JAL-1863 allow RNA secondary structure rows exported by Jalview to be imported again

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 83fb7c0..f04744d 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -20,14 +20,13 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AAFrequency;
 import jalview.analysis.AlignmentSorter;
 import jalview.analysis.AlignmentUtils;
-import jalview.analysis.Conservation;
 import jalview.analysis.CrossRef;
 import jalview.analysis.Dna;
 import jalview.analysis.ParseProperties;
 import jalview.analysis.SequenceIdMatcher;
+import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
@@ -795,7 +794,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       public void internalFrameClosed(
               javax.swing.event.InternalFrameEvent evt)
       {
-        System.out.println("deregistering discoverer listener");
+        // System.out.println("deregistering discoverer listener");
         Desktop.instance.removeJalviewPropertyChangeListener("services",
                 thisListener);
         closeMenuItem_actionPerformed(true);
@@ -1030,7 +1029,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   @Override
   public void addFromText_actionPerformed(ActionEvent e)
   {
-    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport);
+    Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport
+            .getAlignPanel());
   }
 
   @Override
@@ -1146,7 +1146,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         return false;
       }
 
-      AlignmentExportData exportData = getAlignmentForExport(format, viewport);
+      AlignmentExportData exportData = getAlignmentForExport(format,
+              viewport, null);
       if (exportData.getSettings().isCancelled())
       {
         return false;
@@ -1225,7 +1226,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
 
     AlignmentExportData exportData = getAlignmentForExport(
-            e.getActionCommand(), viewport);
+            e.getActionCommand(), viewport, null);
     if (exportData.getSettings().isCancelled())
     {
       return;
@@ -1251,10 +1252,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
-  public static AlignmentExportData getAlignmentForExport(String exportFomat,
-          AlignViewportI viewport)
+  public static AlignmentExportData getAlignmentForExport(String exportFormat,
+ AlignViewportI viewport,
+          AlignExportSettingI exportSettings)
   {
     AlignmentI alignmentToExport = null;
+    AlignExportSettingI settings = exportSettings;
     String[] omitHidden = null;
     int[] alignmentStartEnd = new int[2];
 
@@ -1267,9 +1270,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     { 0, alignmentToExport.getWidth() - 1 };
 
     boolean hasHiddenSeqs = hiddenSeqs.getSize() > 0;
-    AlignExportSettings settings = new AlignExportSettings(hasHiddenSeqs,
-            viewport.hasHiddenColumns(), exportFomat);
-    settings.isExportAnnotations();
+    if (settings == null)
+    {
+      settings = new AlignExportSettings(hasHiddenSeqs,
+            viewport.hasHiddenColumns(), exportFormat);
+    }
+    // settings.isExportAnnotations();
 
     if (viewport.hasHiddenColumns() && !settings.isExportHiddenColumns())
     {
@@ -3491,115 +3497,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    */
   public void changeColour(ColourSchemeI cs)
   {
-    // TODO: compare with applet and pull up to model method
-    int threshold = 0;
+    // TODO: pull up to controller method
 
     if (cs != null)
     {
+      // Make sure viewport is up to date w.r.t. any sliders
       if (viewport.getAbovePIDThreshold())
       {
-        threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
+        int threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
                 "Background");
-        cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
-      }
-      else
-      {
-        cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
+        viewport.setThreshold(threshold);
       }
 
       if (viewport.getConservationSelected())
       {
-
-        Alignment al = (Alignment) viewport.getAlignment();
-        Conservation c = new Conservation("All",
-                ResidueProperties.propHash, 3, al.getSequences(), 0,
-                al.getWidth() - 1);
-
-        c.calculate();
-        c.verdict(false, viewport.getConsPercGaps());
-
-        cs.setConservation(c);
-
         cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
                 cs, "Background"));
       }
-      else
-      {
-        cs.setConservation(null);
-      }
-
-      cs.setConsensus(viewport.getSequenceConsensusHash());
     }
 
     viewport.setGlobalColourScheme(cs);
 
-    if (viewport.getColourAppliesToAllGroups())
-    {
-
-      for (SequenceGroup sg : viewport.getAlignment().getGroups())
-      {
-        if (cs == null)
-        {
-          sg.cs = null;
-          continue;
-        }
-
-        if (cs instanceof ClustalxColourScheme)
-        {
-          sg.cs = new ClustalxColourScheme(sg,
-                  viewport.getHiddenRepSequences());
-        }
-        else if (cs instanceof UserColourScheme)
-        {
-          sg.cs = new UserColourScheme(((UserColourScheme) cs).getColours());
-        }
-        else
-        {
-          try
-          {
-            sg.cs = cs.getClass().newInstance();
-          } catch (Exception ex)
-          {
-          }
-        }
-
-        if (viewport.getAbovePIDThreshold()
-                || cs instanceof PIDColourScheme
-                || cs instanceof Blosum62ColourScheme)
-        {
-          sg.cs.setThreshold(threshold, viewport.isIgnoreGapsConsensus());
-
-          sg.cs.setConsensus(AAFrequency.calculate(
-                  sg.getSequences(viewport.getHiddenRepSequences()),
-                  sg.getStartRes(), sg.getEndRes() + 1));
-        }
-        else
-        {
-          sg.cs.setThreshold(0, viewport.isIgnoreGapsConsensus());
-        }
-
-        if (viewport.getConservationSelected())
-        {
-          Conservation c = new Conservation("Group",
-                  ResidueProperties.propHash, 3, sg.getSequences(viewport
-                          .getHiddenRepSequences()), sg.getStartRes(),
-                  sg.getEndRes() + 1);
-          c.calculate();
-          c.verdict(false, viewport.getConsPercGaps());
-          sg.cs.setConservation(c);
-        }
-        else
-        {
-          sg.cs.setConservation(null);
-        }
-      }
-    }
-
-    if (alignPanel.getOverviewPanel() != null)
-    {
-      alignPanel.getOverviewPanel().updateOverviewImage();
-    }
-
     alignPanel.paintAlignment(true);
   }
 
@@ -4534,8 +4452,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         final List<JMenuItem> legacyItems = new ArrayList<JMenuItem>();
         try
         {
-          System.err.println("Building ws menu again "
-                  + Thread.currentThread());
+          // System.err.println("Building ws menu again "
+          // + Thread.currentThread());
           // TODO: add support for context dependent disabling of services based
           // on
           // alignment and current selection
@@ -4887,7 +4805,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                 al.getCodonFrames().addAll(cf);
                 final StructureSelectionManager ssm = StructureSelectionManager
                         .getStructureSelectionManager(Desktop.instance);
-                ssm.addMappings(cf);
+                ssm.registerMappings(cf);
               }
               else
               {