JAL-3603 load annotation file from RELATIVE_URL in JS, small code tidies

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b7ba75a..7818748 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1489,10 +1489,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     final JalviewFileChooser chooser = new JalviewFileChooser(
             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
     chooser.setFileView(new JalviewFileView());
-    chooser.setDialogTitle(
-            MessageManager.getString("label.load_jalview_annotations"));
-    chooser.setToolTipText(
-            MessageManager.getString("label.load_jalview_annotations"));
+    String tooltip = MessageManager.getString("label.load_jalview_annotations");
+    chooser.setDialogTitle(tooltip);
+    chooser.setToolTipText(tooltip);
     chooser.setResponseHandler(0, new Runnable()
     {
       @Override

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index f0f1ca3..2182b24 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -20,6 +20,17 @@
  */
 package jalview.io;
 
+import java.awt.Color;
+import java.io.BufferedReader;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
 import jalview.analysis.Conservation;
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
@@ -35,51 +46,32 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.ColorUtils;
 
-import java.awt.Color;
-import java.io.BufferedReader;
-import java.io.FileReader;
-import java.io.InputStreamReader;
-import java.io.StringReader;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
 public class AnnotationFile
 {
-  public AnnotationFile()
-  {
-    init();
-  }
+  private static final String GRAPHLINE = "GRAPHLINE";
+
+  private static final String COMBINE = "COMBINE";
 
-  /**
-   * character used to write newlines
-   */
   protected String newline = System.getProperty("line.separator");
 
+  private StringBuffer text;
+
+  private SequenceI refSeq = null;
+
+  private String refSeqId = null;
+
+  private long nlinesread = 0;
+
+  private String lastread = "";
+
   /**
-   * set new line string and reset the output buffer
-   * 
-   * @param nl
+   * Constructor
    */
-  public void setNewlineString(String nl)
+  public AnnotationFile()
   {
-    newline = nl;
     init();
   }
 
-  public String getNewlineString()
-  {
-    return newline;
-  }
-
-  StringBuffer text;
-
   private void init()
   {
     text = new StringBuffer("JALVIEW_ANNOTATION" + newline + "# Created: "
@@ -642,10 +634,6 @@ public class AnnotationFile
     }
   }
 
-  SequenceI refSeq = null;
-
-  String refSeqId = null;
-
   public boolean annotateAlignmentView(AlignViewportI viewport, Object file,
           DataSourceType protocol)
   {
@@ -682,32 +670,11 @@ public class AnnotationFile
     BufferedReader in = null;
     try
     {
-      if (sourceType == DataSourceType.FILE)
-      {
-        in = FileLoader.getBufferedReader(file);
-      }
-      else if (sourceType == DataSourceType.URL)
-      {
-        URL url = new URL(file.toString());
-        in = new BufferedReader(new InputStreamReader(url.openStream()));
-      }
-      else if (sourceType == DataSourceType.PASTE)
-      {
-        in = new BufferedReader(new StringReader(file.toString()));
-      }
-      else if (sourceType == DataSourceType.CLASSLOADER)
-      {
-        java.io.InputStream is = getClass().getResourceAsStream("/" + file);
-        if (is != null)
-        {
-          in = new BufferedReader(new java.io.InputStreamReader(is));
-        }
-      }
+      in = new FileParse().getBufferedReader(file, sourceType);
       if (in != null)
       {
         return parseAnnotationFrom(al, hidden, in);
       }
-
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -722,12 +689,6 @@ public class AnnotationFile
     return false;
   }
 
-  long nlinesread = 0;
-
-  String lastread = "";
-
-  private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
-
   public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,
           BufferedReader in) throws Exception
   {

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 1d5be1b..3aa433e 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -20,6 +20,13 @@
  */
 package jalview.io;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.SwingUtilities;
+
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
@@ -39,21 +46,8 @@ import jalview.project.Jalview2XML;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
-import jalview.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
 
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.SwingUtilities;
-
 public class FileLoader implements Runnable
 {
   String file;
@@ -641,23 +635,4 @@ public class FileLoader implements Runnable
     return tempStructFile.toString();
   }
 
