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total annotation score is a double for maximum precision.
[jalview.git]
/
src
/
jalview
/
commands
/
EditCommand.java
diff --git
a/src/jalview/commands/EditCommand.java
b/src/jalview/commands/EditCommand.java
index
ccc6a81
..
ce88127
100644
(file)
--- a/
src/jalview/commands/EditCommand.java
+++ b/
src/jalview/commands/EditCommand.java
@@
-151,16
+151,16
@@
public class EditCommand
switch(edits[e].command)
{
case INSERT_GAP:
switch(edits[e].command)
{
case INSERT_GAP:
- insertGap(edits[e]);
+ insertGap(edits[e]);
break;
case DELETE_GAP:
break;
case DELETE_GAP:
- deleteGap(edits[e]);
+ deleteGap(edits[e]);
break;
case CUT:
break;
case CUT:
- cut(edits[e]);
+ cut(edits[e]);
break;
case PASTE:
break;
case PASTE:
- paste(edits[e]);
+ paste(edits[e]);
break;
case REPLACE:
replace(edits[e]);
break;
case REPLACE:
replace(edits[e]);
@@
-182,16
+182,16
@@
public class EditCommand
switch (edits[e].command)
{
case INSERT_GAP:
switch (edits[e].command)
{
case INSERT_GAP:
- deleteGap(edits[e]);
+ deleteGap(edits[e]);
break;
case DELETE_GAP:
break;
case DELETE_GAP:
- insertGap(edits[e]);
+ insertGap(edits[e]);
break;
case CUT:
break;
case CUT:
- paste(edits[e]);
+ paste(edits[e]);
break;
case PASTE:
break;
case PASTE:
- cut(edits[e]);
+ cut(edits[e]);
break;
case REPLACE:
replace(edits[e]);
break;
case REPLACE:
replace(edits[e]);
@@
-373,6
+373,7
@@
public class EditCommand
final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility)
{
final void adjustAnnotations(Edit command, boolean insert, boolean modifyVisibility)
{
+
AlignmentAnnotation[] annotations = null;
if (modifyVisibility && !insert)
AlignmentAnnotation[] annotations = null;
if (modifyVisibility && !insert)
@@
-471,7
+472,11
@@
public class EditCommand
}
int tSize = 0;
}
int tSize = 0;
-
+ if (annotations[a].annotations == null)
+ {
+ // nothing to edit here ?
+ continue;
+ }
aSize = annotations[a].annotations.length;
if (insert)
{
aSize = annotations[a].annotations.length;
if (insert)
{
@@
-480,7
+485,7
@@
public class EditCommand
for (int aa = 0; aa < temp.length; aa++)
{
temp[aa] = new Annotation(
for (int aa = 0; aa < temp.length; aa++)
{
temp[aa] = new Annotation(
- command.al.getGapCharacter()+"",
+ command.gapChar+"",
null, ' ', 0);
}
}
null, ' ', 0);
}
}
@@
-760,6
+765,7
@@
public class EditCommand
this.position = position;
this.number = number;
this.al = al;
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 = new char[seqs.length][];
for (int i = 0; i < seqs.length; i++)
{
@@
-769,5
+775,4
@@
public class EditCommand
fullAlignmentHeight = (al.getHeight() == seqs.length);
}
}
fullAlignmentHeight = (al.getHeight() == seqs.length);
}
}
-
}
}