git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-1641 round trip test/refactoring
[jalview.git]
/
src
/
jalview
/
io
/
HtmlFile.java
diff --git
a/src/jalview/io/HtmlFile.java
b/src/jalview/io/HtmlFile.java
index
a4e9bf4
..
0f5cd55
100644
(file)
--- a/
src/jalview/io/HtmlFile.java
+++ b/
src/jalview/io/HtmlFile.java
@@
-21,6
+21,12
@@
package jalview.io;
package jalview.io;
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeI;
+
import java.io.IOException;
import java.io.StringReader;
import java.io.IOException;
import java.io.StringReader;
@@
-28,11
+34,6
@@
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;
-import jalview.api.ComplexAlignFile;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
-
public class HtmlFile extends AlignFile implements ComplexAlignFile
{
public static final String FILE_EXT = "html";
public class HtmlFile extends AlignFile implements ComplexAlignFile
{
public static final String FILE_EXT = "html";
@@
-47,6
+48,8
@@
public class HtmlFile extends AlignFile implements ComplexAlignFile
private SequenceI[] hiddenSequences;
private SequenceI[] hiddenSequences;
+ private FeaturesDisplayedI displayedFeatures;
+
public HtmlFile()
{
super();
public HtmlFile()
{
super();
@@
-92,6
+95,7
@@
public class HtmlFile extends AlignFile implements ComplexAlignFile
this.colourScheme = jsonFile.getColourScheme();
this.hiddenSequences = jsonFile.getHiddenSequences();
this.columnSelection = jsonFile.getColumnSelection();
this.colourScheme = jsonFile.getColourScheme();
this.hiddenSequences = jsonFile.getHiddenSequences();
this.columnSelection = jsonFile.getColumnSelection();
+ this.displayedFeatures = jsonFile.getDisplayedFeatures();
} catch (Exception e)
{
errormessage = "Failed to extract data from HTML document.";
} catch (Exception e)
{
errormessage = "Failed to extract data from HTML document.";
@@
-147,4
+151,10
@@
public class HtmlFile extends AlignFile implements ComplexAlignFile
this.hiddenSequences = hiddenSequences;
}
this.hiddenSequences = hiddenSequences;
}
+ @Override
+ public FeaturesDisplayedI getDisplayedFeatures()
+ {
+ return displayedFeatures;
+ }
+
}
}