(regexSearchString))
+          {
+            itemMatched = true;
+          }
+        }
+
+        if (itemMatched)
+        {
+          cs.addElement(count);
+        }
+      }
+      count++;
+    } while (count < annotations.length);
+    return false;
+  }
+
   @Override
   public void sortAlignmentByFeatureDensity(String[] typ)
   {

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 31b5b64..9f3aa7b 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -1,10 +1,11 @@
 package jalview.gui;
 
-import jalview.api.analysis.AnnotationFilterParameter;
+import jalview.controller.AlignViewController;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 
 import java.awt.BorderLayout;
 import java.awt.CardLayout;
@@ -21,7 +22,6 @@ import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
 import javax.swing.JLayeredPane;
 import javax.swing.JPanel;
 import javax.swing.JRadioButton;
@@ -58,8 +58,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   private JPanel annotationComboBoxPanel = new JPanel();
 
-  private JLabel annotationLabel = new JLabel();
-
   private BorderLayout borderLayout1 = new BorderLayout();
 
   private JComboBox<String> threshold = new JComboBox<String>();
@@ -208,11 +206,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     slider.setOpaque(false);
     slider.setPreferredSize(new Dimension(100, 32));
 
-    annotationLabel.setBackground(Color.white);
-    annotationLabel.setFont(JvSwingUtils.getLabelFont());
-    annotationLabel.setText("Select Annotation : ");
-
-    thresholdPanel.setBorder(new TitledBorder("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]", "[][]"));
@@ -225,6 +220,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
     noGraphFilterView.setBackground(Color.white);
+
     annotationComboBoxPanel.setBackground(Color.white);
     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 
@@ -383,6 +379,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
       {
+        filterParams
+                .setThresholdValue(getCurrentAnnotation().threshold.value);
 
         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
         {
@@ -399,15 +397,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     if (currentStructureFilterPanel != null)
     {
-      if (currentStructureFilterPanel.getAlphaHelix().isSelected())
+      if (currentStructureFilterPanel.alphaHelix.isSelected())
       {
         filterParams.setFilterAlphaHelix(true);
       }
-      if (currentStructureFilterPanel.getBetaStrand().isSelected())
+      if (currentStructureFilterPanel.betaStrand.isSelected())
       {
         filterParams.setFilterBetaSheet(true);
       }
-      if (currentStructureFilterPanel.getTurn().isSelected())
+      if (currentStructureFilterPanel.turn.isSelected())
       {
         filterParams.setFilterTurn(true);
       }
@@ -415,17 +413,18 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     if (currentSearchPanel != null)
     {
-      if (!currentSearchPanel.getSearchString().isEmpty())
+
+      if (!currentSearchPanel.searchBox.getText().isEmpty())
       {
-        currentSearchPanel.getDescription().setEnabled(true);
-        currentSearchPanel.getDisplayName().setEnabled(true);
-        filterParams.setRegexString(currentSearchPanel.getSearchString());
-        if (currentSearchPanel.isDisplayNameChecked())
+        currentSearchPanel.description.setEnabled(true);
+        currentSearchPanel.displayName.setEnabled(true);
+        filterParams.setRegexString(currentSearchPanel.searchBox.getText());
+        if (currentSearchPanel.displayName.isSelected())
         {
           filterParams
                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
         }
-        if (currentSearchPanel.isDescriptionChecked())
+        if (currentSearchPanel.description.isSelected())
         {
           filterParams
                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
@@ -433,12 +432,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
       else
       {
-        currentSearchPanel.getDescription().setEnabled(false);
-        currentSearchPanel.getDisplayName().setEnabled(false);
+        currentSearchPanel.description.setEnabled(false);
+        currentSearchPanel.displayName.setEnabled(false);
       }
     }
 
-    filterAnnotations(getCurrentAnnotation().annotations, filterParams,
+    AlignViewController.filterAnnotations(
+            getCurrentAnnotation().annotations, filterParams,
             av.getColumnSelection());
 
     av.showAllHiddenColumns();
@@ -465,6 +465,48 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
   }
 
