X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=b28ccc7f9afd45b61b509f3db213e1bd038df2ed;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=29a79dddbfff551143dab592acc8764bbc1ba8db;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index 29a79dd..b28ccc7 100755
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -1,31 +1,57 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 java.awt.image.BufferedImage;
-
-import jalview.datamodel.*;
+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;
 
+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
 {
@@ -92,10 +118,13 @@ 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();
+    }
   }
 
   /**
@@ -107,7 +136,8 @@ public class AnnotationLabels extends Panel implements ActionListener,
   int getSelectedRow(int y)
   {
     int row = -2;
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
 
     if (aa == null)
     {
@@ -132,22 +162,23 @@ public class AnnotationLabels extends Panel implements ActionListener,
     return row;
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
 
     if (evt.getActionCommand().equals(ADDNEW))
     {
       AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
-              new Annotation[ap.av.alignment.getWidth()]);
+              new Annotation[ap.av.getAlignment().getWidth()]);
 
       if (!editLabelDescription(newAnnotation))
       {
         return;
       }
 
-      ap.av.alignment.addAnnotation(newAnnotation);
-      ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+      ap.av.getAlignment().addAnnotation(newAnnotation);
+      ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
     }
     else if (evt.getActionCommand().equals(EDITNAME))
     {
@@ -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();
@@ -215,12 +254,15 @@ public class AnnotationLabels extends Panel implements ActionListener,
       return true;
     }
     else
+    {
       return false;
+    }
 
   }
 
   boolean resizePanel = false;
 
+  @Override
   public void mouseMoved(MouseEvent evt)
   {
     resizePanel = evt.getY() < 10 && evt.getX() < 14;
@@ -228,7 +270,10 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
     if (row > -1)
     {
-      ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(av.alignment.getAlignmentAnnotation()[row].getDescription(true), true, "\n");
+      ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
+              av.getAlignment().getAlignmentAnnotation()[row]
+                      .getDescription(true),
+              true, "\n");
       if (tooltip == null)
       {
         tooltip = new Tooltip(phb.getNonHtmlContent(), this);
@@ -263,6 +308,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
     dragCancelled = true;
   }
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     if (dragCancelled)
@@ -278,8 +324,8 @@ 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)
       {
@@ -290,7 +336,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
         ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
                 - dif));
         ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
-                ap.annotationPanel.calcPanelHeight());
+                av.calcPanelHeight());
         f.height += dif;
         ap.seqPanelHolder.setPreferredSize(f);
         ap.setScrollValues(av.getStartRes(), av.getStartSeq());
@@ -322,10 +368,12 @@ public class AnnotationLabels extends Panel implements ActionListener,
     }
   }
 
+  @Override
   public void mouseClicked(MouseEvent evt)
   {
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     if (!resizePanel && !dragCancelled)
@@ -334,20 +382,20 @@ public class AnnotationLabels extends Panel implements ActionListener,
 
       int end = getSelectedRow(evt.getY() + scrollOffset);
 
-      if (start>-1 && start != end)
+      if (start > -1 && start != end)
       {
         // Swap these annotations
-        AlignmentAnnotation startAA = ap.av.alignment
+        AlignmentAnnotation startAA = ap.av.getAlignment()
                 .getAlignmentAnnotation()[start];
         if (end == -1)
         {
-          end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+          end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
         }
-        AlignmentAnnotation endAA = ap.av.alignment
+        AlignmentAnnotation endAA = ap.av.getAlignment()
                 .getAlignmentAnnotation()[end];
 
-        ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
-        ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+        ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+        ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
       }
     }
     resizePanel = false;
@@ -357,6 +405,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
     ap.annotationPanel.repaint();
   }
 
+  @Override
   public void mouseEntered(MouseEvent evt)
   {
     if (evt.getY() < 10 && evt.getX() < 14)
@@ -366,6 +415,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
     }
   }
 
+  @Override
   public void mouseExited(MouseEvent evt)
   {
     dragCancelled = false;
@@ -384,6 +434,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
     repaint();
   }
 
+  @Override
   public void mousePressed(MouseEvent evt)
   {
     oldY = evt.getY();
@@ -391,17 +442,19 @@ public class AnnotationLabels extends Panel implements ActionListener,
     {
       return;
     }
-    dragCancelled=false;
+    dragCancelled = false;
     // todo: move below to mouseClicked ?
     selectedRow = getSelectedRow(evt.getY() + scrollOffset);
 
-    AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = ap.av.getAlignment()
+            .getAlignmentAnnotation();
 