-  /**
-   * 
-   * @param file a File, or a String which is a name of a file
-   * @return
-   * @throws FileNotFoundException 
-   */
-  public static BufferedReader getBufferedReader(Object file) throws FileNotFoundException {
-    if (file instanceof String)
-    {
-      return new BufferedReader(new FileReader((String) file));
-    }
-    byte[] bytes = Platform.getFileBytes((File) file);
-    if (bytes != null)
-    {
-      return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
-    }
-    return  new BufferedReader(new FileReader((File) file));
-  }
-
 }

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 13c0f43..a5a4e36 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -20,13 +20,6 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingsI;
-import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureSettingsModelI;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.File;
@@ -41,6 +34,13 @@ import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.zip.GZIPInputStream;
 
+import jalview.api.AlignExportSettingsI;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 /**
  * implements a random access wrapper around a particular datasource, for
  * passing to identifyFile and AlignFile objects.
@@ -332,7 +332,7 @@ public class FileParse
   }
 
   private void parse(File file, String fileStr, DataSourceType sourceType,
-          boolean isFileObject) throws MalformedURLException, IOException
+          boolean isFileObject) throws IOException
   {
     bytes = Platform.getFileBytes(file);
     dataSourceType = sourceType;
@@ -373,7 +373,8 @@ public class FileParse
     {
       // BH 2018 hack for no support for access-origin
       bytes = Platform.getFileAsBytes(fileStr);
-      dataIn = new BufferedReader(new java.io.InputStreamReader(new ByteArrayInputStream(bytes)));      
+      dataIn = new BufferedReader(
+              new InputStreamReader(new ByteArrayInputStream(bytes)));
       dataName = fileStr;
 
     }
@@ -423,8 +424,7 @@ public class FileParse
     else if (sourceType == DataSourceType.CLASSLOADER)
     {
       errormessage = "RESOURCE CANNOT BE LOCATED";
-      java.io.InputStream is = getClass()
-              .getResourceAsStream("/" + fileStr);
+      InputStream is = getClass().getResourceAsStream("/" + fileStr);
       if (is == null)
       {
         String suffixLess = extractSuffix(fileStr);
@@ -435,7 +435,7 @@ public class FileParse
       }
       if (is != null)
       {
-        dataIn = new BufferedReader(new java.io.InputStreamReader(is));
+        dataIn = new BufferedReader(new InputStreamReader(is));
         dataName = fileStr;
       }
       else
@@ -669,4 +669,61 @@ public class FileParse
   {
     return dataSourceType;
   }
+
+  /**
+   * Returns a buffered reader for the input object. Returns null, or throws
+   * IOException, on failure.
+   * 
+   * @param file
+   *          a File, or a String which is a name of a file
+   * @param sourceType
+   * @return
+   * @throws IOException
+   */
+  public BufferedReader getBufferedReader(Object file,
+          DataSourceType sourceType) throws IOException
+  {
+    BufferedReader in = null;
+    byte[] bytes;
+
+    switch (sourceType)
+    {
+    case FILE:
+      if (file instanceof String)
+      {
+        return new BufferedReader(new FileReader((String) file));
+      }
+      bytes = Platform.getFileBytes((File) file);
+      if (bytes != null)
+      {
+        return new BufferedReader(
+                new InputStreamReader(new ByteArrayInputStream(bytes)));
+      }
+      return new BufferedReader(new FileReader((File) file));
+    case URL:
+      URL url = new URL(file.toString());
+      in = new BufferedReader(new InputStreamReader(url.openStream()));
+      break;
+    case RELATIVE_URL: // JalviewJS only
+      bytes = Platform.getFileAsBytes(file.toString());
+      if (bytes != null)
+      {
+        in = new BufferedReader(
+                new InputStreamReader(new ByteArrayInputStream(bytes)));
+      }
+      break;
+    case PASTE:
+      in = new BufferedReader(new StringReader(file.toString()));
+      break;
+    case CLASSLOADER:
+      InputStream is = getClass().getResourceAsStream("/" + file);
+      if (is != null)
+      {
+        in = new BufferedReader(new InputStreamReader(is));
+      }
+      break;
+    }
+
+    return in;
+  }
 }