+  public FurtherActionPanel getCurrentFutherActionPanel()
+  {
+    return currentFurtherActionPanel;
+  }
+
+  public void setCurrentFutherActionPanel(
+          FurtherActionPanel currentFutherActionPanel)
+  {
+    this.currentFurtherActionPanel = currentFutherActionPanel;
+  }
+
+  public SearchPanel getCurrentSearchPanel()
+  {
+    return currentSearchPanel;
+  }
+
+  public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
+  {
+    this.currentSearchPanel = currentSearchPanel;
+  }
+
+  public int getActionOption()
+  {
+    return actionOption;
+  }
+
+  public void setActionOption(int actionOption)
+  {
+    this.actionOption = actionOption;
+  }
+
+  public StructureFilterPanel getCurrentStructureFilterPanel()
+  {
+    return currentStructureFilterPanel;
+  }
+
+  public void setCurrentStructureFilterPanel(
+          StructureFilterPanel currentStructureFilterPanel)
+  {
+    this.currentStructureFilterPanel = currentStructureFilterPanel;
+  }
+
   public void select_action(ActionEvent actionEvent)
   {
     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
@@ -512,47 +554,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     updateView();
   }
 
-  public FurtherActionPanel getCurrentFutherActionPanel()
-  {
-    return currentFurtherActionPanel;
-  }
-
-  public void setCurrentFutherActionPanel(
-          FurtherActionPanel currentFutherActionPanel)
-  {
-    this.currentFurtherActionPanel = currentFutherActionPanel;
-  }
-
-  public SearchPanel getCurrentSearchPanel()
-  {
-    return currentSearchPanel;
-  }
-
-  public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
-  {
-    this.currentSearchPanel = currentSearchPanel;
-  }
-
-  public int getActionOption()
-  {
-    return actionOption;
-  }
-
-  public void setActionOption(int actionOption)
-  {
-    this.actionOption = actionOption;
-  }
-
-  public StructureFilterPanel getCurrentStructureFilterPanel()
-  {
-    return currentStructureFilterPanel;
-  }
-
-  public void setCurrentStructureFilterPanel(
-          StructureFilterPanel currentStructureFilterPanel)
-  {
-    this.currentStructureFilterPanel = currentStructureFilterPanel;
-  }
 
   public class FurtherActionPanel extends JPanel
   {
@@ -567,10 +568,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
     {
       this.aColChooser = aColChooser;
-      getSelectOption().setBackground(Color.white);
-      getSelectOption().setFont(JvSwingUtils.getLabelFont());
-      getSelectOption().setText("Select");
-      getSelectOption().addActionListener(new ActionListener()
+      JvSwingUtils.jvInitComponent(selectOption, "action.select");
+      selectOption.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent actionEvent)
@@ -579,10 +578,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      getHideOption().setBackground(Color.white);
-      getHideOption().setFont(JvSwingUtils.getLabelFont());
-      getHideOption().setText("Hide");
-      getHideOption().addActionListener(new ActionListener()
+      JvSwingUtils.jvInitComponent(hideOption, "action.hide");
+      hideOption.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent actionEvent)
@@ -591,16 +588,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      getOptionsGroup().add(getSelectOption());
-      getOptionsGroup().add(getHideOption());
-      getOptionsGroup().setSelected(getSelectOption().getModel(), true);
+      optionsGroup.add(selectOption);
+      optionsGroup.add(hideOption);
+      optionsGroup.setSelected(selectOption.getModel(), true);
 
-      this.setBackground(Color.white);
-      this.setFont(JvSwingUtils.getLabelFont());
+      JvSwingUtils.jvInitComponent(this);
       syncState();
 
