Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge

[jalview.git] / src / jalview / appletgui / SliderPanel.java

diff --git a/src/jalview/appletgui/SliderPanel.java b/src/jalview/appletgui/SliderPanel.java
old mode 100755 (executable)
new mode 100644 (file)
index 8a4eb29..340bb64
--- a/src/jalview/appletgui/SliderPanel.java
+++ b/src/jalview/appletgui/SliderPanel.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.0b1)
+ * 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
@@ -24,6 +25,7 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 import jalview.schemes.*;
+import jalview.util.MessageManager;
 
 public class SliderPanel extends Panel implements ActionListener,
         AdjustmentListener, MouseListener
@@ -57,7 +59,7 @@ public class SliderPanel extends Panel implements ActionListener,
 
     conservationSlider.setTitle("Conservation Colour Increment  (" + source
             + ")");
-    if (ap.av.alignment.getGroups() != null)
+    if (ap.av.getAlignment().getGroups() != null)
     {
       sp.setAllGroupsCheckEnabled(true);
     }
@@ -112,7 +114,7 @@ public class SliderPanel extends Panel implements ActionListener,
     }
     PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
 
-    if (ap.av.alignment.getGroups() != null)
+    if (ap.av.getAlignment().getGroups() != null)
     {
       pid.setAllGroupsCheckEnabled(true);
     }
@@ -167,14 +169,14 @@ public class SliderPanel extends Panel implements ActionListener,
     applyButton.setVisible(false);
     if (forConservation)
     {
-      label.setText("Modify conservation visibility");
+      label.setText(MessageManager.getString("label.modify_conservation_visibility"));
       slider.setMinimum(0);
       slider.setMaximum(50 + slider.getVisibleAmount());
       slider.setUnitIncrement(1);
     }
     else
     {
-      label.setText("Colour residues above % occurence");
+      label.setText(MessageManager.getString("label.colour_residues_above_occurence"));
       slider.setMinimum(0);
       slider.setMaximum(100 + slider.getVisibleAmount());
       slider.setBlockIncrement(1);
@@ -195,24 +197,22 @@ public class SliderPanel extends Panel implements ActionListener,
     }
 
     ColourSchemeI toChange = null;
-    Vector allGroups = null;
-    int groupIndex = 0;
+    Iterator<SequenceGroup> allGroups = null;
 
     if (allGroupsCheck.getState())
     {
-      allGroups = ap.av.alignment.getGroups();
-      groupIndex = allGroups.size() - 1;
+      allGroups = ap.av.getAlignment().getGroups().listIterator();
     }
     else
     {
       toChange = cs;
     }
 
-    while (groupIndex > -1)
+    do
     {
       if (allGroups != null)
       {
-        toChange = ((SequenceGroup) allGroups.elementAt(groupIndex)).cs;
+        toChange = allGroups.next().cs;
       }
 
       if (forConservation)
@@ -224,8 +224,7 @@ public class SliderPanel extends Panel implements ActionListener,
         toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
       }
 
-      groupIndex--;
-    }
+    } while (allGroups != null && allGroups.hasNext());
 
     ap.seqPanel.seqCanvas.repaint();
 
@@ -319,20 +318,20 @@ public class SliderPanel extends Panel implements ActionListener,
     valueField.setText("      ");
     valueField.addActionListener(this);
     label.setFont(new java.awt.Font("Verdana", 0, 11));
-    label.setText("set this label text");
+    label.setText(MessageManager.getString("label.set_this_label_text"));
     jPanel1.setLayout(borderLayout1);
     jPanel2.setLayout(flowLayout1);
     applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    applyButton.setLabel("Apply");
+    applyButton.setLabel(MessageManager.getString("action.apply"));
     applyButton.addActionListener(this);
     undoButton.setEnabled(false);
     undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
-    undoButton.setLabel("Undo");
+    undoButton.setLabel(MessageManager.getString("action.undo"));
     undoButton.addActionListener(this);
     allGroupsCheck.setEnabled(false);
     allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
-    allGroupsCheck.setLabel("Apply threshold to all groups");
-    allGroupsCheck.setName("Apply to all Groups");
+    allGroupsCheck.setLabel(MessageManager.getString("action.apply_threshold_all_groups"));
+    allGroupsCheck.setName(MessageManager.getString("action.apply_all_groups"));
     this.setBackground(Color.white);
     this.setForeground(Color.black);
     jPanel2.add(label, null);