X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FEditCommand.java;h=aece057c845053b69bfdfb59bee3c1e364ff8816;hb=a0205942210037198f48eb20480efe88d5eb951e;hp=052b212fed256fcc2efffbc1ab9fcb7361c2c8c0;hpb=537bad6655186ae1c9daf2dbe6746c7c7168aeb0;p=jalview.git

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 052b212..aece057 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -44,6 +44,7 @@ public class EditCommand
   public static final int DELETE_GAP = 1;
   public static final int CUT = 2;
   public static final int PASTE = 3;
+  public static final int REPLACE = 4;
 
   Edit[] edits;
 
@@ -72,7 +73,25 @@ public class EditCommand
           new Edit(command, seqs, position, number, al)};
     }
 
-    performEdit(0);
+    performEdit(0, null);
+  }
+
+  public EditCommand(String description,
+                     int command,
+                     String replace,
+                     SequenceI[] seqs,
+                     int position,
+                     int number,
+                     AlignmentI al)
+  {
+    this.description = description;
+    if (command == REPLACE)
+    {
+      edits = new Edit[]
+          { new Edit(command, seqs, position, number, al, replace)};
+    }
+
+    performEdit(0, null);
   }
 
   final public String getDescription()
@@ -90,12 +109,42 @@ public class EditCommand
     return edits[0].al;
   }
 
+  /**
+   * append a new editCommand
+   * Note. this shouldn't be called if the edit is an operation affects more alignment objects than the one referenced
+   * in al (for example, cut or pasting whole sequences). Use the form with an additional AlignmentI[] views parameter. 
+   * @param command
+   * @param seqs
+   * @param position
+   * @param number
+   * @param al
+   * @param performEdit
+   */
+  final public void appendEdit(int command,
+          SequenceI[] seqs,
+          int position,
+          int number,
+          AlignmentI al,
+          boolean performEdit)
+  {
+    appendEdit(command, seqs, position, number, al, performEdit, null);
+  }
+  /**
+   * append a new edit command with a set of alignment views that may be operated on
+   * @param command
+   * @param seqs
+   * @param position
+   * @param number
+   * @param al
+   * @param performEdit
+   * @param views
+   */
   final public void appendEdit(int command,
                                SequenceI[] seqs,
                                int position,
                                int number,
                                AlignmentI al,
-                               boolean performEdit)
+                               boolean performEdit, AlignmentI[] views)
   {
     Edit edit = new Edit(command, seqs, position, number, al.getGapCharacter());
     if (al.getHeight() == seqs.length)
@@ -120,59 +169,63 @@ public class EditCommand
 
     if (performEdit)
     {
-      performEdit(edits.length - 1);
+      performEdit(edits.length - 1, views);
     }
   }
 
-  final void performEdit(int commandIndex)
+  final void performEdit(int commandIndex, AlignmentI[] views)
   {
     int eSize = edits.length;
     for (int e = commandIndex; e < eSize; e++)
     {
-      if (edits[e].command == INSERT_GAP)
+      switch(edits[e].command)
       {
+        case INSERT_GAP:
         insertGap(edits[e]);
-      }
-      else if (edits[e].command == DELETE_GAP)
-      {
+          break;
+        case DELETE_GAP:
         deleteGap(edits[e]);
-      }
-      else if (edits[e].command == CUT)
-      {
-        cut(edits[e]);
-      }
-      else if (edits[e].command == PASTE)
-      {
-        paste(edits[e]);
+          break;
+        case CUT:
+        cut(edits[e], views);
+          break;
+        case PASTE:
+        paste(edits[e], views);
+          break;
+        case REPLACE:
+          replace(edits[e]);
+          break;
       }
     }
   }
 
-  final public void doCommand()
+  final public void doCommand(AlignmentI[] views)
   {
-    performEdit(0);
+    performEdit(0,views);
   }
 
