X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=92562785557cc57492dace2cab363cadbc99913f;hb=f47ded5b8b48d6372cd1ef8f49e1a630dcadfbdb;hp=73d30dcbc46d0a5bdbe6f0f11ddc05431555caed;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java index 73d30dc..9256278 100644 --- a/src/jalview/io/HtmlFile.java +++ b/src/jalview/io/HtmlFile.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -22,8 +22,9 @@ 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 java.io.IOException; @@ -43,7 +44,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile private boolean showSeqFeatures; - private ColumnSelection columnSelection; + private HiddenColumns hiddenColumns; private SequenceI[] hiddenSequences; @@ -59,9 +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 @@ -109,7 +111,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile this.showSeqFeatures = jsonFile.isShowSeqFeatures(); this.globalColourScheme = jsonFile.getGlobalColourScheme(); this.hiddenSequences = jsonFile.getHiddenSequences(); - this.columnSelection = jsonFile.getColumnSelection(); + this.hiddenColumns = jsonFile.getHiddenColumns(); this.displayedFeatures = jsonFile.getDisplayedFeatures(); } catch (Exception e) { @@ -118,12 +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; @@ -134,6 +137,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile this.showSeqFeatures = showSeqFeatures; } + @Override public String getGlobalColourScheme() { return globalColourScheme; @@ -144,16 +148,18 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile 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; @@ -170,4 +176,19 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile return displayedFeatures; } + /** + * Returns a descriptor for suitable feature display settings with + *