Merge branch 'develop' into bug/JAL-1608createGroups

[jalview.git] / src / jalview / appletgui / AnnotationColourChooser.java

diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index 487b75c..f516bc9 100644 (file)
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -46,7 +46,8 @@ import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
-import java.util.Hashtable;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Vector;
 
 public class AnnotationColourChooser extends Panel implements
@@ -60,9 +61,15 @@ public class AnnotationColourChooser extends Panel implements
 
   ColourSchemeI oldcs;
 
-  Hashtable oldgroupColours;
+  Map<SequenceGroup, ColourSchemeI> oldgroupColours;
 
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  /*
+   * map from annotation to its menu item display label
+   * - so we know which item to pre-select on restore
+   */
+  private Map<AlignmentAnnotation, String> annotationLabels;
+
+  AlignmentAnnotation currentAnnotation;
 
   boolean adjusting = false;
 
@@ -78,17 +85,10 @@ public class AnnotationColourChooser extends Panel implements
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
-      oldgroupColours = new Hashtable();
+      oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        if (sg.getColourScheme() != null)
-        {
-          oldgroupColours.put(sg, sg.getColourScheme());
-        }
-        else
-        {
-          oldgroupColours.put(sg, "null");
-        }
+        oldgroupColours.put(sg, sg.getColourScheme());
       }
     }
     this.av = av;
@@ -119,24 +119,7 @@ public class AnnotationColourChooser extends Panel implements
       // seqAssociated.setState(acg.isSeqAssociated());
     }
 
-    Vector<String> list = new Vector<String>();
-    int index = 1;
-    for (int i = 0; i < anns.length; i++)
-    {
-      String label = anns[i].label;
-      if (anns[i].sequenceRef != null)
-      {
-        label = label + "_" + anns[i].sequenceRef.getName();
-      }
-      if (!list.contains(label))
-      {
-        list.addElement(label);
-      }
-      else
-      {
-        list.addElement(label + "_" + (index++));
-      }
-    }
+    Vector<String> list = getAnnotationItems();
 
     for (int i = 0; i < list.size(); i++)
     {
@@ -153,7 +136,8 @@ public class AnnotationColourChooser extends Panel implements
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      annotations.select(acg.getAnnotation());
+      String label = annotationLabels.get(acg.getAnnotation());
+      annotations.select(label);
       switch (acg.getAboveThreshold())
       {
       case AnnotationColourGradient.NO_THRESHOLD:
@@ -170,7 +154,7 @@ public class AnnotationColourChooser extends Panel implements
                 MessageManager
                         .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient"));
       }
-      thresholdIsMin.setState(acg.thresholdIsMinMax);
+      thresholdIsMin.setState(acg.isThresholdIsMinMax());
       thresholdValue.setText("" + acg.getAnnotationThreshold());
     }
 
@@ -186,6 +170,51 @@ public class AnnotationColourChooser extends Panel implements
     validate();
   }
 
+  /**
+   * Builds and returns a list of menu items (display text) for choice of
+   * annotation. Also builds a map between annotations and their display labels.
+   * 
+   * @return
+   */
+  protected Vector<String> getAnnotationItems()
+  {
+    // TODO remove duplication with gui.AnnotationRowFilter
+    // TODO add 'per sequence only' option / parameter
+
+    annotationLabels = new HashMap<AlignmentAnnotation, String>();
+    Vector<String> list = new Vector<String>();
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
+    {
+      return list;
+    }
+    int index = 1;
+    for (int i = 0; i < anns.length; i++)
+    {
+      String label = anns[i].label;
+      if (anns[i].sequenceRef != null)
+      {
+        /*
+         * be helpful and include sequence id in label for
+         * sequence-associated annotation (JAL-2236)
+         */
+        label = label + "_" + anns[i].sequenceRef.getName();
+      }
+      if (!list.contains(label))
+      {
+        list.addElement(label);
+        annotationLabels.put(anns[i], label);
+      }
+      else
+      {
+        label = label + "_" + (index++);
+        list.addElement(label);
+        annotationLabels.put(anns[i], label);
+      }
+    }
+    return list;
+  }
+
   private void setDefaultMinMax()
   {
     minColour.setBackground(av.applet.getDefaultColourParameter(
@@ -501,7 +530,7 @@ public class AnnotationColourChooser extends Panel implements
       acg.setPredefinedColours(true);
     }
 
-    acg.thresholdIsMinMax = thresholdIsMin.getState();
+    acg.setThresholdIsMinMax(thresholdIsMin.getState());
 
     av.setGlobalColourScheme(acg);
 
@@ -510,7 +539,6 @@ public class AnnotationColourChooser extends Panel implements
     {
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-
         if (sg.getColourScheme() == null)
         {
           continue;
@@ -527,7 +555,6 @@ public class AnnotationColourChooser extends Panel implements
                   currentAnnotation, minColour.getBackground(), maxColour
                           .getBackground(), aboveThreshold));
         }
-
       }
     }
 
@@ -543,20 +570,10 @@ public class AnnotationColourChooser extends Panel implements
     {
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        Object cs = oldgroupColours.get(sg);
-        if (cs instanceof ColourSchemeI)
-        {
-          sg.setColourScheme((ColourSchemeI) cs);
-        }
-        else
-        {
-          // probably the "null" string we set it to if it was null originally.
-          sg.setColourScheme(null);
-        }
+        sg.setColourScheme(oldgroupColours.get(sg));
       }
     }
     ap.paintAlignment(true);
-
   }
 
   @Override