JAL-1066 limit available rows to per-sequence when selected and disable if no sequenc...

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

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index eca0b4c..f53f55a 100755 (executable)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -51,14 +51,11 @@ public class AnnotationColourChooser extends JPanel
   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
     oldcs = av.getGlobalColourScheme();
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
       oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      for (SequenceGroup sg:ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
         if (sg.cs != null)
         {
           oldgroupColours.put(sg, sg.cs);
@@ -91,7 +88,7 @@ public class AnnotationColourChooser extends JPanel
       }
     });
 
-    if (av.alignment.getAlignmentAnnotation() == null)
+    if (av.getAlignment().getAlignmentAnnotation() == null)
     {
       return;
     }
@@ -108,21 +105,10 @@ public class AnnotationColourChooser extends JPanel
        minColour.setBackground(acg.getMinColour());
         maxColour.setBackground(acg.getMaxColour());
       }
+      seqAssociated.setSelected(acg.isSeqAssociated());
     }
-
     adjusting = true;
-    Vector list = new Vector();
-    int index = 1;
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
-    {
-      String label = av.alignment.getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-        list.addElement(label);
-      else
-        list.addElement(label + "_" + (index++));
-    }
-
-    annotations = new JComboBox(list);
+    annotations = new JComboBox(getAnnotationItems(seqAssociated.isSelected()));
 
     threshold.addItem("No Threshold");
     threshold.addItem("Above Threshold");
@@ -159,10 +145,44 @@ public class AnnotationColourChooser extends JPanel
     adjusting = false;
 
     changeColour();
-    validate();
+    frame.invalidate();
+    frame.pack();
 
   }
 
+  private Vector<String> getAnnotationItems(boolean isSeqAssociated) {
+    Vector<String> list = new Vector<String>();
+    int index = 1;
+    int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+    boolean enableSeqAss=false;
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    {
+      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef==null)
+      {
+        if (isSeqAssociated)
+          {
+          continue;
+          }
+      } else {
+        enableSeqAss=true;
+      }
+      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      if (!list.contains(label))
+        {anmap[list.size()] = i;
+        list.addElement(label);
+        
+        }else {
+        if (!isSeqAssociated) {
+          anmap[list.size()] = i;
+          list.addElement(label + "_" + (index++));
+        }
+      }
+    }
+    seqAssociated.setEnabled(enableSeqAss);
+    annmap = new int[list.size()];
+    System.arraycopy(anmap, 0,  annmap,  0,  annmap.length);
+    return list;
+  }
   private void setDefaultMinMax()
   {
     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
@@ -290,6 +310,19 @@ public class AnnotationColourChooser extends JPanel
         thresholdIsMin_actionPerformed(actionEvent);
       }
     });
+    seqAssociated.setBackground(Color.white);
+    seqAssociated.setFont(JvSwingUtils.getLabelFont());
+    seqAssociated.setText("Per-sequence only");
+    seqAssociated.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        seqAssociated_actionPerformed(arg0);
+      }
+    });
+    
     this.setLayout(borderLayout1);
     jPanel2.setLayout(new MigLayout("","[left][center][right]","[][][]"));
     jPanel1.setBackground(Color.white);
@@ -297,14 +330,14 @@ public class AnnotationColourChooser extends JPanel
 
     jPanel1.add(ok);
     jPanel1.add(cancel);
-    jPanel2.add(annotations);
+    jPanel2.add(annotations, "grow, wrap");
+    jPanel2.add(seqAssociated);
     jPanel2.add(currentColours);
     JPanel colpanel = new JPanel(new FlowLayout());
     colpanel.setBackground(Color.white);
     colpanel.add(minColour);
     colpanel.add(maxColour);
     jPanel2.add(colpanel, "wrap");
-    
     jPanel2.add(threshold);
     jPanel2.add(defColours,"skip 1, wrap");
     jPanel2.add(thresholdIsMin);
@@ -312,6 +345,30 @@ public class AnnotationColourChooser extends JPanel
     jPanel2.add(thresholdValue, "grow");
     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
     this.add(jPanel2, java.awt.BorderLayout.CENTER);
+    this.validate();
+  }
+
+  protected void seqAssociated_actionPerformed(ActionEvent arg0)
+  {
+    adjusting=true;
+    String cursel = (String) annotations.getSelectedItem();
+    boolean isvalid=false,isseqs=seqAssociated.isSelected();
+    this.annotations.removeAllItems();
+    for (String anitem:getAnnotationItems(seqAssociated.isSelected()))
+    {
+      if (anitem.equals(            cursel) || (isseqs && cursel.startsWith(anitem)))
+      {
+        isvalid=true;
+        cursel=anitem;
+      }
+      this.annotations.addItem(anitem);
+    }
+    adjusting=false;
+    if (isvalid) { this.annotations.setSelectedItem(cursel); } else {
+      if (annotations.getItemCount()>0) {
+        annotations.setSelectedIndex(0);
+      }
+    }
   }
 
   protected void resetColours_actionPerformed(ActionEvent arg0)
@@ -321,7 +378,7 @@ public class AnnotationColourChooser extends JPanel
   }
 
   JComboBox annotations;
-
+  int[] annmap;
   JPanel minColour = new JPanel();
 
   JPanel maxColour = new JPanel();
@@ -345,6 +402,8 @@ public class AnnotationColourChooser extends JPanel
   JCheckBox currentColours = new JCheckBox();
 
   JCheckBox thresholdIsMin = new JCheckBox();
+  
+  JCheckBox seqAssociated = new JCheckBox();
 
   public void minColour_actionPerformed()
   {
@@ -378,8 +437,8 @@ public class AnnotationColourChooser extends JPanel
       return;
     }
 
-    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
-            .getSelectedIndex()];
+    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+            .getSelectedIndex()]];
 
     int aboveThreshold = -1;
     if (threshold.getSelectedItem().equals("Above Threshold"))
@@ -439,6 +498,7 @@ public class AnnotationColourChooser extends JPanel
               minColour.getBackground(), maxColour.getBackground(),
               aboveThreshold);
     }
+    acg.setSeqAssociated(seqAssociated.isSelected());
 
     if (currentAnnotation.graphMin == 0f
             && currentAnnotation.graphMax == 0f)
@@ -450,14 +510,11 @@ public class AnnotationColourChooser extends JPanel
 
     av.setGlobalColourScheme(acg);
 
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      
+      for (SequenceGroup sg:ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
-
         if (sg.cs == null)
         {
           continue;
@@ -467,16 +524,20 @@ public class AnnotationColourChooser extends JPanel
         {
           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
                   aboveThreshold);
+          ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected());
+
         }
         else
         {
           sg.cs = new AnnotationColourGradient(currentAnnotation,
                   minColour.getBackground(), maxColour.getBackground(),
                   aboveThreshold);
+          ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected());
         }
 
       }
     }
+    ap.alignmentChanged();
     // ensure all associated views (overviews, structures, etc) are notified of updated colours.
     ap.paintAlignment(true);
   }
@@ -508,13 +569,11 @@ public class AnnotationColourChooser extends JPanel
   void reset()
   {
     av.setGlobalColourScheme(oldcs);
-    if (av.alignment.getGroups() != null)
+    if (av.getAlignment().getGroups() != null)
     {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
+      
+      for (SequenceGroup sg:ap.av.getAlignment().getGroups())
       {
-        sg = (SequenceGroup) allGroups.get(g);
         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
       }
     }