X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=e31e78dcc2551fcf2c80df2059c05d0d10834b07;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=75e99a6c7a6641c78d91523e6a7a71a3cf84c224;hpb=ddeb701f639a19574ad9caf87c2db74e4c4dd786;p=jalview.git

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 75e99a6..e31e78d 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -21,25 +21,35 @@
 
 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.ColumnSelection;
+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 ColumnSelection columnSelection;
+
+  private SequenceI[] hiddenSequences;
+
+  private FeaturesDisplayedI displayedFeatures;
+
   public HtmlFile()
   {
     super();
@@ -58,6 +68,8 @@ public class HtmlFile extends AlignFile
   @Override
   public void parse() throws IOException
   {
+    Element content = null;
+    Document doc = null;
     try
     {
       StringBuilder htmlData = new StringBuilder();
@@ -66,31 +78,46 @@ public class HtmlFile extends AlignFile
       {
         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.columnSelection = jsonFile.getColumnSelection();
+      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()
   {
@@ -98,6 +125,7 @@ public class HtmlFile extends AlignFile
             "Print method of HtmlFile is not supported!");
   }
 
+  @Override
   public boolean isShowSeqFeatures()
   {
     return showSeqFeatures;
@@ -108,14 +136,58 @@ public class HtmlFile extends AlignFile
     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 ColumnSelection getColumnSelection()
+  {
+    return columnSelection;
+  }
+
+  public void setColumnSelection(ColumnSelection columnSelection)
+  {
+    this.columnSelection = columnSelection;
+  }
+
+  @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();
   }
 
 }