file format enum wip changes

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 133aab4..cf5766f 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -65,10 +65,14 @@ import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
+import jalview.io.JPredFile;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.JnetAnnotationMaker;
@@ -179,7 +183,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Last format used to load or save alignments in this window
    */
-  String currentFileFormat = null;
+  FileFormatI currentFileFormat = null;
 
   /**
    * Current filename for this alignment
@@ -488,7 +492,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param format
    *          format of file
    */
-  public void setFileName(String file, String format)
+  public void setFileName(String file, FileFormatI format)
   {
     fileName = file;
     setFileFormat(format);
@@ -1138,10 +1142,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       fileName = chooser.getSelectedFile().getPath();
 
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",
-              currentFileFormat);
+      Cache.setProperty("DEFAULT_FILE_FORMAT",
+              currentFileFormat.toString());
 
-      jalview.bin.Cache.setProperty("LAST_DIRECTORY", fileName);
+      Cache.setProperty("LAST_DIRECTORY", fileName);
       if (currentFileFormat.indexOf(" ") > -1)
       {
         currentFileFormat = currentFileFormat.substring(0,
@@ -1151,11 +1155,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-  public boolean saveAlignment(String file, String format)
+  public boolean saveAlignment(String file, FileFormatI format)
   {
     boolean success = true;
 
-    if (format.equalsIgnoreCase("Jalview"))
+    if (format == FileFormat.Jalview)
     {
       String shortName = title;
 
@@ -1273,8 +1277,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     cap.setForInput(null);
     try
     {
+      FileFormatI format = FileFormat.valueOf(e.getActionCommand());
       cap.setText(new FormatAdapter(alignPanel, exportData.getSettings())
-              .formatSequences(e.getActionCommand(),
+              .formatSequences(format,
                       exportData.getAlignment(),
                       exportData.getOmitHidden(),
                       exportData.getStartEndPostions(),
@@ -1291,7 +1296,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   public static AlignmentExportData getAlignmentForExport(
-          String exportFormat, AlignViewportI viewport,
+          FileFormatI format, AlignViewportI viewport,
           AlignExportSettingI exportSettings)
   {
     AlignmentI alignmentToExport = null;
@@ -1307,7 +1312,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     if (settings == null)
     {
       settings = new AlignExportSettings(hasHiddenSeqs,
-              viewport.hasHiddenColumns(), exportFormat);
+              viewport.hasHiddenColumns(), format);
     }
     // settings.isExportAnnotations();
 
@@ -4320,7 +4325,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       jalview.io.NewickFile fin = null;
       try
       {
-        fin = new jalview.io.NewickFile(choice, "File");
+        fin = new NewickFile(choice, DataSourceType.FILE);
         viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());
       } catch (Exception ex)
       {
@@ -4979,11 +4984,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   /**
    * Set the file format
    * 
-   * @param fileFormat
+   * @param format
    */
-  public void setFileFormat(String fileFormat)
+  public void setFileFormat(FileFormatI format)
   {
-    this.currentFileFormat = fileFormat;
+    this.currentFileFormat = format;
   }
 
   /**
@@ -4991,14 +4996,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * 
    * @param file
    *          contents or path to retrieve file
-   * @param type
+   * @param sourceType
    *          access mode of file (see jalview.io.AlignFile)
    * @return true if features file was parsed correctly.
    */
-  public boolean parseFeaturesFile(String file, String type)
+  public boolean parseFeaturesFile(String file, DataSourceType sourceType)
   {
-    return avc.parseFeaturesFile(file, type,
-            jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+    return avc.parseFeaturesFile(file, sourceType,
+            Cache.getDefault("RELAXEDSEQIDMATCHING", false));
 
