JAL-2236 fixes for desktop and applet implementation of 'append seqname'

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

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 722ecdc..8335042 100644 (file)
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -1,10 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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 +29,9 @@ 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 +71,11 @@ 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
@@ -110,7 +131,6 @@ public abstract class AnnotationRowFilter extends JPanel
     });
   }
 
-
   public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
   {
     this.av = av;
@@ -141,11 +161,19 @@ public abstract class AnnotationRowFilter extends JPanel
         enableSeqAss = true;
       }
       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      // add associated sequence ID if available
+      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
+      {
+        label = label
+                + "_"
+                + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef
+                        .getName();
+      }
+      // make label unique
       if (!list.contains(label))
       {
         anmap[list.size()] = i;
         list.add(label);
-
       }
       else
       {
@@ -182,7 +210,6 @@ public abstract class AnnotationRowFilter extends JPanel
 
   public void ok_actionPerformed(ActionEvent e)
   {
-    updateView();
     try
     {
       frame.setClosed(true);
@@ -238,11 +265,11 @@ public abstract class AnnotationRowFilter extends JPanel
   protected void populateThresholdComboBox(JComboBox<String> threshold)
   {
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_no_thereshold"));
+            .getString("label.threshold_feature_no_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_above_thereshold"));
+            .getString("label.threshold_feature_above_threshold"));
     threshold.addItem(MessageManager
-            .getString("label.threshold_feature_below_thereshold"));
+            .getString("label.threshold_feature_below_threshold"));
   }
 
   protected void seqAssociated_actionPerformed(ActionEvent arg0,
@@ -363,89 +390,6 @@ 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()
   {
     return currentAnnotation;