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JAL-1925 update source version in license
[jalview.git]
/
src
/
jalview
/
io
/
FormatAdapter.java
diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
e795925
..
182f2f4
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-29,7
+29,6
@@
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.gui.AlignmentPanel;
/**
* Additional formatting methods used by the application in a number of places.
/**
* Additional formatting methods used by the application in a number of places.
@@
-51,7
+50,7
@@
public class FormatAdapter extends AppletFormatAdapter
init();
}
init();
}
- public FormatAdapter(AlignmentPanel alignPanel,
+ public FormatAdapter(AlignmentViewPanel alignPanel,
AlignExportSettingI settings)
{
super(alignPanel, settings);
AlignExportSettingI settings)
{
super(alignPanel, settings);
@@
-64,9
+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
{
@@
-108,12
+107,10
@@
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)
@@
-129,9
+126,7
@@
public class FormatAdapter extends AppletFormatAdapter
}
startRes = seqs[i].findPosition(startIndex);
}
startRes = seqs[i].findPosition(startIndex);
- startRes = seqs[i].getStart() > 1 ? startRes - seqs[i].getStart()
- : startRes;
- endRes = seqs[i].findPosition(endIndex) - seqs[i].getStart();
+ endRes = seqs[i].findPosition(endIndex);
}
tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
}
tmp[i] = new Sequence(seqs[i].getName(), omitHiddenColumns[i],
@@
-272,14
+267,12
@@
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)
{
@@
-364,5
+357,4
@@
public class FormatAdapter extends AppletFormatAdapter
selectedOnly);
}
selectedOnly);
}
-
}
}