JAL-2446 merged to spike branch

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 4f83ab1..9d5fd93 100755 (executable)
--- 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;
 
@@ -205,6 +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";
 
@@ -325,9 +334,27 @@ public class FileLoader implements Runnable
 
             // 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.
+            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
+            {
+              al = fa.readFile(file, protocol, format);
+              source = fa.getAlignFile(); // keep reference for later if
+                                          // necessary.
+            }
           }
         } catch (java.io.IOException ex)
         {
@@ -372,8 +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)
@@ -556,6 +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)
    *