From f0fcba68c61bd8eddd6a975168ade951e8d9001d Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 31 Jan 2007 14:47:57 +0000
Subject: [PATCH] Adjust features when cutting and pasting

---
 src/jalview/commands/EditCommand.java |  137 ++++++++++++++++++++++++++++++---
 1 file changed, 128 insertions(+), 9 deletions(-)

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index 0c833d0..f3b178f 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -73,7 +73,7 @@ public class EditCommand implements CommandI
   }
 
 
-  public String getDescription()
+  final public String getDescription()
   {
     return description;
   }
@@ -83,13 +83,13 @@ public class EditCommand implements CommandI
     return edits==null?0:edits.length;
   }
 
-  public AlignmentI getAlignment()
+  final public AlignmentI getAlignment()
   {
     return edits[0].al;
   }
 
 
-  public void appendEdit(int command,
+  final public void appendEdit(int command,
                          SequenceI[] seqs,
                          int position,
                          int number,
@@ -117,7 +117,7 @@ public class EditCommand implements CommandI
       performEdit(edits.length - 1);
   }
 
-  void performEdit(int commandIndex)
+  final void performEdit(int commandIndex)
   {
     int eSize = edits.length;
     for (int e = commandIndex; e < eSize; e++)
@@ -141,12 +141,12 @@ public class EditCommand implements CommandI
     }
   }
 
-  public void doCommand()
+  final public void doCommand()
   {
     performEdit(0);
   }
 
-  public void undoCommand()
+  final public void undoCommand()
   {
     int e = 0, eSize = edits.length;
     for (e = eSize-1; e > -1; e--)
@@ -170,7 +170,7 @@ public class EditCommand implements CommandI
     }
   }
 
-  void insertGap(Edit command)
+  final void insertGap(Edit command)
   {
     for(int s=0; s<command.seqs.length; s++)
     {
@@ -182,7 +182,7 @@ public class EditCommand implements CommandI
     adjustAnnotations(command, true);
   }
 
-  void deleteGap(Edit command)
+  final void deleteGap(Edit command)
   {
     for (int s = 0; s < command.seqs.length; s++)
     {
@@ -203,6 +203,23 @@ public class EditCommand implements CommandI
         command.string[i] = command.seqs[i].getSequence(command.position,
             command.position + command.number);
 
+        if(command.seqs[i].getDatasetSequence()!=null
+        || command.seqs[i].getSequenceFeatures()!=null)
+        {
+          for (int s = command.position; s < command.position + command.number; s++)
+          {
+            if (jalview.schemes.ResidueProperties
+                .aaIndex[command.seqs[i].getCharAt(s)] != 23)
+            {
+              adjustFeatures(command, i,
+                             command.seqs[i].findPosition(command.position),
+                             command.seqs[i].findPosition(command.position +
+                                                          command.number),
+                             false);
+              break;
+            }
+          }
+        }
         command.seqs[i].deleteChars(command.position,
                                     command.position + command.number);
       }
@@ -219,8 +236,12 @@ public class EditCommand implements CommandI
   void paste(Edit command)
   {
     StringBuffer tmp;
+    boolean newDSNeeded;
+    int start=0, end=0;
+
     for(int i=0; i<command.seqs.length; i++)
     {
+      newDSNeeded = false;
       if(command.seqs[i].getLength()<1)
       {
         // ie this sequence was deleted, we need to
@@ -248,9 +269,40 @@ public class EditCommand implements CommandI
           }
         }
         tmp.insert(command.position, command.string[i]);
+
+        for (int s = 0; s < command.string[i].length; s++)
+        {
+          if (jalview.schemes.ResidueProperties.aaIndex[command.string[i][s]] != 23)
+          {
+            newDSNeeded = true;
+            start = command.seqs[i].findPosition(command.position);
+            end = command.seqs[i].findPosition(command.position+command.number);
+            break;
+          }
+        }
         command.string[i] = null;
       }
+
+
       command.seqs[i].setSequence(tmp.toString());
+
+      if(newDSNeeded)
+      {
+        if (command.seqs[i].getDatasetSequence() != null)
+        {
+          Sequence ds = new Sequence(command.seqs[i].getName(),
+                                     jalview.analysis.AlignSeq.extractGaps(
+                                         jalview.util.Comparison.GapChars,
+                                         command.seqs[i].getSequenceAsString()
+                                     ),
+                                     command.seqs[i].getStart(),
+                                     command.seqs[i].getEnd());
+          ds.setDescription(command.seqs[i].getDescription());
+          command.seqs[i].setDatasetSequence(ds);
+        }
+
+        adjustFeatures(command, i, start, end, true);
+      }
     }
 
 
@@ -260,7 +312,7 @@ public class EditCommand implements CommandI
   }
 
 
-  void adjustAnnotations(Edit command, boolean insert)
+  final void adjustAnnotations(Edit command, boolean insert)
   {
 
     AlignmentAnnotation [] annotations = null;
@@ -379,11 +431,78 @@ public class EditCommand implements CommandI
      }
   }
 
+  final void adjustFeatures(Edit command, int index, int i, int j, boolean insert)
+  {
+    SequenceI seq = command.seqs[index];
+    SequenceI sequence = seq.getDatasetSequence();
+    if(sequence==null)
+      sequence = seq;
+
+    if(insert)
+    {
+      if (command.editedFeatures != null
+          && command.editedFeatures.containsKey(seq))
+        sequence.setSequenceFeatures(
+            (SequenceFeature[]) command.editedFeatures.get(seq)
+            );
+
+      return;
+    }
+
+
+    SequenceFeature [] sf = sequence.getSequenceFeatures();
+
+
+    if(sf==null)
+    {
+      return;
+    }
+
+    SequenceFeature [] oldsf = new SequenceFeature[sf.length];
+
+    int cSize = j - i;
+
+    for (int s = 0; s < sf.length; s++)
+    {
+      SequenceFeature copy = new SequenceFeature(sf[s]);
+
+      oldsf[s] = copy;
+
+      if (sf[s].getEnd() < i)
+        continue;
+
+      if (sf[s].getBegin() > j)
+      {
+        sf[s].setBegin(copy.getBegin() - cSize);
+        sf[s].setEnd(copy.getEnd() - cSize);
+        continue;
+      }
+
+      if (sf[s].getBegin() >= i)
+        sf[s].setBegin(i);
+
+      if (sf[s].getEnd() < j)
+        sf[s].setEnd(j - 1);
+
+      sf[s].setEnd(sf[s].getEnd() - (cSize));
+
+      if (sf[s].getBegin() > sf[s].getEnd())
+        sequence.deleteFeature(sf[s]);
+    }
+
+    if (command.editedFeatures == null)
+      command.editedFeatures = new Hashtable();
+
+    command.editedFeatures.put(seq, oldsf);
+
+  }
+
 
   class Edit
   {
     boolean fullAlignmentHeight = false;
     Hashtable deletedAnnotations;
+    Hashtable editedFeatures;
     AlignmentI al;
     int command;
     char [][] string;
-- 
1.7.10.2