X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FHtmlFile.java;h=92562785557cc57492dace2cab363cadbc99913f;hb=8f992e8f0ecac1cfb85903ee8dce8f3dbf73d323;hp=d19a2030a2982ba1674898d1a740d6dbb06101a3;hpb=a8362b85de4f21440433bc9385bd9b3a24354532;p=jalview.git

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index d19a203..9256278 100644
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -24,16 +24,11 @@ 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.BufferedReader;
-import java.io.File;
 import java.io.IOException;
-import java.io.InputStreamReader;
 import java.io.StringReader;
-import java.net.URL;
-import java.util.Objects;
 
 import org.jsoup.Jsoup;
 import org.jsoup.nodes.Document;
@@ -49,7 +44,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
 
   private boolean showSeqFeatures;
 
-  private ColumnSelection columnSelection;
+  private HiddenColumns hiddenColumns;
 
   private SequenceI[] hiddenSequences;
 
@@ -65,9 +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
@@ -115,7 +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)
     {
@@ -124,7 +120,7 @@ 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!");
@@ -153,14 +149,14 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
   }
 
   @Override
-  public ColumnSelection getColumnSelection()
+  public HiddenColumns getHiddenColumns()
   {
-    return columnSelection;
+    return hiddenColumns;
   }
 
-  public void setColumnSelection(ColumnSelection columnSelection)
+  public void setHiddenColumns(HiddenColumns hidden)
   {
-    this.columnSelection = columnSelection;
+    this.hiddenColumns = hidden;
   }
 
   @Override
@@ -195,52 +191,4 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     return new PDBFeatureSettings();
   }
 
-  /**
-   * Read a template file content as string
-   * 
-   * @param file
-   *          - the file to be read
-   * @return File content as String
-   * @throws IOException
-   */
-  public static String readFileAsString(File file) throws IOException
-  {
-    InputStreamReader isReader = null;
-    BufferedReader buffReader = null;
-    StringBuilder sb = new StringBuilder();
-    Objects.requireNonNull(file, "File must not be null!");
-    @SuppressWarnings("deprecation")
-    URL url = file.toURL();
-    if (url != null)
-    {
-      try
-      {
-        isReader = new InputStreamReader(url.openStream());
-        buffReader = new BufferedReader(isReader);
-        String line;
-        String lineSeparator = System.getProperty("line.separator");
-        while ((line = buffReader.readLine()) != null)
-        {
-          sb.append(line).append(lineSeparator);
-        }
-  
-      } catch (Exception ex)
-      {
-        ex.printStackTrace();
-      } finally
-      {
-        if (isReader != null)
-        {
-          isReader.close();
-        }
-  
-        if (buffReader != null)
-        {
-          buffReader.close();
-        }
-      }
-    }
-    return sb.toString();
-  }
-
 }