X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=92562785557cc57492dace2cab363cadbc99913f;hb=08c7bee16c16563cc7cec7ea4d336b3e0c4c937a;hp=a4e9bf4bb15b024746f52691ca8d39086f73e811;hpb=263ae64817c7604150961e1c9c76554936ab994b;p=jalview.git

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index a4e9bf4..9256278 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -21,6 +21,12 @@
 
 package jalview.io;
 
+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;
 
@@ -28,25 +34,22 @@ import org.jsoup.Jsoup;
 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 ColumnSelection columnSelection;
+  private HiddenColumns hiddenColumns;
 
   private SequenceI[] hiddenSequences;
 
+  private FeaturesDisplayedI displayedFeatures;
+
   public HtmlFile()
   {
     super();
@@ -57,56 +60,73 @@ 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
   public void parse() throws IOException
   {
+    Element content = null;
+    Document doc = null;
     try
     {
-      Element content = null;
-      Document doc = null;
-      try {
-    	  StringBuilder htmlData = new StringBuilder();
-          String currentLine;
-          while ((currentLine = nextLine()) != null)
-          {
-            htmlData.append(currentLine);
-          }
-
-          doc = Jsoup.parse(htmlData.toString());
-      } catch (OutOfMemoryError oom) {
-    	  errormessage = "Not enough memory to process HTML document";
-    	  throw new IOException(errormessage);
+      StringBuilder htmlData = new StringBuilder();
+      String currentLine;
+      while ((currentLine = nextLine()) != null)
+      {
+        htmlData.append(currentLine);
+      }
+      doc = Jsoup.parse(htmlData.toString());
+    } catch (OutOfMemoryError oom)
+    {
+      errormessage = "Not enough memory to process HTML document";
+      throw new IOException(errormessage);
+    }
+
+    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);
       }
-      content = doc.getElementById("seqData");
-      
-      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)
     {
-      errormessage = "Failed to extract data from HTML document.";
-      throw new IOException("Unexpected exception whilst extracting JSon from HTML.",e);
+      throw e;
     }
   }
 
-
   @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;
@@ -117,26 +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;
@@ -147,4 +170,25 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     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()
+  {
+    return new PDBFeatureSettings();
+  }
+
 }