X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=b6f89295e012843d7c3addfa39019b7b40f06231;hb=refs%2Fheads%2Ftask%2FJAL-3763_newDatasetForCds;hp=0bc45e24c6a4e0db69593253b0bc5affc0b41a69;hpb=0e7325771ec658d66194b7abab05616681f03a57;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 0bc45e2..b6f8929 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -418,7 +418,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         viewport.featureSettings.refreshTable();
       }
       alignPanel.paintAlignment(true, true);
-      statusBar.setText(MessageManager
+      setStatus(MessageManager
               .getString("label.successfully_added_features_alignment"));
     }
     return featuresFile;
@@ -576,7 +576,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     case KeyEvent.VK_F2:
       viewport.cursorMode = !viewport.cursorMode;
-      statusBar.setText(MessageManager
+      setStatus(MessageManager
               .formatMessage("label.keyboard_editing_mode", new String[]
               { (viewport.cursorMode ? "on" : "off") }));
       if (viewport.cursorMode)
@@ -2081,7 +2081,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             seqs, 0, viewport.getAlignment().getWidth(),
             viewport.getAlignment()));
 
-    viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
+    viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight() - 1); // BH
+                                                                             // 2019.04.18
     viewport.getAlignment().getWidth();
     viewport.firePropertyChange("alignment", null,
             viewport.getAlignment().getSequences());
@@ -2357,7 +2358,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
                 column, al);
       }
 
-      statusBar.setText(MessageManager
+      setStatus(MessageManager
               .formatMessage("label.removed_columns", new String[]
               { Integer.valueOf(trimRegion.getSize()).toString() }));
       addHistoryItem(trimRegion);
@@ -2401,7 +2402,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
     addHistoryItem(removeGapCols);
 
-    statusBar.setText(MessageManager
+    setStatus(MessageManager
             .formatMessage("label.removed_empty_columns", new String[]
             { Integer.valueOf(removeGapCols.getSize()).toString() }));
 
@@ -3521,16 +3522,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
             MessageManager.getString("label.colourScheme_hydrophobic"));
     hydrophobicityColour.addActionListener(this);
     helixColour.setLabel(MessageManager
-            .getString("label.colourScheme_helix_propensity"));
+            .getString("label.colourScheme_helixpropensity"));
     helixColour.addActionListener(this);
     strandColour.setLabel(MessageManager
-            .getString("label.colourScheme_strand_propensity"));
+            .getString("label.colourScheme_strandpropensity"));
     strandColour.addActionListener(this);
     turnColour.setLabel(
-            MessageManager.getString("label.colourScheme_turn_propensity"));
+            MessageManager.getString("label.colourScheme_turnpropensity"));
     turnColour.addActionListener(this);
     buriedColour.setLabel(
-            MessageManager.getString("label.colourScheme_buried_index"));
+            MessageManager.getString("label.colourScheme_buriedindex"));
     buriedColour.addActionListener(this);
     purinePyrimidineColour.setLabel(MessageManager
             .getString("label.colourScheme_purine/pyrimidine"));
@@ -3539,19 +3540,19 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // .getString("label.rna_interaction"));
     // RNAInteractionColour.addActionListener(this);
     RNAHelixColour.setLabel(
-            MessageManager.getString("label.colourScheme_rna_helices"));
+            MessageManager.getString("label.colourScheme_rnahelices"));
     RNAHelixColour.addActionListener(this);
     userDefinedColour
             .setLabel(MessageManager.getString("action.user_defined"));
     userDefinedColour.addActionListener(this);
     PIDColour.setLabel(
-            MessageManager.getString("label.colourScheme_%_identity"));
+            MessageManager.getString("label.colourScheme_%identity"));
     PIDColour.addActionListener(this);
     BLOSUM62Colour.setLabel(
             MessageManager.getString("label.colourScheme_blosum62"));
     BLOSUM62Colour.addActionListener(this);
     tcoffeeColour.setLabel(
-            MessageManager.getString("label.colourScheme_t-coffee_scores"));
+            MessageManager.getString("label.colourScheme_t-coffeescores"));
     // it will be enabled only if a score file is provided
     tcoffeeColour.setEnabled(false);
     tcoffeeColour.addActionListener(this);
@@ -3823,7 +3824,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
      */
     statusBar.setBackground(Color.white);
     statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
-    statusBar.setText(MessageManager.getString("label.status_bar"));
+    setStatus(MessageManager.getString("label.status_bar"));
     this.add(statusBar, BorderLayout.SOUTH);
   }
 
@@ -3963,7 +3964,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * without an additional javascript library to exchange messages between the
    * distinct applets. See http://issues.jalview.org/browse/JAL-621
    * 
-   * @param viewer
+   * @param jmolViewer
    *          JmolViewer instance
    * @param sequenceIds
    *          - sequence Ids to search for associations
@@ -4191,7 +4192,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else
     {
-      new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+      new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
     }
 
   }