package jalview.io;
-import jalview.api.AlignViewControllerGuiI;
-import jalview.schemes.ColourSchemeI;
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceI;
import java.io.IOException;
+import java.io.StringReader;
import org.jsoup.Jsoup;
import org.jsoup.nodes.Document;
import org.jsoup.nodes.Element;
-public class HtmlFile extends AlignFile
+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 HiddenColumns hiddenColumns;
+
+ private SequenceI[] hiddenSequences;
+
+ private FeaturesDisplayedI displayedFeatures;
+
public HtmlFile()
{
super();
super(source);
}
- public HtmlFile(String inFile, String type) throws IOException
+ public HtmlFile(String inFile, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ super(inFile, sourceType);
}
@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");
- String alignmentJsonString = 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");
+ }
- JSONFile jsonFile = new JSONFile().parse(alignmentJsonString);
- seqs = jsonFile.getSeqs();
- seqGroups = jsonFile.getSeqGroups();
- annotations = jsonFile.getAnnotations();
- showSeqFeatures = jsonFile.isShowSeqFeatures();
- colourScheme = jsonFile.getColourScheme();
+ 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.globalColourScheme = jsonFile.getGlobalColourScheme();
+ this.hiddenSequences = jsonFile.getHiddenSequences();
+ this.hiddenColumns = jsonFile.getHiddenColumns();
+ this.displayedFeatures = jsonFile.getDisplayedFeatures();
} catch (Exception e)
{
- e.printStackTrace();
+ throw e;
}
}
- public void applySettingsToAlignFrame(AlignViewControllerGuiI af)
- {
- af.setShowSeqFeatures(isShowSeqFeatures());
- af.changeColour(getColourScheme());
- af.setMenusForViewport();
- }
-
-
@Override
- public String print()
+ public String print(SequenceI[] sqs, boolean jvsuffix)
{
throw new UnsupportedOperationException(
"Print method of HtmlFile is not supported!");
}
+ @Override
public boolean isShowSeqFeatures()
{
return showSeqFeatures;
this.showSeqFeatures = showSeqFeatures;
}
- public ColourSchemeI getColourScheme()
+ @Override
+ public String getGlobalColourScheme()
+ {
+ return globalColourScheme;
+ }
+
+ public void setColourScheme(String globalColourScheme)
{
- return colourScheme;
+ this.globalColourScheme = globalColourScheme;
}
- public void setColourScheme(ColourSchemeI colourScheme)
+ @Override
+ public HiddenColumns getHiddenColumns()
+ {
+ return hiddenColumns;
+ }
+
+ public void setHiddenColumns(HiddenColumns hidden)
+ {
+ this.hiddenColumns = hidden;
+ }
+
+ @Override
+ public SequenceI[] getHiddenSequences()
+ {
+ return hiddenSequences;
+ }
+
+ public void setHiddenSequences(SequenceI[] hiddenSequences)
+ {
+ this.hiddenSequences = hiddenSequences;
+ }
+
+ @Override
+ public FeaturesDisplayedI getDisplayedFeatures()
+ {
+ return displayedFeatures;
+ }
+
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ * <ul>
+ * <li>ResNums or insertions features visible</li>
+ * <li>insertions features coloured red</li>
+ * <li>ResNum features coloured by label</li>
+ * <li>Insertions displayed above (on top of) ResNums</li>
+ * </ul>
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
{
- this.colourScheme = colourScheme;
+ return new PDBFeatureSettings();
}
}