fix for JAL-2072

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index c12cb54..28ff0a1 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -96,6 +96,8 @@ import jalview.schemes.ZappoColourScheme;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
 import jalview.ws.SequenceFetcher;
 import jalview.ws.jws1.Discoverer;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -1274,13 +1276,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     AlignmentI alignmentToExport = null;
     AlignExportSettingI settings = exportSettings;
     String[] omitHidden = null;
-    int[] alignmentStartEnd = new int[2];
 
     HiddenSequences hiddenSeqs = viewport.getAlignment()
             .getHiddenSequences();
 
     alignmentToExport = viewport.getAlignment();
-    alignmentStartEnd = new int[] { 0, alignmentToExport.getWidth() - 1 };
 
     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
     if (settings == null)
@@ -1295,6 +1295,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       omitHidden = viewport.getViewAsString(false);
     }
 
+    int[] alignmentStartEnd = new int[2];
     if (hasHiddenSeqs && settings.isExportHiddenSequences())
     {
       alignmentToExport = hiddenSeqs.getFullAlignment();
@@ -1302,7 +1303,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     else
     {
       alignmentToExport = viewport.getAlignment();
-      alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
+      alignmentStartEnd = viewport.getAlignment()
+              .getVisibleStartAndEndIndex(
+                      viewport
               .getColumnSelection().getHiddenColumns());
     }
     AlignmentExportData ed = new AlignmentExportData(alignmentToExport,
@@ -1310,55 +1313,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return ed;
   }
 
-  public static int[] getStartEnd(int[] aligmentStartEnd,
-          List<int[]> hiddenCols)
-  {
-    int startPos = aligmentStartEnd[0];
-    int endPos = aligmentStartEnd[1];
-
-    int[] lowestRange = new int[] { -1, -1 };
-    int[] higestRange = new int[] { -1, -1 };
-
-    for (int[] hiddenCol : hiddenCols)
-    {
-      lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange;
-      higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange;
-    }
-
-    if (lowestRange[0] == -1 && lowestRange[1] == -1)
-    {
-      startPos = aligmentStartEnd[0];
-    }
-    else
-    {
-      startPos = lowestRange[1] + 1;
-    }
-
-    if (higestRange[0] == -1 && higestRange[1] == -1)
-    {
-      endPos = aligmentStartEnd[1];
-    }
-    else
-    {
-      endPos = higestRange[0] - 1;
-    }
-
-    // System.out.println("Export range : " + startPos + " - " + endPos);
-    return new int[] { startPos, endPos };
-  }
-
-  public static void main(String[] args)
-  {
-    ArrayList<int[]> hiddenCols = new ArrayList<int[]>();
-    hiddenCols.add(new int[] { 0, 0 });
-    hiddenCols.add(new int[] { 6, 9 });
-    hiddenCols.add(new int[] { 11, 12 });
-    hiddenCols.add(new int[] { 33, 33 });
-    hiddenCols.add(new int[] { 50, 50 });
-
-    int[] x = getStartEnd(new int[] { 0, 50 }, hiddenCols);
-    // System.out.println("Export range : " + x[0] + " - " + x[1]);
-  }
 