-      this.add(getSelectOption());
-      this.add(getHideOption());
+      this.add(selectOption);
+      this.add(hideOption);
     }
 
     public void selectRadioAction(ActionEvent actionEvent)
@@ -615,47 +611,16 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       aColChooser.hide_action(actionEvent);
     }
 
-    public JRadioButton getHideOption()
-    {
-      return hideOption;
-    }
-
-    public void setHideOption(JRadioButton hideOption)
-    {
-      this.hideOption = hideOption;
-    }
-
-    public JRadioButton getSelectOption()
-    {
-      return selectOption;
-    }
-
-    public void setSelectOption(JRadioButton selectOption)
-    {
-      this.selectOption = selectOption;
-    }
-
-    public ButtonGroup getOptionsGroup()
-    {
-      return optionsGroup;
-    }
-
-    public void setOptionsGroup(ButtonGroup optionsGroup)
-    {
-      this.optionsGroup = optionsGroup;
-    }
-
     public void syncState()
     {
       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
       {
-        this.getOptionsGroup().setSelected(this.getHideOption().getModel(),
+        this.optionsGroup.setSelected(this.hideOption.getModel(),
                 true);
       }
       else
       {
-        this.getOptionsGroup().setSelected(
-                this.getSelectOption().getModel(), true);
+        this.optionsGroup.setSelected(this.selectOption.getModel(), true);
       }
     }
   }
@@ -676,9 +641,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       this.aColChooser = aColChooser;
 
-      alphaHelix.setBackground(Color.white);
-      alphaHelix.setFont(JvSwingUtils.getLabelFont());
-      alphaHelix.setText("Alpha Helix");
+      JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
       alphaHelix.addActionListener(new ActionListener()
       {
         @Override
@@ -688,9 +651,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      betaStrand.setBackground(Color.white);
-      betaStrand.setFont(JvSwingUtils.getLabelFont());
-      betaStrand.setText("Beta Strand");
+      JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
       betaStrand.addActionListener(new ActionListener()
       {
         @Override
@@ -700,9 +661,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      turn.setBackground(Color.white);
-      turn.setFont(JvSwingUtils.getLabelFont());
-      turn.setText("Turn");
+      JvSwingUtils.jvInitComponent(turn, "label.turn");
       turn.addActionListener(new ActionListener()
       {
         @Override
@@ -712,9 +671,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      all.setBackground(Color.white);
-      all.setFont(JvSwingUtils.getLabelFont());
-      all.setText("Select all");
+      JvSwingUtils.jvInitComponent(all, "label.select_all");
       all.addActionListener(new ActionListener()
       {
         @Override
@@ -724,9 +681,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      this.setBorder(new TitledBorder("Structures Filter"));
-      this.setBackground(Color.white);
-      this.setFont(JvSwingUtils.getLabelFont());
+      this.setBorder(new TitledBorder(MessageManager
+              .getString("label.structures_filter")));
+      JvSwingUtils.jvInitComponent(this);
 
       this.add(all);
       this.add(alphaHelix);
@@ -792,10 +749,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
               .getCurrentStructureFilterPanel();
       if (sfp != null)
       {
-        alphaHelix.setSelected(sfp.getAlphaHelix().isSelected());
-        betaStrand.setSelected(sfp.getBetaStrand().isSelected());
-        turn.setSelected(sfp.getTurn().isSelected());
-        if (sfp.getAll().isSelected())
+        alphaHelix.setSelected(sfp.alphaHelix.isSelected());
+        betaStrand.setSelected(sfp.betaStrand.isSelected());
+        turn.setSelected(sfp.turn.isSelected());
+        if (sfp.all.isSelected())
         {
           all.setSelected(true);
           alphaHelix.setSelected(true);
@@ -805,47 +762,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
 
