X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=fdb3975704379fa3ce0b1aeece782ad0d08c8d83;hb=7e8241cdc284ef2586e36a3abbe3bd385dad10dc;hp=2178e37ef8abb920386662214a112048dc40761c;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 2178e37..fdb3975 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 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.gui;
@@ -41,21 +43,21 @@ import jalview.util.MessageManager;
 public class AnnotationLabels extends JPanel implements MouseListener,
         MouseMotionListener, ActionListener
 {
-  static String TOGGLE_LABELSCALE = "Scale Label to Column";
+  String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
 
-  static String ADDNEW = "Add New Row";
+  String ADDNEW = MessageManager.getString("label.add_new_row");
 
-  static String EDITNAME = "Edit Label/Description";
+  String EDITNAME = MessageManager.getString("label.edit_label_description");
 
-  static String HIDE = "Hide This Row";
+  String HIDE = MessageManager.getString("label.hide_row");
 
-  static String DELETE = "Delete This Row";
+  String DELETE = MessageManager.getString("label.delete_row");
 
-  static String SHOWALL = "Show All Hidden Rows";
+  String SHOWALL = MessageManager.getString("label.show_all_hidden_rows");
 
-  static String OUTPUT_TEXT = "Export Annotation";
+  String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
 
-  static String COPYCONS_SEQ = "Copy Consensus Sequence";
+  String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence");
 
   boolean resizePanel = false;
 
@@ -507,17 +509,40 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         }
         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.av.sendSelection();
             ap.paintAlignment(false);
@@ -532,7 +557,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
       return;
     }
 
-    JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.annotations"));
+    JPopupMenu pop = new JPopupMenu(
+            MessageManager.getString("label.annotations"));
     JMenuItem item = new JMenuItem(ADDNEW);
     item.addActionListener(this);
     pop.add(item);
@@ -823,11 +849,14 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   }
 
   /**
-   * Draw the full set of annotation Labels for the alignment at the given cursor
+   * Draw the full set of annotation Labels for the alignment at the given
+   * cursor
+   * 
+   * @param g
+   *          Graphics2D instance (needed for font scaling)
+   * @param width
+   *          Width for scaling labels
    * 
-   * @param g Graphics2D instance (needed for font scaling)
-   * @param width Width for scaling labels
-   *          
    */
   public void drawComponent(Graphics g, int width)
   {
@@ -835,12 +864,18 @@ public class AnnotationLabels extends JPanel implements MouseListener,
   }
 
   private final boolean debugRedraw = false;
+
   /**
-   * Draw the full set of annotation Labels for the alignment at the given cursor
+   * Draw the full set of annotation Labels for the alignment at the given
+   * cursor
    * 
-   * @param g Graphics2D instance (needed for font scaling)
-   * @param clip - true indicates that only current visible area needs to be rendered
-   * @param width Width for scaling labels         
+   * @param g
+   *          Graphics2D instance (needed for font scaling)
+   * @param clip
+   *          - true indicates that only current visible area needs to be
+   *          rendered
+   * @param width
+   *          Width for scaling labels
    */
   public void drawComponent(Graphics g, boolean clip, int width)
   {
@@ -859,7 +894,7 @@ public class AnnotationLabels extends JPanel implements MouseListener,
 
     g.translate(0, scrollOffset);
     g.setColor(Color.black);
-    
+
     AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
     int fontHeight = g.getFont().getSize();
     int y = 0;
@@ -869,18 +904,20 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     Font baseFont = g.getFont();
     FontMetrics baseMetrics = fm;
     int ofontH = fontHeight;
-    int sOffset=0;
+    int sOffset = 0;
     int visHeight = 0;
-    int[] visr = (ap!=null && ap.annotationPanel!=null) ? ap.annotationPanel.getVisibleVRange() : null;
-    if (clip && visr!=null){ 
-      sOffset = visr[0]; 
+    int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel
+            .getVisibleVRange() : null;
+    if (clip && visr != null)
+    {
+      sOffset = visr[0];
       visHeight = visr[1];
     }
-    boolean visible = true,before=false,after=false;
+    boolean visible = true, before = false, after = false;
     if (aa != null)
     {
       hasHiddenRows = false;
-      int olY=0;
+      int olY = 0;
       for (int i = 0; i < aa.length; i++)
       {
         visible = true;
@@ -889,33 +926,39 @@ public class AnnotationLabels extends JPanel implements MouseListener,
           hasHiddenRows = true;
           continue;
         }
-        olY=y;
+        olY = y;
         y += aa[i].height;
-        if (clip) {if (y<sOffset)
+        if (clip)
         {
-          if (!before)
+          if (y < sOffset)
           {
-            if (debugRedraw) {
-              System.out.println("before vis: "+i);
+            if (!before)
+            {
+              if (debugRedraw)
+              {
+                System.out.println("before vis: " + i);
+              }
+              before = true;
             }
-          before=true;
+            // don't draw what isn't visible
+            continue;
           }
-          // don't draw what isn't visible
-          continue;
-        }
-        if (olY>visHeight)
-        {
-
-          if (!after)
+          if (olY > visHeight)
           {
-            if (debugRedraw) {
-              System.out.println("Scroll offset: "+sOffset+" after vis: "+i);
+
+            if (!after)
+            {
+              if (debugRedraw)
+              {
+                System.out.println("Scroll offset: " + sOffset
+                        + " after vis: " + i);
+              }
+              after = true;
             }
-          after=true;
+            // don't draw what isn't visible
+            continue;
           }
-          // don't draw what isn't visible
-          continue;
-        }}
+        }
         g.setColor(Color.black);
 
         offset = -aa[i].height / 2;
@@ -933,7 +976,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
         if (aa[i].graphGroup > -1)
         {
           int groupSize = 0;
-          // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels
+          // TODO: JAL-1291 revise rendering model so the graphGroup map is
+          // computed efficiently for all visible labels
           for (int gg = 0; gg < aa.length; gg++)
           {
             if (aa[gg].graphGroup == aa[i].graphGroup)
@@ -1012,7 +1056,8 @@ public class AnnotationLabels extends JPanel implements MouseListener,
     if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
     {
       g.drawString(MessageManager.getString("label.right_click"), 2, 8);
-      g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18);
+      g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+              18);
     }
   }
 }