-  final public void undoCommand()
+  final public void undoCommand(AlignmentI[] views)
   {
     int e = 0, eSize = edits.length;
     for (e = eSize - 1; e > -1; e--)
     {
-      if (edits[e].command == INSERT_GAP)
+      switch (edits[e].command)
       {
+        case INSERT_GAP:
         deleteGap(edits[e]);
-      }
-      else if (edits[e].command == DELETE_GAP)
-      {
+          break;
+        case DELETE_GAP:
         insertGap(edits[e]);
-      }
-      else if (edits[e].command == CUT)
-      {
-        paste(edits[e]);
-      }
-      else if (edits[e].command == PASTE)
-      {
-        cut(edits[e]);
+          break;
+        case CUT:
+        paste(edits[e], views);
+          break;
+        case PASTE:
+        cut(edits[e], views);
+          break;
+        case REPLACE:
+          replace(edits[e]);
+          break;
       }
     }
   }
@@ -186,7 +239,7 @@ public class EditCommand
                                    command.gapChar);
     }
 
-    adjustAnnotations(command, true, false);
+    adjustAnnotations(command, true, false, null);
   }
 
   final void deleteGap(Edit command)
@@ -197,10 +250,10 @@ public class EditCommand
                                   command.position + command.number);
     }
 
-    adjustAnnotations(command, false, false);
+    adjustAnnotations(command, false, false, null);
   }
 
-  void cut(Edit command)
+  void cut(Edit command, AlignmentI[] views)
   {
     boolean seqDeleted=false;
     command.string = new char[command.seqs.length][];
@@ -241,10 +294,10 @@ public class EditCommand
       }
     }
 
-    adjustAnnotations(command, false, seqDeleted);
+    adjustAnnotations(command, false, seqDeleted, views);
   }
 
-  void paste(Edit command)
+  void paste(Edit command, AlignmentI[] views)
   {
     StringBuffer tmp;
     boolean newDSNeeded;
@@ -322,12 +375,33 @@ public class EditCommand
         adjustFeatures(command, i, start, end, true);
       }
     }
-    adjustAnnotations(command, true, seqWasDeleted);
+    adjustAnnotations(command, true, seqWasDeleted, views);
 
     command.string = null;
   }
 
-  final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility)
+  void replace(Edit command)
+  {
+    StringBuffer tmp;
+    String oldstring;
+    int start = command.position;
+    int end = command.number;
+
+    command.number = start + command.string[0].length;
+    for (int i = 0; i < command.seqs.length; i++)
+    {
+      oldstring = command.seqs[i].getSequenceAsString();
+      tmp = new StringBuffer(oldstring.substring(0, start));
+      tmp.append(command.string[i]);
+      tmp.append(oldstring.substring(end));
+      command.seqs[i].setSequence(tmp.toString());
+      command.string[i] = oldstring.substring(start, end).toCharArray();
+      tmp = null;
+      oldstring = null;
+    }
+  }
+
+  final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility, AlignmentI[] views)
   {
 