     // DETECT RIGHT MOUSE BUTTON IN AWT
     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);
@@ -426,6 +479,32 @@ 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);
@@ -444,13 +523,14 @@ 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()
             {
+              @Override
               public void itemStateChanged(ItemEvent e)
               {
                 if (aaa.groupRef != null)
@@ -460,7 +540,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
                 }
                 else
                 {
-                  ap.av.setIgnoreGapsConsensus(cbmi.getState());
+                  ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
                 }
                 ap.paintAlignment(true);
               }
@@ -469,10 +549,12 @@ 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()
               {
+                @Override
                 public void itemStateChanged(ItemEvent e)
                 {
                   // TODO: pass on reference
@@ -488,10 +570,11 @@ 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()
               {
+                @Override
                 public void itemStateChanged(ItemEvent e)
                 {
                   // TODO: pass on reference
@@ -505,14 +588,39 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
                 }
               });
+
               popup.add(cprofl);
+              final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+                      MessageManager
+                              .getString("label.normalise_group_logo"),
+                      aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+              cprofn.addItemListener(new ItemListener()
+              {
+                @Override
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  aaa.groupRef.setshowSequenceLogo(true);
+                  aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(cprofn);
             }
             else
             {
               final CheckboxMenuItem chist = new CheckboxMenuItem(
-                      "Show Histogram", av.isShowConsensusHistogram());
+                      MessageManager.getString("label.show_histogram"),
+                      av.isShowConsensusHistogram());
               chist.addItemListener(new ItemListener()
               {
+                @Override
                 public void itemStateChanged(ItemEvent e)
                 {
                   // TODO: pass on reference
@@ -522,15 +630,21 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // can be
                   // updated.
                   av.setShowConsensusHistogram(chist.getState());
+                  ap.alignFrame.showConsensusHistogram.setState(chist
+                          .getState()); // TODO: implement
+                                        // ap.updateGUI()/alignFrame.updateGUI
+                                        // for applet
                   ap.repaint();
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
                 }
               });
               popup.add(chist);
               final CheckboxMenuItem cprof = new CheckboxMenuItem(
-                      "Show Logo", av.isShowSequenceLogo());
+                      MessageManager.getString("label.show_logo"),
+                      av.isShowSequenceLogo());
               cprof.addItemListener(new ItemListener()
               {
+                @Override
                 public void itemStateChanged(ItemEvent e)
                 {
                   // TODO: pass on reference
@@ -540,11 +654,42 @@ public class AnnotationLabels extends Panel implements ActionListener,
                   // can be
                   // updated.
                   av.setShowSequenceLogo(cprof.getState());
+                  ap.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
+                                                                             // implement
+                                                                             // ap.updateGUI()/alignFrame.updateGUI
+                                                                             // for
+                                                                             // applet
                   ap.repaint();
                   // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
                 }
               });
               popup.add(cprof);
+              final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+                      MessageManager.getString("label.normalise_logo"),
+                      av.isNormaliseSequenceLogo());
+              cprofn.addItemListener(new ItemListener()
+              {
+                @Override
+                public void itemStateChanged(ItemEvent e)
+                {
+                  // TODO: pass on reference
+                  // to ap
+                  // so the
+                  // view
+                  // can be
+                  // updated.
+                  av.setShowSequenceLogo(true);
+                  ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
+                                                                              // implement
+                                                                              // ap.updateGUI()/alignFrame.updateGUI
+                                                                              // for
+                                                                              // applet
+                  av.setNormaliseSequenceLogo(cprofn.getState());
+                  ap.repaint();
+                  // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+                }
+              });
+              popup.add(cprofn);
             }
 
             item = new MenuItem(COPYCONS_SEQ);
@@ -567,11 +712,47 @@ public class AnnotationLabels extends Panel implements ActionListener,
             // todo: make the ap scroll to the selection - not necessary, first
             // click highlights/scrolls, second selects
             ap.seqPanel.ap.idPanel.highlightSearchResults(null);
-            ap.av.setSelectionGroup(// new SequenceGroup(
-            aa[selectedRow].groupRef); // );
-            ap.av.sendSelection();
+            // process modifiers
+            SequenceGroup sg = ap.av.getSelectionGroup();
+            if (sg == null
+                    || sg == aa[selectedRow].groupRef
+                    || !(jalview.util.Platform.isControlDown(evt) || evt
+                            .isShiftDown()))
+            {
+              if (jalview.util.Platform.isControlDown(evt)
+                      || evt.isShiftDown())
+              {
+                // clone a new selection group from the associated group
+                ap.av.setSelectionGroup(new SequenceGroup(
+                        aa[selectedRow].groupRef));
+              }
+              else
+              {
+                // set selection to the associated group so it can be edited
+                ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+              }
+            }
+            else
+            {
+              // modify current selection with associated group
+              int remainToAdd = aa[selectedRow].groupRef.getSize();
+              for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+              {
+                if (jalview.util.Platform.isControlDown(evt))
+                {
+                  sg.addOrRemove(sgs, --remainToAdd == 0);
+                }
+                else
+                {
+                  // notionally, we should also add intermediate sequences from
+                  // last added sequence ?
+                  sg.addSequence(sgs, --remainToAdd == 0);
+                }
+              }
+            }
             ap.paintAlignment(false);
             PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+            ap.av.sendSelection();
           }
           else
           {
@@ -583,17 +764,49 @@ 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 (!(jalview.util.Platform.isControlDown(evt) || evt
+                      .isShiftDown()))
+              {
+                sg = new SequenceGroup(sg);
+                sg.clear();
+                sg.addSequence(aa[selectedRow].sequenceRef, false);
+              }
+              else
+              {
+                if (jalview.util.Platform.isControlDown(evt))
+                {
+                  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());
@@ -622,31 +835,30 @@ public class AnnotationLabels extends Panel implements ActionListener,
     jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
             + sq.getStart() + "\t" + sq.getEnd() + "\t"
             + sq.getSequenceAsString() + "\n");
-    if (av.hasHiddenColumns)
+    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] });
+                .addElement(new int[] { region[0], region[1] });
       }
     }
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
   }
 
+  @Override
   public void paint(Graphics g)
   {
     int w = getSize().width;
     int h = getSize().height;
-    if (image == null || w != image.getWidth(this) || h!=image.getHeight(this) )
+    if (image == null || w != image.getWidth(this)
+            || h != image.getHeight(this))
     {
       image = createImage(w, ap.annotationPanel.getSize().height);
     }
@@ -665,7 +877,7 @@ public class AnnotationLabels extends Panel implements ActionListener,
     g.translate(0, -scrollOffset);
     g.setColor(Color.black);
 
-    AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+    AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     int y = 0, fy = g.getFont().getSize();
     int x = 0, offset;
 
@@ -703,11 +915,12 @@ public class AnnotationLabels extends Panel implements ActionListener,
               dragEvent.getY());
     }
 
-    if ((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);
     }
   }
 }