X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=4adeb839e3f8786f3400583e7d75d70389ed7133;hb=057f733ab390518a3641f1dedebd36c028bf03d6;hp=92cd407c90a9977b4c936ce1c4af56bb0f499d1e;hpb=4cea7a0328724b90a6a7c16ae8c926e0cc12cedd;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 92cd407..4adeb83 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,19 +1,22 @@
 /*
- * 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 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;
 
@@ -39,20 +42,20 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         MouseListener, MouseWheelListener, MouseMotionListener,
         ActionListener, AdjustmentListener, Scrollable
 {
-  final String HELIX = "Helix";
+  String HELIX = MessageManager.getString("label.helix");
 
-  final String SHEET = "Sheet";
+  String SHEET = MessageManager.getString("label.sheet");
 
   /**
    * For RNA secondary structure "stems" aka helices
    */
-  final String STEM = "RNA Helix";
+  String STEM = MessageManager.getString("label.rna_helix");
 
-  final String LABEL = "Label";
+  String LABEL = MessageManager.getString("label.label");
 
-  final String REMOVE = "Remove Annotation";
+  String REMOVE = MessageManager.getString("label.remove_annotation");
 
-  final String COLOUR = "Colour";
+  String COLOUR = MessageManager.getString("action.colour");
 
   public final Color HELIX_COLOUR = Color.red.darker();
 
@@ -268,8 +271,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else if (evt.getActionCommand().equals(LABEL))
     {
       String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
-      String label = JOptionPane.showInputDialog(this, MessageManager.getString("label.enter_label"),
-              exMesg);
+      String label = JOptionPane.showInputDialog(this,
+              MessageManager.getString("label.enter_label"), exMesg);
 
       if (label == null)
       {
@@ -304,7 +307,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     else if (evt.getActionCommand().equals(COLOUR))
     {
       Color col = JColorChooser.showDialog(this,
-              "Choose foreground colour", Color.black);
+              MessageManager.getString("label.select_foreground_colour"), Color.black);
 
       for (int i = 0; i < av.getColumnSelection().size(); i++)
       {
@@ -349,8 +352,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         aa[activeRow].hasIcons = true;
       }
 
-      String label = JOptionPane.showInputDialog(
-              MessageManager.getString("label.enter_label_for_the_structure"), symbol);
+      String label = JOptionPane.showInputDialog(MessageManager
+              .getString("label.enter_label_for_the_structure"), symbol);
 
       if (label == null)
       {
@@ -360,8 +363,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       if ((label.length() > 0) && !aa[activeRow].hasText)
       {
         aa[activeRow].hasText = true;
+        if (evt.getActionCommand().equals(STEM))
+        {
+          aa[activeRow].showAllColLabels = true;
+        }
       }
-
       for (int i = 0; i < av.getColumnSelection().size(); i++)
       {
         int index = av.getColumnSelection().columnAt(i);
@@ -376,11 +382,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
         anot[index].secondaryStructure = type;
         anot[index].displayCharacter = label;
+
       }
     }
     av.getAlignment().validateAnnotation(aa[activeRow]);
     ap.alignmentChanged();
-    
+
     adjustPanelHeight();
     repaint();
 
@@ -483,7 +490,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         return;
       }
 
-      JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.structure_type"));
+      JPopupMenu pop = new JPopupMenu(
+              MessageManager.getString("label.structure_type"));
       JMenuItem item;
       /*
        * Just display the needed structure options
@@ -665,7 +673,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
               && aa[row].annotations[res].description != null
               && aa[row].annotations[res].description.length() > 0)
       {
-        this.setToolTipText("<html>"+JvSwingUtils.wrapTooltip(aa[row].annotations[res].description)+"</html>");
+        this.setToolTipText(JvSwingUtils
+                        .wrapTooltip(true, aa[row].annotations[res].description));
       }
       else
       {
@@ -701,11 +710,11 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   @Override
   public void mouseClicked(MouseEvent evt)
   {
-//    if (activeRow != -1)
-//    {
-//      AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
-//      AlignmentAnnotation anot = aa[activeRow];
-//    }
+    // if (activeRow != -1)
+    // {
+    // AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+    // AlignmentAnnotation anot = aa[activeRow];
+    // }
   }
 
   // TODO mouseClicked-content and drawCursor are quite experimental!
@@ -797,10 +806,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     imageFresh = false;
     g.drawImage(image, 0, 0, this);
   }
+
   /**
    * set true to enable redraw timing debug output on stderr
    */
   private final boolean debugRedraw = false;
+
   /**
    * non-Thread safe repaint
    * 
@@ -817,9 +828,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       repaint();
       return;
     }
-    long stime=System.currentTimeMillis();
+    long stime = System.currentTimeMillis();
     gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
-    long mtime=System.currentTimeMillis();
+    long mtime = System.currentTimeMillis();
     int sr = av.startRes;
     int er = av.endRes + 1;
     int transX = 0;
@@ -839,12 +850,15 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     drawComponent(gg, sr, er);
 
     gg.translate(-transX, 0);
-    long dtime=System.currentTimeMillis();
+    long dtime = System.currentTimeMillis();
     fastPaint = true;
     repaint();
-    long rtime=System.currentTimeMillis();
-    if (debugRedraw) {
-      System.err.println("Scroll:\t"+horizontal+"\tCopyArea:\t"+(mtime-stime)+"\tDraw component:\t"+(dtime-mtime)+"\tRepaint call:\t"+(rtime-dtime));
+    long rtime = System.currentTimeMillis();
+    if (debugRedraw)
+    {
+      System.err.println("Scroll:\t" + horizontal + "\tCopyArea:\t"
+              + (mtime - stime) + "\tDraw component:\t" + (dtime - mtime)
+              + "\tRepaint call:\t" + (rtime - dtime));
     }
 
   }
@@ -906,7 +920,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
       fadedImage = null;
     }
-    
+
     g.setColor(Color.white);
     g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
 
@@ -924,7 +938,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       g.setColor(Color.black);
       if (av.validCharWidth)
       {
-        g.drawString(MessageManager.getString("label.alignment_has_no_annotations"), 20, 15);
+        g.drawString(MessageManager
+                .getString("label.alignment_has_no_annotations"), 20, 15);
       }
 
       return;
@@ -954,16 +969,21 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   {
     return imgWidth;
   }
+
   private int[] bounds = new int[2];
+
   @Override
   public int[] getVisibleVRange()
   {
-    if (ap!=null && ap.alabels!=null)
+    if (ap != null && ap.alabels != null)
     {
-    int sOffset=-ap.alabels.scrollOffset;
-    int visHeight = sOffset+ap.annotationSpaceFillerHolder.getHeight();
-    bounds[0] = sOffset; bounds[1]=visHeight;
-    return bounds;
-    } else return null;
+      int sOffset = -ap.alabels.scrollOffset;
+      int visHeight = sOffset + ap.annotationSpaceFillerHolder.getHeight();
+      bounds[0] = sOffset;
+      bounds[1] = visHeight;
+      return bounds;
+    }
+    else
+      return null;
   }
 }