X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=592fd4f402a68601b86474d697c4e36f80a4021c;hb=e2e6110281b107d8cc5d79ca567f830f7b06e17e;hp=a5dfb83cf5a2b5dc4f9f409302ea2c173c0b79ee;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index a5dfb83..592fd4f 100644
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,33 +1,49 @@
 /*
- * 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 2.8.2)
+ * 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.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
 import jalview.structure.SelectionSource;
 import jalview.structure.SequenceListener;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Vector;
 
 public class SeqPanel extends Panel implements MouseMotionListener,
         MouseListener, SequenceListener
@@ -143,10 +159,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   void setCursorPosition()
   {
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+    SequenceI sequence = av.getAlignment().getSequenceAt(
             seqCanvas.cursorY);
 
-    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+    seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
     scrollToVisible();
   }
 
@@ -236,7 +252,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   void setSelectionAreaAtCursor(boolean topLeft)
   {
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+    SequenceI sequence = av.getAlignment().getSequenceAt(
             seqCanvas.cursorY);
 
     if (av.getSelectionGroup() != null)
@@ -345,26 +361,36 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   int getKeyboardNo1()
   {
-    if (keyboardNo1 == null)
-      return 1;
-    else
+    try
+    {
+      if (keyboardNo1 != null)
+      {
+        int value = Integer.parseInt(keyboardNo1.toString());
+        keyboardNo1 = null;
+        return value;
+      }
+    } catch (Exception x)
     {
-      int value = Integer.parseInt(keyboardNo1.toString());
-      keyboardNo1 = null;
-      return value;
     }
+    keyboardNo1 = null;
+    return 1;
   }
 
   int getKeyboardNo2()
   {
-    if (keyboardNo2 == null)
-      return 1;
-    else
+    try
+    {
+      if (keyboardNo2 != null)
+      {
+        int value = Integer.parseInt(keyboardNo2.toString());
+        keyboardNo2 = null;
+        return value;
+      }
+    } catch (Exception x)
     {
-      int value = Integer.parseInt(keyboardNo2.toString());
-      keyboardNo2 = null;
-      return value;
     }
+    keyboardNo2 = null;
+    return 1;
   }
 
   void setStatusMessage(SequenceI sequence, int res, int seq)
@@ -634,7 +660,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     String tmp = sequence.hashCode() + index + "";
     if (lastMessage == null || !lastMessage.equals(tmp))
+    {
       ssm.mouseOverSequence(sequence, index, pos, av);
+    }
 
     lastMessage = tmp;
   }
@@ -684,7 +712,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     int respos = sequence.findPosition(res);
     if (ssm != null)
+    {
       mouseOverSequence(sequence, res, respos);
+    }
 
     StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: "
             + sequence.getName());
@@ -799,7 +829,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
                         .containsKey(features[i].featureGroup)
                 && !((Boolean) seqCanvas.fr.featureGroups
                         .get(features[i].featureGroup)).booleanValue())
+        {
           continue;
+        }
 
         if ((features[i].getBegin() <= res)
                 && (features[i].getEnd() >= res))
@@ -924,7 +956,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       if (av.isHiddenRepSequence(seq))
       {
-        sg = (SequenceGroup) av.getRepresentedSequences(seq);
+        sg = av.getRepresentedSequences(seq);
         groupEditing = true;
       }
     }
@@ -932,15 +964,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     StringBuffer message = new StringBuffer();
     if (groupEditing)
     {
-      message.append("Edit group:");
+      message.append(MessageManager.getString("action.edit_group")).append(":");
       if (editCommand == null)
       {
-        editCommand = new EditCommand("Edit Group");
+        editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
       }
     }
     else
     {
-      message.append("Edit sequence: " + seq.getName());
+      message.append(MessageManager.getString("label.edit_sequence")).append(" " + seq.getName());
       String label = seq.getName();
       if (label.length() > 10)
       {
@@ -948,7 +980,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
       if (editCommand == null)
       {
-        editCommand = new EditCommand("Edit " + label);
+        editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
       }
     }
 
@@ -1150,7 +1182,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+          editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
                   startres, startres - lastres, av.getAlignment(), true);
         }
       }
@@ -1166,7 +1198,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+          editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
                   startres, lastres - startres, av.getAlignment(), true);
         }
 
@@ -1188,7 +1220,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+          editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
           { seq }, lastres, startres - lastres, av.getAlignment(), true);
         }
       }
@@ -1223,7 +1255,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
           if (max > 0)
           {
-            editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+            editCommand.appendEdit(Action.DELETE_GAP, new SequenceI[]
             { seq }, startres, max, av.getAlignment(), true);
           }
         }
@@ -1259,10 +1291,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
     }
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+    editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
             av.getAlignment(), true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1,
+    editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
             av.getAlignment(), true);
 
   }
@@ -1270,10 +1302,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
+    editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
             av.getAlignment(), true);
 
-    editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+    editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
             av.getAlignment(), true);
   }
 
@@ -1298,7 +1330,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       return;
     }
 
-    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
     if (sequence == null || res > sequence.getLength())
     {