   }
 
@@ -5040,7 +5045,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void drop(DropTargetDropEvent evt)
   {
     Transferable t = evt.getTransferable();
-    java.util.List<String> files = new ArrayList<String>(), protocols = new ArrayList<String>();
+    List<String> files = new ArrayList<String>();
+    List<DataSourceType> protocols = new ArrayList<DataSourceType>();
 
     try
     {
@@ -5066,13 +5072,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           String file = files.get(i).toString();
           String pdbfn = "";
-          String protocol = FormatAdapter.checkProtocol(file);
-          if (protocol == jalview.io.FormatAdapter.FILE)
+          DataSourceType protocol = FormatAdapter.checkProtocol(file);
+          if (protocol == DataSourceType.FILE)
           {
             File fl = new File(file);
             pdbfn = fl.getName();
           }
-          else if (protocol == jalview.io.FormatAdapter.URL)
+          else if (protocol == DataSourceType.URL)
           {
             URL url = new URL(file);
             pdbfn = url.getFile();
@@ -5205,21 +5211,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * @param file
    *          either a filename or a URL string.
    */
-  public void loadJalviewDataFile(String file, String protocol,
-          String format, SequenceI assocSeq)
+  public void loadJalviewDataFile(String file, DataSourceType sourceType,
+          FileFormatI format, SequenceI assocSeq)
   {
     try
     {
-      if (protocol == null)
+      if (sourceType == null)
       {
-        protocol = FormatAdapter.checkProtocol(file);
+        sourceType = FormatAdapter.checkProtocol(file);
       }
       // if the file isn't identified, or not positively identified as some
       // other filetype (PFAM is default unidentified alignment file type) then
       // try to parse as annotation.
-      boolean isAnnotation = (format == null || format
-              .equalsIgnoreCase("PFAM")) ? new AnnotationFile()
-              .annotateAlignmentView(viewport, file, protocol) : false;
+      boolean isAnnotation = (format == null || format == FileFormat.Pfam) ? new AnnotationFile()
+              .annotateAlignmentView(viewport, file, sourceType) : false;
 
       if (!isAnnotation)
       {
@@ -5227,7 +5232,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         TCoffeeScoreFile tcf = null;
         try
         {
-          tcf = new TCoffeeScoreFile(file, protocol);
+          tcf = new TCoffeeScoreFile(file, sourceType);
           if (tcf.isValid())
           {
             if (tcf.annotateAlignment(viewport.getAlignment(), true))
@@ -5273,12 +5278,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           // try to parse it as a features file
           if (format == null)
           {
-            format = new IdentifyFile().identify(file, protocol);
+            format = new IdentifyFile().identify(file, sourceType);
           }
-          if (format.equalsIgnoreCase("JnetFile"))
+          if (format == FileFormat.Jnet)
           {
-            jalview.io.JPredFile predictions = new jalview.io.JPredFile(
-                    file, protocol);
+            JPredFile predictions = new JPredFile(
+                    file, sourceType);
             new JnetAnnotationMaker();
             JnetAnnotationMaker.add_annotation(predictions,
                     viewport.getAlignment(), 0, false);
@@ -5291,14 +5296,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           }
           else if (IdentifyFile.FeaturesFile.equals(format))
           {
-            if (parseFeaturesFile(file, protocol))
+            if (parseFeaturesFile(file, sourceType))
             {
               alignPanel.paintAlignment(true);
             }
           }
           else
           {
-            new FileLoader().LoadFile(viewport, file, protocol, format);
+            new FileLoader().LoadFile(viewport, file, sourceType, format);
           }
         }
       }
@@ -5323,8 +5328,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       new OOMWarning(
               "loading data "
-                      + (protocol != null ? (protocol.equals(FormatAdapter.PASTE) ? "from clipboard."
-                              : "using " + protocol + " from " + file)
+                      + (sourceType != null ? (sourceType == DataSourceType.PASTE ? "from clipboard."
+                              : "using " + sourceType + " from " + file)
                               : ".")
                       + (format != null ? "(parsing as '" + format
                               + "' file)" : ""), oom, Desktop.desktop);