JAL-2416 order score models by order of addition rather than name

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d6dfd9d..0da8381 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -69,6 +69,7 @@ import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FileFormats;
 import jalview.io.FileLoader;
+import jalview.io.FileParse;
 import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
@@ -77,6 +78,7 @@ import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.io.JnetAnnotationMaker;
 import jalview.io.NewickFile;
+import jalview.io.ScoreMatrixFile;
 import jalview.io.TCoffeeScoreFile;
 import jalview.jbgui.GAlignFrame;
 import jalview.schemes.ColourSchemeI;
@@ -4605,10 +4607,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
-   * Attempt to load a "dropped" file or URL string: First by testing whether
-   * it's an Annotation file, then a JNet file, and finally a features file. If
-   * all are false then the user may have dropped an alignment file onto this
-   * AlignFrame.
+   * Attempt to load a "dropped" file or URL string, by testing in turn for
+   * <ul>
+   * <li>an Annotation file</li>
+   * <li>a JNet file</li>
+   * <li>a features file</li>
+   * <li>else try to interpret as an alignment file</li>
+   * </ul>
    * 
    * @param file
    *          either a filename or a URL string.
@@ -4682,7 +4687,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
           {
             format = new IdentifyFile().identify(file, sourceType);
           }
-          if (FileFormat.Jnet.equals(format))
+          if (FileFormat.ScoreMatrix == format)
+          {
+            ScoreMatrixFile sm = new ScoreMatrixFile(new FileParse(file,
+                    sourceType));
+            sm.parse();
+            // todo: i18n this message
+            statusBar
+                    .setText(MessageManager.formatMessage(
+                            "label.successfully_loaded_matrix",
+                            sm.getMatrixName()));
+          }
+          else if (FileFormat.Jnet.equals(format))
           {
             JPredFile predictions = new JPredFile(file, sourceType);
             new JnetAnnotationMaker();