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Merge branch 'develop' into Release_2_9_Branch
[jalview.git]
/
src
/
jalview
/
io
/
FormatAdapter.java
diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
8a563fa
..
ebca31b
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-63,9
+63,9
@@
public class FormatAdapter extends AppletFormatAdapter
annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
true);
localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
annotFromStructure = jalview.bin.Cache.getDefault("ADD_TEMPFACT_ANN",
true);
localSecondaryStruct = jalview.bin.Cache.getDefault("ADD_SS_ANN",
- true);
- serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
- true);
+ true);
+ serviceSecondaryStruct = jalview.bin.Cache.getDefault("USE_RNAVIEW",
+ true);
}
else
{
}
else
{
@@
-108,11
+108,10
@@
public class FormatAdapter extends AppletFormatAdapter
startRes = seqs[i].getStart();
endRes = seqs[i].getEnd();
startRes = seqs[i].getStart();
endRes = seqs[i].getEnd();
- startIndex = startEnd[0];
- endIndex = startEnd[1];
-
if (startEnd != null)
{
if (startEnd != null)
{
+ startIndex = startEnd[0];
+ endIndex = startEnd[1];
// get first non-gaped residue start position
while (jalview.util.Comparison.isGap(seqs[i]
.getCharAt(startIndex)) && startIndex < endIndex)
// get first non-gaped residue start position
while (jalview.util.Comparison.isGap(seqs[i]
.getCharAt(startIndex)) && startIndex < endIndex)
@@
-271,14
+270,12
@@
public class FormatAdapter extends AppletFormatAdapter
ColumnSelection colSel)
{
return formatSequences(format, alignment, omitHidden, exportRange,
ColumnSelection colSel)
{
return formatSequences(format, alignment, omitHidden, exportRange,
- suffix, colSel,
- null);
+ suffix, colSel, null);
}
public String formatSequences(String format, AlignmentI alignment,
String[] omitHidden, int[] exportRange, boolean suffix,
}
public String formatSequences(String format, AlignmentI alignment,
String[] omitHidden, int[] exportRange, boolean suffix,
- ColumnSelection colSel,
- jalview.datamodel.SequenceGroup selgp)
+ ColumnSelection colSel, jalview.datamodel.SequenceGroup selgp)
{
if (omitHidden != null)
{
{
if (omitHidden != null)
{
@@
-363,5
+360,4
@@
public class FormatAdapter extends AppletFormatAdapter
selectedOnly);
}
selectedOnly);
}
-
}
}