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 9e205c4..8335042 100644 (file)
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -1,9 +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.AnnotationRowFilterI;
 import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
@@ -14,6 +31,7 @@ import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.util.Vector;
 
+import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
@@ -24,8 +42,7 @@ import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 
 @SuppressWarnings("serial")
-public abstract class AnnotationRowFilter extends JPanel implements
-        AnnotationRowFilterI
+public abstract class AnnotationRowFilter extends JPanel
 {
   protected AlignViewport av;
 
@@ -54,6 +71,11 @@ public abstract class AnnotationRowFilter extends JPanel implements
   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
@@ -109,7 +131,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
     });
   }
 
-
   public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
   {
     this.av = av;
@@ -121,7 +142,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
 
   }
 
-  @Override
   public Vector<String> getAnnotationItems(boolean isSeqAssociated)
   {
     Vector<String> list = new Vector<String>();
@@ -141,11 +161,19 @@ public abstract class AnnotationRowFilter extends JPanel implements
         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
       {
@@ -156,7 +184,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
         }
       }
     }
-    // seqAssociated.setEnabled(enableSeqAss);
     this.annmap = new int[list.size()];
     System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
     return list;
@@ -183,7 +210,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
 
   public void ok_actionPerformed(ActionEvent e)
   {
-    updateView();
     try
     {
       frame.setClosed(true);
@@ -239,11 +265,11 @@ public abstract class AnnotationRowFilter extends JPanel implements
   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,
@@ -364,78 +390,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
     return false;
   }
 
-  protected boolean markColumnsContaining(
-          AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
-  {
-    try
-    {
-      if (currentAnnotation != null)
-      {
-        Annotation[] annotations = currentAnnotation.annotations;
-        ColumnSelection cs = av.getColumnSelection();
-        cs.clear();
-        if (thresholdComparisonType == AnnotationColourGradient.NO_THRESHOLD)
-        {
-          int count = 0;
-          do
-          {
-            if (annotations[count] != null)
-            {
-              if (currentAnnotation.label.equals("Secondary Structure")
-                      && annotations[count].secondaryStructure != ' ')
-              {
-                cs.addElement(count);
-              }
-              else if (currentAnnotation.label
-                      .equals("Iron Sulphur Contacts"))
-              {
-                cs.addElement(count);
-              }
-              else if (annotations[count].value != 0.0)
-              {
-                cs.addElement(count);
-              }
-
-            }
-            count++;
-          } while (count < annotations.length);
-        }
-        else
-        {
-          int count = 0;
-          do
-          {
-            if (annotations[count] != null)
-            {
-              if (thresholdComparisonType == AnnotationColourGradient.ABOVE_THRESHOLD)
-              {
-                if (annotations[count].value > currentAnnotation.threshold.value)
-                {
-                  cs.addElement(count);
-                }
-              }
-              else if (thresholdComparisonType == AnnotationColourGradient.BELOW_THRESHOLD)
-              {
-                if (annotations[count].value < currentAnnotation.threshold.value)
-                {
-                  cs.addElement(count);
-                }
-              }
-
-            }
-            count++;
-          } while (count < annotations.length);
-        }
-      }
-
-      return true;
-    } catch (Exception e)
-    {
-      e.printStackTrace();
-      return false;
-    }
-  }
-
   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
   {
     return currentAnnotation;
@@ -447,4 +401,9 @@ public abstract class AnnotationRowFilter extends JPanel implements
     this.currentAnnotation = currentAnnotation;
   }
 
+  public abstract void valueChanged(boolean updateAllAnnotation);
+
+  public abstract void updateView();
+
+  public abstract void reset();
 }