     }
-
-    public JCheckBox getAlphaHelix()
-    {
-      return alphaHelix;
-    }
-
-    public void setAlphaHelix(JCheckBox alphaHelix)
-    {
-      this.alphaHelix = alphaHelix;
-    }
-
-    public JCheckBox getBetaStrand()
-    {
-      return betaStrand;
-    }
-
-    public void setBetaStrand(JCheckBox betaStrand)
-    {
-      this.betaStrand = betaStrand;
-    }
-
-    public JCheckBox getTurn()
-    {
-      return turn;
-    }
-
-    public void setTurn(JCheckBox turn)
-    {
-      this.turn = turn;
-    }
-
-    public JCheckBox getAll()
-    {
-      return all;
-    }
-
-    public void setAll(JCheckBox all)
-    {
-      this.all = all;
-
-    }
   }
 
   public class SearchPanel extends JPanel
@@ -858,19 +774,16 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     private JTextField searchBox = new JTextField(10);
 
-    private JCheckBox structuresFilter = new JCheckBox();
-
     public SearchPanel(AnnotationColumnChooser aColChooser)
     {
 
       this.aColChooser = aColChooser;
-      this.setBorder(new TitledBorder("Search Filter"));
-      this.setBackground(Color.white);
-      this.setFont(JvSwingUtils.getLabelFont());
+      JvSwingUtils.jvInitComponent(this);
+      this.setBorder(new TitledBorder(MessageManager
+              .getString("label.search_filter")));
 
-      getSearchBox().setBackground(Color.white);
-      getSearchBox().setFont(JvSwingUtils.getLabelFont());
-      getSearchBox().getDocument().addDocumentListener(
+      JvSwingUtils.jvInitComponent(searchBox);
+      searchBox.getDocument().addDocumentListener(
               new DocumentListener()
               {
                 @Override
@@ -892,11 +805,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
                 }
               });
 
-      getDisplayName().setBackground(Color.white);
-      getDisplayName().setFont(JvSwingUtils.getLabelFont());
-      getDisplayName().setText("Display Name");
-      getDisplayName().setEnabled(false);
-      getDisplayName().addActionListener(new ActionListener()
+      JvSwingUtils.jvInitComponent(displayName, "label.display_name");
+      displayName.setEnabled(false);
+      displayName.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent actionEvent)
@@ -905,11 +816,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      getDescription().setBackground(Color.white);
-      getDescription().setFont(JvSwingUtils.getLabelFont());
-      getDescription().setText("Description");
-      getDescription().setEnabled(false);
-      getDescription().addActionListener(new ActionListener()
+      JvSwingUtils.jvInitComponent(description, "label.description");
+      description.setEnabled(false);
+      description.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent actionEvent)
@@ -919,24 +828,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       });
 
       syncState();
-      this.add(getSearchBox());
-      this.add(getDisplayName());
-      this.add(getDescription());
-    }
-
-    public boolean isDescriptionChecked()
-    {
-      return getDescription().isSelected();
-    }
-
-    public boolean isDisplayNameChecked()
-    {
-      return getDisplayName().isSelected();
-    }
-
-    public String getSearchString()
-    {
-      return getSearchBox().getText();
+      this.add(searchBox);
+      this.add(displayName);
+      this.add(description);
     }
 
     public void displayNameCheckboxAction()
@@ -957,58 +851,18 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       aColChooser.updateView();
     }
 
-    public JCheckBox getDisplayName()
-    {
-      return displayName;
-    }
-
-    public void setDisplayName(JCheckBox displayName)
-    {
-      this.displayName = displayName;
-    }
-
-    public JCheckBox getDescription()
-    {
-      return description;
-    }
-
-    public void setDescription(JCheckBox description)
-    {
-      this.description = description;
-    }
-
-    public JTextField getSearchBox()
-    {
-      return searchBox;
-    }
-
-    public void setSearchBox(JTextField searchBox)
-    {
-      this.searchBox = searchBox;
-    }
-
-    public JCheckBox getStructuresFilter()
-    {
-      return structuresFilter;
-    }
-
-    public void setStructuresFilter(JCheckBox structuresFilter)
-    {
-      this.structuresFilter = structuresFilter;
-    }
-
     public void syncState()
     {
       SearchPanel sp = aColChooser.getCurrentSearchPanel();
       if (sp != null)
       {
-        description.setEnabled(sp.getDescription().isEnabled());
-        description.setSelected(sp.getDescription().isSelected());
+        description.setEnabled(sp.description.isEnabled());
+        description.setSelected(sp.description.isSelected());
 
