X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=9d5fd934d3ce5df299c5b75af4b8c36c9c468ceb;hb=2d3be0b3f26fa3e35480976cd5a90a5562d43dcf;hp=3ad74c71ff2bed320f08579b9f1081459f15751f;hpb=483e7163b1fb8d4bcb9393014816c944befce328;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3ad74c7..9d5fd93 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -27,7 +27,7 @@ import jalview.api.FeaturesSourceI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -39,7 +39,10 @@ import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
+import jalview.ws.utils.UrlDownloadClient;
 
+import java.io.File;
+import java.io.IOException;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
@@ -53,7 +56,8 @@ public class FileLoader implements Runnable
 
   FileFormatI format;
 
-  AlignmentFileI source = null; // alternative specification of where data comes
+  AlignmentFileReaderI source = null; // alternative specification of where data
+                                      // comes
 
   // from
 
@@ -160,7 +164,7 @@ public class FileLoader implements Runnable
    * @param format
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source,
+  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
           FileFormatI format)
   {
     this.source = source;
@@ -204,6 +208,12 @@ public class FileLoader implements Runnable
       // refer to it as.
       return;
     }
+    if (file != null
+            && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+    {
+      // ignore files loaded from the system's temporary directory
+      return;
+    }
     String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
             : "RECENT_URL";
 
@@ -237,7 +247,7 @@ public class FileLoader implements Runnable
 
     if (protocol == DataSourceType.FILE)
     {
-      Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString());
+      Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
     }
   }
 
@@ -279,7 +289,7 @@ public class FileLoader implements Runnable
                   Desktop.desktop,
                   MessageManager.getString("label.couldnt_read_data")
                           + " in " + file + "\n"
-                          + AppletFormatAdapter.SUPPORTED_FORMATS,
+                          + AppletFormatAdapter.getSupportedFormats(),
                   MessageManager.getString("label.couldnt_read_data"),
                   JvOptionPane.WARNING_MESSAGE);
         }
@@ -311,27 +321,45 @@ public class FileLoader implements Runnable
       }
       else
       {
-        String error = AppletFormatAdapter.SUPPORTED_FORMATS;
-          try
+        String error = AppletFormatAdapter.getSupportedFormats();
+        try
+        {
+          if (source != null)
           {
-            if (source != null)
-            {
-              // read from the provided source
+            // read from the provided source
             al = new FormatAdapter().readFromFile(source, format);
+          }
+          else
+          {
+
+            // open a new source and read from it
+            FormatAdapter fa = new FormatAdapter();
+            boolean downloadStructureFile = format.isStructureFile()
+                    && protocol.equals(DataSourceType.URL);
+            if (downloadStructureFile)
+            {
+              String structExt = format.getExtensions().split(",")[0];
+              String urlLeafName = file.substring(file.lastIndexOf(System
+                      .getProperty("file.separator")), file
+                      .lastIndexOf("."));
+              String tempStructureFileStr = createNamedJvTempFile(
+                      urlLeafName, structExt);
+              UrlDownloadClient.download(file, tempStructureFileStr);
+              al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+                      format);
+              source = fa.getAlignFile();
             }
             else
             {
-
-              // open a new source and read from it
-              FormatAdapter fa = new FormatAdapter();
               al = fa.readFile(file, protocol, format);
               source = fa.getAlignFile(); // keep reference for later if
                                           // necessary.
             }
-          } catch (java.io.IOException ex)
-          {
-            error = ex.getMessage();
           }
+        } catch (java.io.IOException ex)
+        {
+          error = ex.getMessage();
+        }
 
         if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
         {
@@ -371,8 +399,8 @@ public class FileLoader implements Runnable
 
             if (source instanceof ComplexAlignFile)
             {
-              ColumnSelection colSel = ((ComplexAlignFile) source)
-                      .getColumnSelection();
+              HiddenColumns colSel = ((ComplexAlignFile) source)
+                      .getHiddenColumns();
               SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
                       .getHiddenSequences();
               String colourSchemeName = ((ComplexAlignFile) source)
@@ -555,6 +583,29 @@ public class FileLoader implements Runnable
 
   }
 
+  /**
+   * This method creates the file -
+   * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied
+   * file name and extension
+   * 
+   * @param fileName
+   *          the name of the temp file to be created
+   * @param extension
+   *          the extension of the temp file to be created
+   * @return
+   */
+  private static String createNamedJvTempFile(String fileName,
+          String extension) throws IOException
+  {
+    String seprator = System.getProperty("file.separator");
+    String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview"
+            + seprator + System.currentTimeMillis();
+    File tempStructFile = new File(jvTempDir + seprator + fileName + "."
+            + extension);
+    tempStructFile.mkdirs();
+    return tempStructFile.toString();
+  }
+
   /*
    * (non-Javadoc)
    *