X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=c490fbaf9c60bffe23736da109cb982e917feb97;hb=a4677746324adeea9632d7306c83dfd94dff6181;hp=3d54ae1b429067d07ae13e8310a8d34f9f427f64;hpb=830518dd02bbe8858347dbdcf5604e47af03faf3;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 3d54ae1..c490fba 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,30 +1,58 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 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.
+ * 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/>.
+ * 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.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.analysis.AlignmentUtils;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
 import jalview.util.ParseHtmlBodyAndLinks;
 
+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;
+
 public class AnnotationLabels extends Panel implements ActionListener,
         MouseListener, MouseMotionListener
 {
@@ -91,10 +119,13 @@ public class AnnotationLabels extends Panel implements ActionListener,
     this.av = av;
   }
 
-  public void setScrollOffset(int y)
+  public void setScrollOffset(int y, boolean repaint)
   {
     scrollOffset = y;
-    repaint();
+    if (repaint)
+    {
+      repaint();
+    }
   }
 
   /**
@@ -170,7 +201,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
               ap.alignFrame);
       Frame frame = new Frame();
       frame.add(cap);
-      jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
+      JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
               + " - " + aa[selectedRow].label, 500, 100);
       cap.setText(aa[selectedRow].toString());
     }
@@ -183,6 +214,14 @@ 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();
@@ -215,7 +254,9 @@ public class AnnotationLabels extends Panel implements ActionListener,
       return true;
     }
     else
+    {
       return false;
+    }
 
   }
 
@@ -281,8 +322,8 @@ 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)
       {
@@ -405,7 +446,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
     if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
 
-      PopupMenu popup = new PopupMenu("Annotations");
+      PopupMenu popup = new PopupMenu(
+              MessageManager.getString("label.annotations"));
 
       MenuItem item = new MenuItem(ADDNEW);
       item.addActionListener(this);
@@ -430,6 +472,32 @@ 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);
@@ -448,10 +516,10 @@ 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()
             {
@@ -464,7 +532,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
                 }
                 else
                 {
-                  ap.av.setIgnoreGapsConsensus(cbmi.getState());
+                  ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
                 }
                 ap.paintAlignment(true);
               }
@@ -473,7 +541,7 @@ 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()
               {
@@ -492,7 +560,7 @@ 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()
               {
@@ -512,7 +580,7 @@ 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()
               {
@@ -535,7 +603,7 @@ 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)
@@ -557,7 +625,7 @@ 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)
@@ -580,7 +648,7 @@ 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)
@@ -641,17 +709,40 @@ 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());
@@ -676,19 +767,16 @@ public class AnnotationLabels extends Panel implements ActionListener,
     {
       return;
     }
-    jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
-    jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
+    AlignFrame.copiedSequences = new StringBuffer();
+    AlignFrame.copiedSequences.append(sq.getName() + "\t"
             + sq.getStart() + "\t" + sq.getEnd() + "\t"
             + sq.getSequenceAsString() + "\n");
     if (av.hasHiddenColumns())
     {
-      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
-      for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+      AlignFrame.copiedHiddenColumns = new Vector();
+      for (int[] region : av.getColumnSelection().getHiddenColumns())
       {
-        int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
-                .elementAt(i);
-
-        jalview.appletgui.AlignFrame.copiedHiddenColumns
+        AlignFrame.copiedHiddenColumns
                 .addElement(new int[]
                 { region[0], region[1] });
       }
@@ -762,11 +850,12 @@ 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("Right click", 2, 8);
-      g.drawString("to add annotation", 2, 18);
+      g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+      g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+              18);
     }
   }
 }