     AlignmentAnnotation[] annotations = null;
@@ -347,19 +421,62 @@ public class EditCommand
       AlignmentAnnotation[] tmp;
       for (int s = 0; s < command.seqs.length; s++)
       {
-        if (modifyVisibility) 
+        if (modifyVisibility)
         {
           // Rows are only removed or added to sequence object.
           if (!insert) {
             // remove rows
             tmp = command.seqs[s].getAnnotation();
             if (tmp!=null) {
-              command.deletedAnnotationRows.put(command.seqs[s], tmp);
+              int alen=tmp.length;
               for (int aa =0; aa<tmp.length; aa++)
               {
-                command.al.deleteAnnotation(tmp[aa]);
+                if (!command.al.deleteAnnotation(tmp[aa]))
+                {
+                  // strip out annotation not in the current al (will be put back on insert in all views)
+                  tmp[aa] = null;
+                  alen--;
+                }
               }
               command.seqs[s].setAlignmentAnnotation(null);
+              if (alen!=tmp.length)
+              { 
+                // save the non-null annotation references only
+                AlignmentAnnotation[] saved = new AlignmentAnnotation[alen];
+                for (int aa=0,aapos=0;aa<tmp.length;aa++)
+                {
+                  if (tmp[aa]!=null)
+                  {
+                    saved[aapos++] = tmp[aa];
+                    tmp[aa] = null;
+                  }
+                }
+                tmp = saved;
+                command.deletedAnnotationRows.put(command.seqs[s], saved);
+                // and then remove any annotation in the other views
+                for (int alview=0; views!=null && alview<views.length; alview++)
+                {
+                  if (views[alview]!=command.al)
+                  {
+                    AlignmentAnnotation[] toremove = views[alview].getAlignmentAnnotation();
+                    if (toremove==null || toremove.length==0)
+                    {
+                      continue;
+                    }
+                    // remove any alignment annotation on this sequence that's on that alignment view.
+                    for (int aa = 0; aa<toremove.length; aa++)
+                    {
+                      if (toremove[aa].sequenceRef==command.seqs[s])
+                      {
+                        views[alview].deleteAnnotation(toremove[aa]);
+                      }
+                    }
+                  }
+                }
+              } else {
+                // save all the annotation
+                command.deletedAnnotationRows.put(command.seqs[s], tmp);
+              }
             }
           } else {
             // recover rows
@@ -370,12 +487,30 @@ public class EditCommand
               if (revealed!=null) {
                 for (int aa =0; aa<revealed.length; aa++)
                 {
+                  // iterate through al adding original annotation
                   command.al.addAnnotation(revealed[aa]);
                 }
                 for (int aa =0; aa<revealed.length; aa++)
                 {
                   command.al.setAnnotationIndex(revealed[aa], aa);
                 }
+                // and then duplicate added annotation on every other alignment view
+                for (int vnum=0; views!=null && vnum<views.length; vnum++)
+                {
+                  if (views[vnum]!=command.al)
+                  {
+                    int avwidth = views[vnum].getWidth()+1;
+                    // duplicate in this view
+                    for (int a=0; a<revealed.length; a++)
+                    {
+                      AlignmentAnnotation newann = new AlignmentAnnotation(revealed[a]);
+                      command.seqs[s].addAlignmentAnnotation(newann);
+                      newann.padAnnotation(avwidth);
+                      views[vnum].addAnnotation(newann);
+                      views[vnum].setAnnotationIndex(newann, a);
+                    }
+                  }
+                }
               }
             }
           }
@@ -428,11 +563,22 @@ public class EditCommand
       }
 
       int tSize = 0;
-
+      if (annotations[a].annotations == null)
+      {
+        // nothing to edit here ?
+        continue;
+      }
       aSize = annotations[a].annotations.length;
       if (insert)
       {
         temp = new Annotation[aSize + command.number];
+        if(annotations[a].padGaps)
+          for (int aa = 0; aa < temp.length; aa++)
+          {
+            temp[aa] = new Annotation(
+                command.gapChar+"",
+                null, ' ', 0);
+          }
       }
       else
       {
@@ -522,7 +668,7 @@ public class EditCommand
                            0, temp, 0, copylen); //command.position);
 
           Annotation[] deleted = new Annotation[command.number];
-          if (copylen>command.position) {
+          if (copylen>=command.position) {
             copylen = Math.min(command.number, annotations[a].annotations.length-command.position);
             if (copylen>0)
             {
@@ -697,6 +843,27 @@ public class EditCommand
 
       fullAlignmentHeight = (al.getHeight() == seqs.length);
     }
-  }
 
+    Edit(int command,
+         SequenceI[] seqs,
+         int position,
+         int number,
+         AlignmentI al,
+         String replace)
+    {
+      this.command = command;
+      this.seqs = seqs;
+      this.position = position;
+      this.number = number;
+      this.al = al;
+      this.gapChar = al.getGapCharacter();
+      string = new char[seqs.length][];
+      for (int i = 0; i < seqs.length; i++)
+      {
+        string[i] = replace.toCharArray();
+      }
+
+      fullAlignmentHeight = (al.getHeight() == seqs.length);
+    }
+  }
 }