JAL-629 implementation of --tempfac options

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

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 2362010..8b1525c 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,22 +20,24 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentAnnotation.TFType;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SeqDistanceContactMatrix;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
+import jalview.util.Platform;
 
 /**
  * A low level class for alignment and feature IO with alignment formatting
@@ -74,7 +76,9 @@ public class AppletFormatAdapter
    */
   protected String newline = System.getProperty("line.separator");
 
-  private AlignExportSettingI exportSettings;
+  private AlignExportSettingsI exportSettings;
+
+  private File selectedFile;
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
@@ -99,7 +103,7 @@ public class AppletFormatAdapter
   }
 
   public AppletFormatAdapter(AlignmentViewPanel alignPanel,
-          AlignExportSettingI settings)
+          AlignExportSettingsI settings)
   {
     viewpanel = alignPanel;
     exportSettings = settings;
@@ -148,6 +152,26 @@ public class AppletFormatAdapter
   public AlignmentI readFile(String file, DataSourceType sourceType,
           FileFormatI fileFormat) throws IOException
   {
+    return readFile(null, file, sourceType, fileFormat);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat)
+          throws IOException
+  {
+    return readFile(selectedFile, file, sourceType, fileFormat, null);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat,
+          AlignmentAnnotation.TFType tempfacType) throws IOException
+  {
+
+    this.selectedFile = selectedFile;
+    if (selectedFile != null)
+    {
+      this.inFile = selectedFile.getPath();
+    }
     this.inFile = file;
     try
     {
@@ -162,19 +186,27 @@ public class AppletFormatAdapter
                 localSecondaryStruct, serviceSecondaryStruct);
         if (isParseWithJMOL)
         {
-          alignFile = new JmolParser(inFile, sourceType);
+          // needs a File option
+          alignFile = new JmolParser(
+                  selectedFile == null ? inFile : selectedFile, sourceType,
+                  tempfacType);
         }
         else
         {
-          // todo is MCview parsing obsolete yet? JAL-2120
+          // todo is mc_view parsing obsolete yet? JAL-2120
           StructureImportSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
+          alignFile = new mc_view.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   sourceType);
         }
         ((StructureFile) alignFile).setDbRefType(
                 FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
       }
+      else if (selectedFile != null)
+      {
+        alignFile = fileFormat
+                .getReader(new FileParse(selectedFile, sourceType));
+      }
       else
       {
         // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
@@ -251,7 +283,7 @@ public class AppletFormatAdapter
         else
         {
           StructureImportSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
+          alignFile = new mc_view.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, source);
         }
         ((StructureFile) alignFile).setDbRefType(Type.PDB);
@@ -318,8 +350,6 @@ public class AppletFormatAdapter
 
     alignFile.addGroups(al);
 
-    al.addContactList(new SeqDistanceContactMatrix(al.getWidth()));
-
     return al;
   }
 
@@ -412,19 +442,32 @@ public class AppletFormatAdapter
   /**
    * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
    * data
+   * 
+   * BH 2018 allows File or String, and can return RELATIVE_URL
    *
-   * @param data
+   * @param dataObject
+   *          File or String
    * @return the protocol for the input data
    */
-  public static DataSourceType checkProtocol(String data)
+  public static DataSourceType checkProtocol(Object dataObject)
   {
+    if (dataObject instanceof File)
+    {
+      return DataSourceType.FILE;
+    }
+
+    String data = dataObject.toString();
     DataSourceType protocol = DataSourceType.PASTE;
-    String ft = data.toLowerCase().trim();
+    String ft = data.toLowerCase(Locale.ROOT).trim();
     if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
             || ft.indexOf("file:") == 0)
     {
       protocol = DataSourceType.URL;
     }
+    else if (Platform.isJS())
+    {
+      protocol = DataSourceType.RELATIVE_URL;
+    }
     else if (new File(data).exists())
     {
       protocol = DataSourceType.FILE;
@@ -432,6 +475,10 @@ public class AppletFormatAdapter
     return protocol;
   }
 
+  /**
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     int i = 0;