JAL-2557 removal of Sequence.sequenceFeatures

[jalview.git] / src / jalview / commands / EditCommand.java

diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index f36b55f..bba0dfb 100644 (file)
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -122,15 +122,15 @@ public class EditCommand implements CommandI
   {
   }
 
-  public EditCommand(String description)
+  public EditCommand(String desc)
   {
-    this.description = description;
+    this.description = desc;
   }
 
-  public EditCommand(String description, Action command, SequenceI[] seqs,
+  public EditCommand(String desc, Action command, SequenceI[] seqs,
           int position, int number, AlignmentI al)
   {
-    this.description = description;
+    this.description = desc;
     if (command == Action.CUT || command == Action.PASTE)
     {
       setEdit(new Edit(command, seqs, position, number, al));
@@ -139,10 +139,10 @@ public class EditCommand implements CommandI
     performEdit(0, null);
   }
 
-  public EditCommand(String description, Action command, String replace,
+  public EditCommand(String desc, Action command, String replace,
           SequenceI[] seqs, int position, int number, AlignmentI al)
   {
-    this.description = description;
+    this.description = desc;
     if (command == Action.REPLACE)
     {
       setEdit(new Edit(command, seqs, position, number, al, replace));
@@ -548,7 +548,7 @@ public class EditCommand implements CommandI
         {
           // modify the oldds if necessary
           if (oldds != sequence.getDatasetSequence()
-                  || sequence.getSequenceFeatures() != null)
+                  || sequence.getFeatures().hasFeatures())
           {
             if (command.oldds == null)
             {
@@ -1131,16 +1131,15 @@ public class EditCommand implements CommandI
       return;
     }
 
-    SequenceFeature[] oldsf = new SequenceFeature[sf.size()];
+    List<SequenceFeature> oldsf = new ArrayList<SequenceFeature>();
 
     int cSize = j - i;
 
-    int s = 0;
     for (SequenceFeature feature : sf)
     {
       SequenceFeature copy = new SequenceFeature(feature);
 
-      oldsf[s++] = copy;
+      oldsf.add(copy);
 
       if (feature.getEnd() < i)
       {
@@ -1190,7 +1189,7 @@ public class EditCommand implements CommandI
 
     if (command.editedFeatures == null)
     {
-      command.editedFeatures = new Hashtable<SequenceI, SequenceFeature[]>();
+      command.editedFeatures = new Hashtable<SequenceI, List<SequenceFeature>>();
     }
 
     command.editedFeatures.put(seq, oldsf);
@@ -1317,7 +1316,7 @@ public class EditCommand implements CommandI
 
     Hashtable<String, Annotation[]> deletedAnnotations;
 
-    Hashtable<SequenceI, SequenceFeature[]> editedFeatures;
+    Hashtable<SequenceI, List<SequenceFeature>> editedFeatures;
 
     AlignmentI al;
 
@@ -1333,51 +1332,51 @@ public class EditCommand implements CommandI
 
     char gapChar;
 
-    public Edit(Action command, SequenceI[] seqs, int position, int number,
-            char gapChar)
+    public Edit(Action cmd, SequenceI[] sqs, int pos, int count,
+            char gap)
     {
-      this.command = command;
-      this.seqs = seqs;
-      this.position = position;
-      this.number = number;
-      this.gapChar = gapChar;
+      this.command = cmd;
+      this.seqs = sqs;
+      this.position = pos;
+      this.number = count;
+      this.gapChar = gap;
     }
 
-    Edit(Action command, SequenceI[] seqs, int position, int number,
-            AlignmentI al)
+    Edit(Action cmd, SequenceI[] sqs, int pos, int count,
+            AlignmentI align)
     {
-      this.gapChar = al.getGapCharacter();
-      this.command = command;
-      this.seqs = seqs;
-      this.position = position;
-      this.number = number;
-      this.al = al;
-
-      alIndex = new int[seqs.length];
-      for (int i = 0; i < seqs.length; i++)
+      this.gapChar = align.getGapCharacter();
+      this.command = cmd;
+      this.seqs = sqs;
+      this.position = pos;
+      this.number = count;
+      this.al = align;
+
+      alIndex = new int[sqs.length];
+      for (int i = 0; i < sqs.length; i++)
       {
-        alIndex[i] = al.findIndex(seqs[i]);
+        alIndex[i] = align.findIndex(sqs[i]);
       }
 
-      fullAlignmentHeight = (al.getHeight() == seqs.length);
+      fullAlignmentHeight = (align.getHeight() == sqs.length);
     }
 
-    Edit(Action command, SequenceI[] seqs, int position, int number,
-            AlignmentI al, String replace)
+    Edit(Action cmd, SequenceI[] sqs, int pos, int count,
+            AlignmentI align, 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++)
+      this.command = cmd;
+      this.seqs = sqs;
+      this.position = pos;
+      this.number = count;
+      this.al = align;
+      this.gapChar = align.getGapCharacter();
+      string = new char[sqs.length][];
+      for (int i = 0; i < sqs.length; i++)
       {
         string[i] = replace.toCharArray();
       }
 
-      fullAlignmentHeight = (al.getHeight() == seqs.length);
+      fullAlignmentHeight = (align.getHeight() == sqs.length);
     }
 
     public SequenceI[] getSequences()