-        displayName.setEnabled(sp.getDisplayName().isEnabled());
-        displayName.setSelected(sp.getDisplayName().isSelected());
+        displayName.setEnabled(sp.displayName.isEnabled());
+        displayName.setSelected(sp.displayName.isSelected());
 
-        searchBox.setText(sp.getSearchBox().getText());
+        searchBox.setText(sp.searchBox.getText());
       }
     }
   }

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 722ecdc..c0eea38 100644 (file)
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -1,10 +1,6 @@
 package jalview.gui;
 
-import jalview.api.analysis.AnnotationFilterParameter;
-import jalview.api.analysis.AnnotationFilterParameter.SearchableAnnotationField;
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
@@ -13,7 +9,6 @@ import jalview.util.MessageManager;
 import java.awt.event.ActionEvent;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
-import java.util.List;
 import java.util.Vector;
 
 import javax.swing.JCheckBox;
@@ -363,88 +358,6 @@ public abstract class AnnotationRowFilter extends JPanel
     return false;
   }
 
-  protected boolean filterAnnotations(Annotation[] annotations,
-          AnnotationFilterParameter filterParams, ColumnSelection cs)
-  {
-    av.showAllHiddenColumns();
-    cs.clear();
-    int count = 0;
-    do
-    {
-      if (annotations[count] != null)
-      {
-
-        boolean itemMatched = false;
-
-        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
-                && annotations[count].value > currentAnnotation.threshold.value)
-        {
-          itemMatched = true;
-        }
-        if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
-                && annotations[count].value < currentAnnotation.threshold.value)
-        {
-          itemMatched = true;
-        }
-
-        if (filterParams.isFilterAlphaHelix()
-                && annotations[count].secondaryStructure == 'H')
-        {
-          itemMatched = true;
-        }
-
-        if (filterParams.isFilterBetaSheet()
-                && annotations[count].secondaryStructure == 'E')
-        {
-          itemMatched = true;
-        }
-
-        if (filterParams.isFilterTurn()
-                && annotations[count].secondaryStructure == 'S')
-        {
-          itemMatched = true;
-        }
-
-        String regexSearchString = filterParams.getRegexString();
-        if (regexSearchString != null
-                && !filterParams.getRegexSearchFields().isEmpty())
-        {
-          List<SearchableAnnotationField> fields = filterParams
-                  .getRegexSearchFields();
-          try
-          {
-            if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
-                    && annotations[count].displayCharacter
-                            .matches(regexSearchString))
-            {
-              itemMatched = true;
-            }
-          } catch (java.util.regex.PatternSyntaxException pse)
-          {
-            if (annotations[count].displayCharacter
-                    .equals(regexSearchString))
-            {
-              itemMatched = true;
-            }
-          }
-          if (fields.contains(SearchableAnnotationField.DESCRIPTION)
-                  && annotations[count].description != null
-                  && annotations[count].description
-                          .matches(regexSearchString))
-          {
-            itemMatched = true;
-          }
-        }
-
-        if (itemMatched)
-        {
-          cs.addElement(count);
-        }
-      }
-      count++;
-    } while (count < annotations.length);
-    return false;
-  }
 
   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
   {

diff --git a/src/jalview/gui/JvSwingUtils.java b/src/jalview/gui/JvSwingUtils.java
index e433243..c404e2f 100644 (file)
--- a/src/jalview/gui/JvSwingUtils.java
+++ b/src/jalview/gui/JvSwingUtils.java
@@ -20,11 +20,14 @@
  */
 package jalview.gui;
 
