X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=92562785557cc57492dace2cab363cadbc99913f;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=06c271740a128fce710dd0ddb749d8291ec8d70a;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java index 06c2717..9256278 100644 --- a/src/jalview/io/HtmlFile.java +++ b/src/jalview/io/HtmlFile.java @@ -22,10 +22,10 @@ package jalview.io; import jalview.api.ComplexAlignFile; +import jalview.api.FeatureSettingsModelI; import jalview.api.FeaturesDisplayedI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; -import jalview.schemes.ColourSchemeI; import java.io.IOException; import java.io.StringReader; @@ -40,11 +40,11 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile public static final String FILE_DESC = "HTML"; - private ColourSchemeI colourScheme; + private String globalColourScheme; private boolean showSeqFeatures; - private ColumnSelection columnSelection; + private HiddenColumns hiddenColumns; private SequenceI[] hiddenSequences; @@ -60,9 +60,10 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile 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 @@ -108,9 +109,9 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile 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.hiddenColumns = jsonFile.getHiddenColumns(); this.displayedFeatures = jsonFile.getDisplayedFeatures(); } catch (Exception e) { @@ -119,12 +120,13 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile } @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; @@ -135,26 +137,29 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile this.showSeqFeatures = showSeqFeatures; } - public ColourSchemeI getColourScheme() + @Override + 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() + @Override + public HiddenColumns getHiddenColumns() { - return columnSelection; + return hiddenColumns; } - public void setColumnSelection(ColumnSelection columnSelection) + public void setHiddenColumns(HiddenColumns hidden) { - this.columnSelection = columnSelection; + this.hiddenColumns = hidden; } + @Override public SequenceI[] getHiddenSequences() { return hiddenSequences; @@ -171,4 +176,19 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile return displayedFeatures; } + /** + * Returns a descriptor for suitable feature display settings with + *