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JAL-1705 isFromForwardStrand added; toString (for debug) tweaked
[jalview.git]
/
src
/
jalview
/
io
/
FormatAdapter.java
diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
d241308
..
4ec077f
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-20,7
+20,8
@@
*/
package jalview.io;
*/
package jalview.io;
-import jalview.api.AlignViewportI;
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
@@
-37,9
+38,9
@@
import jalview.datamodel.SequenceI;
*/
public class FormatAdapter extends AppletFormatAdapter
{
*/
public class FormatAdapter extends AppletFormatAdapter
{
- public FormatAdapter(AlignViewportI viewport)
+ public FormatAdapter(AlignmentViewPanel viewpanel)
{
{
- super(viewport);
+ super(viewpanel);
init();
}
init();
}
@@
-49,6
+50,12
@@
public class FormatAdapter extends AppletFormatAdapter
init();
}
init();
}
+ public FormatAdapter(AlignmentViewPanel alignPanel,
+ AlignExportSettingI settings)
+ {
+ super(alignPanel, settings);
+ }
+
private void init()
{
if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
private void init()
{
if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
@@
-56,9
+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
{
@@
-100,12
+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)
@@
-121,9
+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],
@@
-264,14
+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)
{
@@
-304,17
+305,17
@@
public class FormatAdapter extends AppletFormatAdapter
return this.formatSequences(format, alignment, suffix);
}
return this.formatSequences(format, alignment, suffix);
}
- public Alignment readFile(String inFile, String type, String format)
+ public AlignmentI readFile(String inFile, String type, String format)
throws java.io.IOException
{
throws java.io.IOException
{
- Alignment al = super.readFile(inFile, type, format);
+ AlignmentI al = super.readFile(inFile, type, format);
return al;
}
public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
return al;
}
public AlignmentI readFromFile(FileParse source, String format)
throws java.io.IOException
{
- Alignment al = (Alignment) super.readFromFile(source, format);
+ AlignmentI al = super.readFromFile(source, format);
return al;
}
return al;
}
@@
-341,15
+342,19
@@
public class FormatAdapter extends AppletFormatAdapter
}
/**
}
/**
- * Create a flat file representation of a given view or selected region of a view
+ * Create a flat file representation of a given view or selected region of a
+ * view
+ *
* @param format
* @param format
- * @param av
+ * @param ap
+ * alignment panel originating the view
* @return String containing flat file
*/
* @return String containing flat file
*/
- public String formatSequences(String format, AlignViewportI av, boolean selectedOnly)
+ public String formatSequences(String format, AlignmentViewPanel ap,
+ boolean selectedOnly)
{
{
- return formatSequences(format, getCacheSuffixDefault(format), av, selectedOnly);
+ return formatSequences(format, getCacheSuffixDefault(format), ap,
+ selectedOnly);
}
}
-
}
}