+import jalview.util.MessageManager;
+
 import java.awt.Color;
 import java.awt.Font;
 import java.awt.Rectangle;
 import java.awt.event.ActionListener;
 
+import javax.swing.AbstractButton;
 import javax.swing.JButton;
 import javax.swing.JComponent;
 import javax.swing.JLabel;
@@ -209,4 +212,28 @@ public final class JvSwingUtils
     }
   }
 
+  public static void jvInitComponent(AbstractButton comp, String i18nString)
+  {
+    setColorAndFont(comp);
+    if (i18nString != null && !i18nString.isEmpty())
+    {
+      comp.setText(MessageManager.getString(i18nString));
+    }
+  }
+
+  public static void jvInitComponent(JComponent comp)
+  {
+    setColorAndFont(comp);
+  }
+
+  // public static void jvInitComponent(JComponent comp, String name){
+  // setColorAndFont(comp);
+  // comp.setText(MessageManager.getString("label.select_all"));
+  // }
+
+  private static void setColorAndFont(JComponent comp)
+  {
+    comp.setBackground(Color.white);
+    comp.setFont(JvSwingUtils.getLabelFont());
+  }
 }

diff --git a/src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java b/src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java
new file mode 100644 (file)
index 0000000..3cd4ef7
--- /dev/null
+++ b/src/jalview/viewmodel/annotationfilter/AnnotationFilterParameter.java
@@ -0,0 +1,101 @@
+package jalview.viewmodel.annotationfilter;
+
+import java.util.ArrayList;
+import java.util.List;
+
+public class AnnotationFilterParameter
+{
+  public enum ThresholdType
+  {
+    NO_THRESHOLD, BELOW_THRESHOLD, ABOVE_THRESHOLD;
+  }
+
+  public enum SearchableAnnotationField
+  {
+    DISPLAY_STRING, DESCRIPTION;
+  }
+  private ThresholdType thresholdType;
+
+  private float thresholdValue;
+
+  private boolean filterAlphaHelix = false;
+
+  private boolean filterBetaSheet = false;
+
+  private boolean filterTurn = false;
+
+  private String regexString;
+
+  private List<SearchableAnnotationField> regexSearchFields = new ArrayList<SearchableAnnotationField>();
+
+  public ThresholdType getThresholdType()
+  {
+    return thresholdType;
+  }
+
+  public void setThresholdType(ThresholdType thresholdType)
+  {
+    this.thresholdType = thresholdType;
+  }
+
+  public float getThresholdValue()
+  {
+    return thresholdValue;
+  }
+
+  public void setThresholdValue(float thresholdValue)
+  {
+    this.thresholdValue = thresholdValue;
+  }
+
+  public String getRegexString()
+  {
+    return regexString;
+  }
+
+  public void setRegexString(String regexString)
+  {
+    this.regexString = regexString;
+  }
+
+  public List<SearchableAnnotationField> getRegexSearchFields()
+  {
+    return regexSearchFields;
+  }
+
+  public void addRegexSearchField(SearchableAnnotationField regexSearchField)
+  {
+    this.regexSearchFields.add(regexSearchField);
+  }
+
+  public boolean isFilterAlphaHelix()
+  {
+    return filterAlphaHelix;
+  }
+
+  public void setFilterAlphaHelix(boolean alphaHelix)
+  {
+    this.filterAlphaHelix = alphaHelix;
+  }
+
+  public boolean isFilterBetaSheet()
+  {
+    return filterBetaSheet;
+  }
+
+  public void setFilterBetaSheet(boolean betaSheet)
+  {
+    this.filterBetaSheet = betaSheet;
+  }
+
+  public boolean isFilterTurn()
+  {
+    return filterTurn;
+  }
+
+  public void setFilterTurn(boolean turn)
+  {
+    this.filterTurn = turn;
+  }
+
+}