X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=67faf1109487b9ce45576da9fac5b00a0277fe20;hb=06e3a52df5af8243cdb67c023c8ddd834711ad36;hp=a286e0685004b7fc3885a83da4fedbf3239d7761;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index a286e06..67faf11 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,12 +20,35 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import java.awt.Checkbox;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Vector;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
 import jalview.util.ParseHtmlBodyAndLinks;
 
@@ -190,6 +213,14 @@ public class AnnotationLabels extends Panel implements ActionListener,
       }
 
     }
+    refresh();
+  }
+
+  /**
+   * Adjust size and repaint
+   */
+  protected void refresh()
+  {
     ap.annotationPanel.adjustPanelHeight();
     setSize(getSize().width, ap.annotationPanel.getSize().height);
     ap.validate();
@@ -222,7 +253,9 @@ public class AnnotationLabels extends Panel implements ActionListener,
       return true;
     }
     else
+    {
       return false;
+    }
 
   }
 
@@ -288,8 +321,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
               .getSize(), f = ap.seqPanelHolder.getSize();
       int dif = evt.getY() - oldY;
 
-      dif /= ap.av.charHeight;
-      dif *= ap.av.charHeight;
+      dif /= ap.av.getCharHeight();
+      dif *= ap.av.getCharHeight();
 
       if ((d.height - dif) > 20 && (f.height + dif) > 20)
       {
@@ -438,6 +471,32 @@ public class AnnotationLabels extends Panel implements ActionListener,
       item = new MenuItem(HIDE);
       item.addActionListener(this);
       popup.add(item);
+
+      /*
+       * Hide all <label>:
+       */
+      if (selectedRow < aa.length)
+      {
+        if (aa[selectedRow].sequenceRef != null)
+        {
+          final String label = aa[selectedRow].label;
+          MenuItem hideType = new MenuItem(
+                  MessageManager.getString("label.hide_all") + " " + label);
+          hideType.addActionListener(new ActionListener()
+          {
+            @Override
+            public void actionPerformed(ActionEvent e)
+            {
+              AlignmentUtils.showOrHideSequenceAnnotations(
+                      ap.av.getAlignment(), Collections.singleton(label),
+                      null, false, false);
+              refresh();
+            }
+          });
+          popup.add(hideType);
+        }
+      }
+
       if (hasHiddenRows)
       {
         item = new MenuItem(SHOWALL);
@@ -456,10 +515,10 @@ public class AnnotationLabels extends Panel implements ActionListener,
           {
             popup.addSeparator();
             final CheckboxMenuItem cbmi = new CheckboxMenuItem(
-                    "Ignore Gaps In Consensus",
+                    MessageManager.getString("label.ignore_gaps_consensus"),
                     (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
                             .getIgnoreGapsConsensus() : ap.av
-                            .getIgnoreGapsConsensus());
+                            .isIgnoreGapsConsensus());
             final AlignmentAnnotation aaa = aa[selectedRow];
             cbmi.addItemListener(new ItemListener()
             {
@@ -472,7 +531,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
                 }
                 else
                 {
-                  ap.av.setIgnoreGapsConsensus(cbmi.getState());
+                  ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
                 }
                 ap.paintAlignment(true);
               }
@@ -481,7 +540,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
             if (aaa.groupRef != null)
             {
               final CheckboxMenuItem chist = new CheckboxMenuItem(
-                      "Show Group Histogram",
+                      MessageManager.getString("label.show_group_histogram"),
                       aa[selectedRow].groupRef.isShowConsensusHistogram());
               chist.addItemListener(new ItemListener()
               {
@@ -500,7 +559,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               });
               popup.add(chist);
               final CheckboxMenuItem cprofl = new CheckboxMenuItem(
-                      "Show Group Logo",
+                      MessageManager.getString("label.show_group_logo"),
                       aa[selectedRow].groupRef.isShowSequenceLogo());
               cprofl.addItemListener(new ItemListener()
               {
@@ -520,7 +579,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
               popup.add(cprofl);
               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
-                      "Normalise Group Logo",
+                      MessageManager.getString("label.normalise_group_logo"),
                       aa[selectedRow].groupRef.isNormaliseSequenceLogo());
               cprofn.addItemListener(new ItemListener()
               {
@@ -543,7 +602,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
             else
             {
               final CheckboxMenuItem chist = new CheckboxMenuItem(
-                      "Show Histogram", av.isShowConsensusHistogram());
+                      MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram());
               chist.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -565,7 +624,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               });
               popup.add(chist);
               final CheckboxMenuItem cprof = new CheckboxMenuItem(
-                      "Show Logo", av.isShowSequenceLogo());
+                      MessageManager.getString("label.show_logo"), av.isShowSequenceLogo());
               cprof.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -588,7 +647,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               });
               popup.add(cprof);
               final CheckboxMenuItem cprofn = new CheckboxMenuItem(
-                      "Normalise Logo", av.isNormaliseSequenceLogo());
+                      MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
               cprofn.addItemListener(new ItemListener()
               {
                 public void itemStateChanged(ItemEvent e)
@@ -649,17 +708,40 @@ public class AnnotationLabels extends Panel implements ActionListener,
         }
         else if (aa[selectedRow].sequenceRef != null)
         {
-          Vector sr = new Vector();
-          sr.addElement(aa[selectedRow].sequenceRef);
           if (evt.getClickCount() == 1)
           {
-            ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+            ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
+                    .asList(new SequenceI[]
+                    { aa[selectedRow].sequenceRef }));
           }
           else if (evt.getClickCount() >= 2)
           {
             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
-            SequenceGroup sg = new SequenceGroup();
-            sg.addSequence(aa[selectedRow].sequenceRef, false);
+            SequenceGroup sg = ap.av.getSelectionGroup();
+            if (sg!=null)
+            {
+              // we make a copy rather than edit the current selection if no modifiers pressed
+              // see Enhancement JAL-1557
+              if (!(evt.isControlDown() || evt.isShiftDown()))
+              {
+                sg = new SequenceGroup(sg);
+                sg.clear();
+                sg.addSequence(aa[selectedRow].sequenceRef, false);
+              } else {
+                if (evt.isControlDown())
+                {
+                  sg.addOrRemove(aa[selectedRow].sequenceRef, true);
+                } else {
+                  // notionally, we should also add intermediate sequences from last added sequence ?
+                  sg.addSequence(aa[selectedRow].sequenceRef, true);
+                }
+              }
+            } else {
+              sg = new SequenceGroup();
+              sg.setStartRes(0);
+              sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+              sg.addSequence(aa[selectedRow].sequenceRef, false);
+            }
             ap.av.setSelectionGroup(sg);
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
@@ -691,11 +773,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
     if (av.hasHiddenColumns())
     {
       jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
-      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+      for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
-                .elementAt(i);
-
         jalview.appletgui.AlignFrame.copiedHiddenColumns
                 .addElement(new int[]
                 { region[0], region[1] });
@@ -770,7 +849,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               dragEvent.getY());
     }
 
-    if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+    if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
     {
       g.setColor(Color.black);
       g.drawString(MessageManager.getString("label.right_click"), 2, 8);