X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=21c91d85a014989a050443abe2591df8e30fff16;hb=31a33833640b743a506f7801388b17f96e915ef3;hp=722ecdc6b13a3fe106654a7d70ef82b437ba3295;hpb=ca5a59c203b85a6c0f26c3d52d7827c5fa9fa4c5;p=jalview.git

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 722ecdc..21c91d8 100644
--- 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;
@@ -13,9 +9,9 @@ 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.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
@@ -55,6 +51,11 @@ public abstract class AnnotationRowFilter extends JPanel
   protected JTextField thresholdValue = new JTextField(20);
 
   protected JInternalFrame frame;
+
+  protected JButton ok = new JButton();
+
+  protected JButton cancel = new JButton();
+
   /**
    * enabled if the user is dragging the slider - try to keep updates to a
    * minimun
@@ -363,88 +364,6 @@ 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()
   {