Merge branch 'patch/JAL-2197_jpredforjnets' into develop

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index af91399..175b171 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -49,7 +49,9 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 import jalview.io.FeaturesFile;
+import jalview.io.FileFormat;
 import jalview.io.TCoffeeScoreFile;
 import jalview.schemes.Blosum62ColourScheme;
 import jalview.schemes.BuriedColourScheme;
@@ -345,7 +347,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    *          is protocol for accessing data referred to by file
    */
 
-  public boolean parseFeaturesFile(String file, String type)
+  public boolean parseFeaturesFile(String file, DataSourceType type)
   {
     return parseFeaturesFile(file, type, true);
   }
@@ -355,14 +357,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
    * 
    * @param file
    *          file URL, content, or other resolvable path
-   * @param type
+   * @param sourceType
    *          is protocol for accessing data referred to by file
    * @param autoenabledisplay
    *          when true, display features flag will be automatically enabled if
    *          features are loaded
    * @return true if data parsed as a features file
    */
-  public boolean parseFeaturesFile(String file, String type,
+  public boolean parseFeaturesFile(String file, DataSourceType sourceType,
           boolean autoenabledisplay)
   {
     boolean featuresFile = false;
@@ -372,7 +374,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
               .getFeatureRenderer().getFeatureColours();
       boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
               "relaxedidmatch", false);
-      featuresFile = new FeaturesFile(file, type).parse(
+      featuresFile = new FeaturesFile(file, sourceType).parse(
               viewport.getAlignment(), colours, true, relaxedIdMatching);
     } catch (Exception ex)
     {
@@ -1356,13 +1358,13 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
     Frame frame = new Frame();
     frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
+    JalviewLite.addFrame(frame, MessageManager.formatMessage(
             "label.alignment_output_command",
             new Object[] { e.getActionCommand() }), 600, 500);
 
-    FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
+    FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
     cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
-            e.getActionCommand(), viewport.getAlignment(),
+            fileFormat, viewport.getAlignment(),
             viewport.getShowJVSuffix()));
   }
 
@@ -3237,11 +3239,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     inputText.addActionListener(this);
     Menu outputTextboxMenu = new Menu(
             MessageManager.getString("label.out_to_textbox"));
-    for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
+    for (String ff : FileFormat.getWritableFormats(true))
     {
-
-      MenuItem item = new MenuItem(
-              jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
+      MenuItem item = new MenuItem(ff);
 
       item.addActionListener(new java.awt.event.ActionListener()
       {
@@ -4019,7 +4019,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
       // resolve data source
       // TODO: this code should be a refactored to an io package
-      String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
+      DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
+              pdbFile, FileFormat.PDB);
       if (protocol == null)
       {
         return false;
@@ -4063,7 +4064,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   }
 
   public void newStructureView(JalviewLite applet, PDBEntry pdb,
-          SequenceI[] seqs, String[] chains, String protocol)
+          SequenceI[] seqs, String[] chains, DataSourceType protocol)
   {
     // Scrub any null sequences from the array
     Object[] sqch = cleanSeqChainArrays(seqs, chains);
@@ -4074,10 +4075,16 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       System.err
               .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
     }
-    if (protocol == null || protocol.trim().length() == 0
-            || protocol.equals("null"))
+    if (protocol == null)
     {
-      protocol = (String) pdb.getProperty("protocol");
+      String sourceType = (String) pdb.getProperty("protocol");
+      try
+      {
+        protocol = DataSourceType.valueOf(sourceType);
+      } catch (IllegalArgumentException e)
+      {
+        // ignore
+      }
       if (protocol == null)
       {
         System.err.println("Couldn't work out protocol to open structure: "
@@ -4100,12 +4107,11 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       // can only do alignments with Jmol
       // find the last jmol window assigned to this alignment
-      jalview.appletgui.AppletJmol ajm = null, tajm;
-      Vector jmols = applet
-              .getAppletWindow(jalview.appletgui.AppletJmol.class);
+      AppletJmol ajm = null, tajm;
+      Vector jmols = applet.getAppletWindow(AppletJmol.class);
       for (int i = 0, iSize = jmols.size(); i < iSize; i++)
       {
-        tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
+        tajm = (AppletJmol) jmols.elementAt(i);
         if (tajm.ap.alignFrame == this)
         {
           ajm = tajm;
@@ -4124,7 +4130,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // otherwise, create a new window
     if (applet.jmolAvailable)
     {
-      new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
+      new AppletJmol(pdb, seqs, chains, alignPanel,
               protocol);
       applet.lastFrameX += 40;
       applet.lastFrameY += 40;