X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=ba8c6abe4d5b490ad9861c6685e3802cc418fa54;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=a7345db13d926133c2605b6752f45ffdc6ecdc21;hpb=0899f9541714086b75987a4ba3d35037a6d6224b;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index a7345db..ba8c6ab 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 2.8.2b1)
+ * 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();
   }
 
@@ -154,7 +170,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
   {
     seqCanvas.cursorX += dx;
     seqCanvas.cursorY += dy;
-    if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+    if (av.hasHiddenColumns()
+            && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
     {
       int original = seqCanvas.cursorX - dx;
       int maxWidth = av.getAlignment().getWidth();
@@ -235,7 +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)
@@ -344,26 +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)
@@ -458,7 +485,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
     if (evt.getClickCount() > 1)
     {
-      if (av.getSelectionGroup()!=null && av.getSelectionGroup().getSize() == 1
+      if (av.getSelectionGroup() != null
+              && av.getSelectionGroup().getSize() == 1
               && av.getSelectionGroup().getEndRes()
                       - av.getSelectionGroup().getStartRes() < 2)
       {
@@ -581,8 +609,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
       y -= hgap;
 
-      seq = Math.min((y % cHeight) / av.getCharHeight(),
-              av.getAlignment().getHeight() - 1);
+      seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
+              .getHeight() - 1);
       if (seq < 0)
       {
         seq = -1;
@@ -590,8 +618,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     }
     else
     {
-      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
-              av.getAlignment().getHeight() - 1);
+      seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+              .getAlignment().getHeight() - 1);
       if (seq < 0)
       {
         seq = -1;
@@ -632,7 +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;
   }
@@ -682,7 +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());
@@ -797,7 +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))
@@ -922,7 +956,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     {
       if (av.isHiddenRepSequence(seq))
       {
-        sg = (SequenceGroup) av.getRepresentedSequences(seq);
+        sg = av.getRepresentedSequences(seq);
         groupEditing = true;
       }
     }
@@ -930,15 +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)
       {
@@ -946,7 +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}));
       }
     }
 
@@ -1036,7 +1070,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
     if (groupEditing)
     {
-      SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences()).toArray(new SequenceI[0]);
+      SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
+              .toArray(new SequenceI[0]);
 
       // drag to right
       if (insertGap)
@@ -1058,12 +1093,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           blank = true;
 
-          for (SequenceI gs:groupSeqs)
+          for (SequenceI gs : groupSeqs)
           {
             for (int j = 0; j < startres - lastres; j++)
             {
-              if (!jalview.util.Comparison.isGap(gs
-                      .getCharAt(fixedRight - j)))
+              if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
+                      - j)))
               {
                 blank = false;
                 break;
@@ -1080,8 +1115,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         {
           if (sg.getSize() == av.getAlignment().getHeight())
           {
-            if ((av.hasHiddenColumns() && startres < av.getColumnSelection()
-                    .getHiddenBoundaryRight(startres)))
+            if ((av.hasHiddenColumns() && startres < av
+                    .getColumnSelection().getHiddenBoundaryRight(startres)))
             {
               endEditing();
               return;
@@ -1090,7 +1125,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
             int alWidth = av.getAlignment().getWidth();
             if (av.hasHiddenRows())
             {
-              int hwidth = av.getAlignment().getHiddenSequences().getWidth();
+              int hwidth = av.getAlignment().getHiddenSequences()
+                      .getWidth();
               if (hwidth > alWidth)
               {
                 alWidth = hwidth;
@@ -1115,7 +1151,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         // / Are we able to delete?
         // ie are all columns blank?
 
-        for (SequenceI gs:groupSeqs)
+        for (SequenceI gs : groupSeqs)
         {
           for (int j = startres; j < lastres; j++)
           {
@@ -1146,7 +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);
         }
       }
@@ -1162,7 +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);
         }
 
@@ -1184,7 +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);
         }
       }
@@ -1219,7 +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);
           }
         }
@@ -1255,21 +1291,21 @@ 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, av.getAlignment(),
-            true);
+    editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
+            av.getAlignment(), true);
 
   }
 
   void deleteChar(int j, SequenceI[] seq, int fixedColumn)
   {
 
-    editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(),
-            true);
+    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);
   }
 
@@ -1294,7 +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())
     {
@@ -1415,8 +1451,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
                                        // state
     if (stretchGroup.cs != null)
     {
-      stretchGroup.cs.alignmentChanged(stretchGroup,av.getHiddenRepSequences());
-      
+      stretchGroup.cs.alignmentChanged(stretchGroup,
+              av.getHiddenRepSequences());
+
       if (stretchGroup.cs.conservationApplied())
       {
         SliderPanel.setConservationSlider(ap, stretchGroup.cs,
@@ -1505,7 +1542,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       dragDirection = -1;
     }
 
-    while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight()))
+    while ((y != oldSeq) && (oldSeq > -1)
+            && (y < av.getAlignment().getHeight()))
     {
       // This routine ensures we don't skip any sequences, as the
       // selection is quite slow.
@@ -1692,7 +1730,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
     {
       SequenceGroup sgroup = null;
-      if (seqsel != null && seqsel.getSize()>0)
+      if (seqsel != null && seqsel.getSize() > 0)
       {
         if (av.getAlignment() == null)
         {
@@ -1722,7 +1760,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
       repaint = av.isSelectionGroupChanged(true);
     }
-    if (copycolsel && (av.getColumnSelection() == null || !av.isColSelChanged(true)))
+    if (copycolsel
+            && (av.getColumnSelection() == null || !av
+                    .isColSelChanged(true)))
     {
       // the current selection is unset or from a previous message
       // so import the new colsel.
@@ -1747,8 +1787,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       }
       repaint |= av.isColSelChanged(true);
     }
-    if (copycolsel && av.hasHiddenColumns()
-            && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null))
+    if (copycolsel
+            && av.hasHiddenColumns()
+            && (av.getColumnSelection() == null || av.getColumnSelection()
+                    .getHiddenColumns() == null))
     {
       System.err.println("Bad things");
     }
@@ -1761,35 +1803,40 @@ public class SeqPanel extends Panel implements MouseMotionListener,
 
   /**
    * scroll to the given row/column - or nearest visible location
+   * 
    * @param row
    * @param column
    */
   public void scrollTo(int row, int column)
   {
-    
-    row = row<0 ? ap.av.startSeq : row;
-    column = column<0 ? ap.av.startRes : column;
+
+    row = row < 0 ? ap.av.startSeq : row;
+    column = column < 0 ? ap.av.startRes : column;
     ap.scrollTo(column, column, row, true, true);
   }
+
   /**
    * scroll to the given row - or nearest visible location
+   * 
    * @param row
    */
   public void scrollToRow(int row)
   {
-    
-    row = row<0 ? ap.av.startSeq : row;
+
+    row = row < 0 ? ap.av.startSeq : row;
     ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
   }
+
   /**
    * scroll to the given column - or nearest visible location
+   * 
    * @param column
    */
   public void scrollToColumn(int column)
   {
-    
-    column = column<0 ? ap.av.startRes : column;
-    ap.scrollTo( column, column, ap.av.startSeq, true, true);
+
+    column = column < 0 ? ap.av.startRes : column;
+    ap.scrollTo(column, column, ap.av.startSeq, true, true);
   }
 
 }