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JAL-2629 add basic parameter adjustment to hmmsearch/align
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentOrder.java
diff --git
a/src/jalview/datamodel/AlignmentOrder.java
b/src/jalview/datamodel/AlignmentOrder.java
index
ccc9bfa
..
ef46d79
100755
(executable)
--- a/
src/jalview/datamodel/AlignmentOrder.java
+++ b/
src/jalview/datamodel/AlignmentOrder.java
@@
-80,7
+80,7
@@
public class AlignmentOrder
*/
public AlignmentOrder(AlignmentI orderFrom)
{
*/
public AlignmentOrder(AlignmentI orderFrom)
{
- Order = new ArrayList<SequenceI>();
+ Order = new ArrayList<>();
for (SequenceI seq : orderFrom.getSequences())
{
for (SequenceI seq : orderFrom.getSequences())
{
@@
-96,7
+96,7
@@
public class AlignmentOrder
*/
public AlignmentOrder(SequenceI[] orderFrom)
{
*/
public AlignmentOrder(SequenceI[] orderFrom)
{
- Order = new ArrayList<SequenceI>(Arrays.asList(orderFrom));
+ Order = new ArrayList<>(Arrays.asList(orderFrom));
}
/**
}
/**
@@
-218,7
+218,8
@@
public class AlignmentOrder
{
if (!identity)
{
{
if (!identity)
{
- throw new Error("Weak sequenceI equivalence not yet implemented.");
+ throw new Error(
+ "Weak sequenceI equivalence not yet implemented.");
}
else
{
}
else
{
@@
-285,7
+286,8
@@
public class AlignmentOrder
}
if (!identity)
{
}
if (!identity)
{
- throw new Error("Weak sequenceI equivalence not yet implemented.");
+ throw new Error(
+ "Weak sequenceI equivalence not yet implemented.");
}
else
{
}
else
{