package jalview.io;
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+
import java.io.IOException;
import java.io.StringReader;
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 static final String FILE_DESC = "HTML";
- private ColourSchemeI colourScheme;
+ private String globalColourScheme;
private boolean showSeqFeatures;
private SequenceI[] hiddenSequences;
+ private FeaturesDisplayedI displayedFeatures;
+
public HtmlFile()
{
super();
@Override
public void parse() throws IOException
{
+ Element content = null;
+ Document doc = null;
try
{
StringBuilder htmlData = new StringBuilder();
{
htmlData.append(currentLine);
}
+ doc = Jsoup.parse(htmlData.toString());
+ } catch (OutOfMemoryError oom)
+ {
+ errormessage = "Not enough memory to process HTML document";
+ throw new IOException(errormessage);
+ }
- Document doc = Jsoup.parse(htmlData.toString());
- Element content = doc.getElementById("seqData");
- JSONFile jsonFile = new JSONFile().parse(new StringReader(content.val()));
+ try
+ {
+ boolean contentFromDiv = true;
+ // search for BioJSON data in div element with id seqData
+ content = doc.select("div[id=seqData]").first();
+ if (content == null)
+ {
+ contentFromDiv = false;
+ // search for BioJSON data in input element with id seqData
+ content = doc.getElementById("seqData");
+ }
+
+ if (content == null)
+ {
+ errormessage = "The html document is not embedded with BioJSON data";
+ throw new IOException(errormessage);
+ }
+ JSONFile jsonFile = new JSONFile().parse(new StringReader(
+ contentFromDiv ? content.text() : content.val()));
this.seqs = jsonFile.getSeqs();
this.seqGroups = jsonFile.getSeqGroups();
this.annotations = jsonFile.getAnnotations();
this.showSeqFeatures = jsonFile.isShowSeqFeatures();
- this.colourScheme = jsonFile.getColourScheme();
+ this.globalColourScheme = jsonFile.getGlobalColourScheme();
this.hiddenSequences = jsonFile.getHiddenSequences();
this.columnSelection = jsonFile.getColumnSelection();
+ this.displayedFeatures = jsonFile.getDisplayedFeatures();
} catch (Exception e)
{
- e.printStackTrace();
+ throw e;
}
}
-
@Override
public String print()
{
this.showSeqFeatures = showSeqFeatures;
}
- public ColourSchemeI getColourScheme()
+ public String getGlobalColourScheme()
{
- return colourScheme;
+ return globalColourScheme;
}
- public void setColourScheme(ColourSchemeI colourScheme)
+ public void setColourScheme(String globalColourScheme)
{
- this.colourScheme = colourScheme;
+ this.globalColourScheme = globalColourScheme;
}
public ColumnSelection getColumnSelection()
this.hiddenSequences = hiddenSequences;
}
+ @Override
+ public FeaturesDisplayedI getDisplayedFeatures()
+ {
+ return displayedFeatures;
+ }
+
}