   /**
    * DOCUMENT ME!
@@ -4170,7 +4124,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         JMenuItem tm = new JMenuItem();
         ScoreModelI sm = ResidueProperties.scoreMatrices.get(pwtype);
-        if (sm.isProtein() == !viewport.getAlignment().isNucleotide())
+        if (sm.isDNA() == viewport.getAlignment().isNucleotide()
+                || sm.isProtein() == !viewport.getAlignment()
+                        .isNucleotide())
         {
           String smn = MessageManager.getStringOrReturn(
                   "label.score_model_", sm.getName());
@@ -4777,8 +4733,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                * pending getting Embl transcripts to 'align', 
                * we are only doing this for Ensembl
                */
-              // TODO want to do this also when fetching UNIPROT for Ensembl
-              if (DBRefSource.ENSEMBL.equalsIgnoreCase(source))
+              // TODO proper criteria for 'can align as cdna'
+              if (DBRefSource.ENSEMBL.equalsIgnoreCase(source)
+                      || AlignmentUtils.looksLikeEnsembl(alignment))
               {
                 copyAlignment.alignAs(alignment);
                 copyAlignmentIsAligned = true;
@@ -5549,15 +5506,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         new Thread(new Runnable()
         {
-
           @Override
           public void run()
           {
-            boolean isNuclueotide = alignPanel.alignFrame.getViewport()
+            boolean isNucleotide = alignPanel.alignFrame.getViewport()
                     .getAlignment().isNucleotide();
-            new jalview.ws.DBRefFetcher(alignPanel.av
+            DBRefFetcher dbRefFetcher = new DBRefFetcher(alignPanel.av
                     .getSequenceSelection(), alignPanel.alignFrame, null,
-                    alignPanel.alignFrame.featureSettings, isNuclueotide)
+                    alignPanel.alignFrame.featureSettings, isNucleotide);
+            dbRefFetcher.addListener(new FetchFinishedListenerI()
+            {
+              @Override
+              public void finished()
+              {
+                AlignFrame.this.setMenusForViewport();
+              }
+            });
+            dbRefFetcher
                     .fetchDBRefs(false);
           }
         }).start();
@@ -5626,14 +5591,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       @Override
                       public void run()
                       {
-                        boolean isNuclueotide = alignPanel.alignFrame
+                        boolean isNucleotide = alignPanel.alignFrame
                                 .getViewport().getAlignment()
                                 .isNucleotide();
-                        new jalview.ws.DBRefFetcher(alignPanel.av
-                                .getSequenceSelection(),
+                        DBRefFetcher dbRefFetcher = new DBRefFetcher(
+                                alignPanel.av.getSequenceSelection(),
                                 alignPanel.alignFrame, dassource,
                                 alignPanel.alignFrame.featureSettings,
-                                isNuclueotide).fetchDBRefs(false);
+                                isNucleotide);
+                        dbRefFetcher
+                                .addListener(new FetchFinishedListenerI()
+                                {
+                                  @Override
+                                  public void finished()
+                                  {
+                                    AlignFrame.this.setMenusForViewport();
+                                  }
+                                });
+                        dbRefFetcher.fetchDBRefs(false);
                       }
                     }).start();
                   }
@@ -5666,14 +5641,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                       @Override
                       public void run()
                       {
-                        boolean isNuclueotide = alignPanel.alignFrame
+                        boolean isNucleotide = alignPanel.alignFrame
                                 .getViewport().getAlignment()
                                 .isNucleotide();
-                        new jalview.ws.DBRefFetcher(alignPanel.av
-                                .getSequenceSelection(),
+                        DBRefFetcher dbRefFetcher = new DBRefFetcher(
+                                alignPanel.av.getSequenceSelection(),
                                 alignPanel.alignFrame, dassource,
                                 alignPanel.alignFrame.featureSettings,
-                                isNuclueotide).fetchDBRefs(false);
+                                isNucleotide);
+                        dbRefFetcher
+                                .addListener(new FetchFinishedListenerI()
+                                {
+                                  @Override
+                                  public void finished()
+                                  {
+                                    AlignFrame.this.setMenusForViewport();
+                                  }
+                                });
+                        dbRefFetcher.fetchDBRefs(false);
                       }
                     }).start();
                   }
@@ -5721,14 +5706,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                         @Override
                         public void run()
                         {
-                          boolean isNuclueotide = alignPanel.alignFrame
+                          boolean isNucleotide = alignPanel.alignFrame
                                   .getViewport().getAlignment()
                                   .isNucleotide();
-                          new jalview.ws.DBRefFetcher(alignPanel.av
-                                  .getSequenceSelection(),
+                          DBRefFetcher dbRefFetcher = new DBRefFetcher(
+                                  alignPanel.av.getSequenceSelection(),
                                   alignPanel.alignFrame, dassrc,
                                   alignPanel.alignFrame.featureSettings,
-                                  isNuclueotide).fetchDBRefs(false);
+                                  isNucleotide);
+                          dbRefFetcher
+                                  .addListener(new FetchFinishedListenerI()
+                                  {
+                                    @Override
+                                    public void finished()
+                                    {
+                                      AlignFrame.this.setMenusForViewport();
+                                    }
+                                  });
+                          dbRefFetcher.fetchDBRefs(false);
                         }
                       }).start();
                     }