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JAL-1953 fix test and expected for canonical name for PFAM!
[jalview.git]
/
src
/
jalview
/
io
/
FormatAdapter.java
diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
ce584f2
..
735619f
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-20,18
+20,21
@@
*/
package jalview.io;
*/
package jalview.io;
-import jalview.api.AlignExportSettingI;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
+import java.io.File;
import java.io.IOException;
/**
import java.io.IOException;
/**
@@
-55,21
+58,18
@@
public class FormatAdapter extends AppletFormatAdapter
}
public FormatAdapter(AlignmentViewPanel alignPanel,
}
public FormatAdapter(AlignmentViewPanel alignPanel,
- AlignExportSettingI settings)
+ AlignExportSettingsI settings)
{
super(alignPanel, settings);
}
private void init()
{
{
super(alignPanel, settings);
}
private void init()
{
- if (jalview.bin.Cache.getDefault("STRUCT_FROM_PDB", true))
+ if (Cache.getDefault("STRUCT_FROM_PDB", true))
{
{
- 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);
+ annotFromStructure = Cache.getDefault("ADD_TEMPFACT_ANN", true);
+ localSecondaryStruct = Cache.getDefault("ADD_SS_ANN", true);
+ serviceSecondaryStruct = Cache.getDefault("USE_RNAVIEW", true);
}
else
{
}
else
{
@@
-116,8
+116,8
@@
public class FormatAdapter extends AppletFormatAdapter
startIndex = startEnd[0];
endIndex = startEnd[1];
// get first non-gaped residue start position
startIndex = startEnd[0];
endIndex = startEnd[1];
// get first non-gaped residue start position
- while (Comparison.isGap(seqs[i]
- .getCharAt(startIndex)) && startIndex < endIndex)
+ while (Comparison.isGap(seqs[i].getCharAt(startIndex))
+ && startIndex < endIndex)
{
startIndex++;
}
{
startIndex++;
}
@@
-161,18
+161,19
@@
public class FormatAdapter extends AppletFormatAdapter
public boolean getCacheSuffixDefault(FileFormatI format)
{
public boolean getCacheSuffixDefault(FileFormatI format)
{
- return Cache.getDefault(format.getName() + "_JVSUFFIX", true);
+ return Cache.getDefault(
+ format.getName().toUpperCase(Locale.ROOT) + "_JVSUFFIX", true);
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
- String[] omitHidden, int[] exportRange, ColumnSelection colSel)
+ String[] omitHidden, int[] exportRange, HiddenColumns hidden)
{
return formatSequences(format, alignment, omitHidden, exportRange,
{
return formatSequences(format, alignment, omitHidden, exportRange,
- getCacheSuffixDefault(format), colSel, null);
+ getCacheSuffixDefault(format), hidden, null);
}
/**
}
/**
- * hack function to replace seuqences with visible sequence strings before
+ * hack function to replace sequences with visible sequence strings before
* generating a string of the alignment in the given format.
*
* @param format
* generating a string of the alignment in the given format.
*
* @param format
@@
-185,15
+186,15
@@
public class FormatAdapter extends AppletFormatAdapter
*/
public String formatSequences(FileFormatI format, AlignmentI alignment,
String[] omitHidden, int[] exportRange, boolean suffix,
*/
public String formatSequences(FileFormatI format, AlignmentI alignment,
String[] omitHidden, int[] exportRange, boolean suffix,
- ColumnSelection colSel)
+ HiddenColumns hidden)
{
return formatSequences(format, alignment, omitHidden, exportRange,
{
return formatSequences(format, alignment, omitHidden, exportRange,
- suffix, colSel, null);
+ suffix, hidden, null);
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
String[] omitHidden, int[] exportRange, boolean suffix,
}
public String formatSequences(FileFormatI format, AlignmentI alignment,
String[] omitHidden, int[] exportRange, boolean suffix,
- ColumnSelection colSel, SequenceGroup selgp)
+ HiddenColumns hidden, SequenceGroup selgp)
{
if (omitHidden != null)
{
{
if (omitHidden != null)
{
@@
-211,12
+212,12
@@
public class FormatAdapter extends AppletFormatAdapter
AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
if (selgp != null)
{
AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
if (selgp != null)
{
- colSel.makeVisibleAnnotation(selgp.getStartRes(),
- selgp.getEndRes(), na);
+ na.makeVisibleAnnotation(selgp.getStartRes(), selgp.getEndRes(),
+ hidden);
}
else
{
}
else
{
- colSel.makeVisibleAnnotation(na);
+ na.makeVisibleAnnotation(hidden);
}
alv.addAnnotation(na);
}
}
alv.addAnnotation(na);
}
@@
-234,6
+235,13
@@
public class FormatAdapter extends AppletFormatAdapter
return al;
}
return al;
}
+ public AlignmentI readFile(File file, DataSourceType sourceType,
+ FileFormatI fileFormat) throws IOException
+ {
+ AlignmentI al = super.readFile(file, null, sourceType, fileFormat);
+ return al;
+ }
+
@Override
public AlignmentI readFromFile(FileParse source, FileFormatI format)
throws IOException
@Override
public AlignmentI readFromFile(FileParse source, FileFormatI format)
throws IOException
@@
-258,8
+266,8
@@
public class FormatAdapter extends AppletFormatAdapter
selectedOnly);
}
selectedOnly);
}
- public AlignmentI readFromFile(AlignmentFileI source, FileFormatI format)
- throws IOException
+ public AlignmentI readFromFile(AlignmentFileReaderI source,
+ FileFormatI format) throws IOException
{
FileParse fp = new FileParse(source.getInFile(),
source.getDataSourceType());
{
FileParse fp = new FileParse(source.getInFile(),
source.getDataSourceType());