X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=92562785557cc57492dace2cab363cadbc99913f;hb=7428d315297907b3bb52ddb099a348acffb87636;hp=4805b8e6434caa8efa48c5987de4d1bfdc803bb3;hpb=e58c9b0c6d453c75810eb08cb2651769fccf7f8a;p=jalview.git

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 4805b8e..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
@@ -87,21 +88,30 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
 
     try
     {
-      content = doc.getElementById("seqData");
+      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(content
-              .val()));
+      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.hiddenColumns = jsonFile.getHiddenColumns();
       this.displayedFeatures = jsonFile.getDisplayedFeatures();
     } catch (Exception e)
     {
@@ -109,14 +119,14 @@ 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;
@@ -127,26 +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;
@@ -163,4 +176,19 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     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()
+  {
+    return new PDBFeatureSettings();
+  }
+
 }