JAL-1482 JAL-653 refactor feature file import code to alignview controller

diff --git a/src/jalview/api/AlignViewControllerGuiI.java b/src/jalview/api/AlignViewControllerGuiI.java
index f768451..4896b35 100644 (file)
--- a/src/jalview/api/AlignViewControllerGuiI.java
+++ b/src/jalview/api/AlignViewControllerGuiI.java
@@ -47,4 +47,19 @@ public interface AlignViewControllerGuiI
   void setMenusForViewport();
   
   void changeColour(ColourSchemeI cs);
+
+  /**
+   * trigger an update of the UI in response to a model data change, and if
+   * necessary enable the display of sequence feature annotation on the view.
+   * 
+   * @param enableIfNecessary
+   */
+  void refreshFeatureUI(boolean enableIfNecessary);
+
+  /**
+   * get the Feature Settings control panel for the alignment view if one exists
+   * 
+   * @return
+   */
+  FeatureSettingsControllerI getFeatureSettingsUI();
 }

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 235a656..fef9f14 100644 (file)
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -76,4 +76,17 @@ public interface AlignViewControllerI
    */
   void sortAlignmentByFeatureDensity(String[] typ);
 
+  /**
+   * add a features file of some kind to the current view
+   * 
+   * @param file
+   * @param protocol
+   * @param relaxedIdMatching
+   *          if true, try harder to match up IDs with local sequence data
+   * @return true if parsing resulted in something being imported to the view or
+   *         dataset
+   */
+  public boolean parseFeaturesFile(String file, String protocol,
+          boolean relaxedIdMatching);
+
 }

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 478aa09..77747d1 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -26,6 +26,7 @@ import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SequenceStructureBinding;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
@@ -4178,7 +4179,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   {
     this.splitFrame = sf;
   }
-
+    // may not need this
   @Override
   public void setShowSeqFeatures(boolean b)
   {
@@ -4193,4 +4194,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     // setMenusFromViewport(viewport);
 
   }
+  @Override
+  public void refreshFeatureUI(boolean enableIfNecessary)
+  {
+    if (enableIfNecessary)
+    {
+      sequenceFeatures.setState(true);
+      alignPanel.av.setShowSequenceFeatures(true);
+    }
+  }
+
+  @Override
+  public FeatureSettingsControllerI getFeatureSettingsUI()
+  {
+    return alignPanel.av.featureSettings;
+  }
+
 }

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 972b6ab..3be32bb 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.FeaturesFile;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -379,4 +380,38 @@ public class AlignViewController implements AlignViewControllerI
   {
     sortBy(typ, "Sort by Feature Score", AlignmentSorter.FEATURE_SCORE);
   }
+
+  @Override
+  public boolean parseFeaturesFile(String file, String protocol,
+          boolean relaxedIdMatching)
+  {
+    boolean featuresFile = false;
+    try
+    {
+      featuresFile = new FeaturesFile(file, protocol).parse(viewport
+              .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
+              .getFeatureColours(), false, relaxedIdMatching);
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+    if (featuresFile)
+    {
+      avcg.refreshFeatureUI(true);
+      if (alignPanel.getFeatureRenderer() != null)
+      {
+        // update the min/max ranges where necessary
+        alignPanel.getFeatureRenderer().findAllFeatures(true);
+      }
+      if (avcg.getFeatureSettingsUI() != null)
+      {
+        avcg.getFeatureSettingsUI().discoverAllFeatureData();
+      }
+      alignPanel.paintAlignment(true);
+    }
+
+    return featuresFile;
+
+  }
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 553ddd2..90b9f6a 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -32,7 +32,6 @@ import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
-import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.ScoreModelI;
 import jalview.bin.Cache;
@@ -60,7 +59,6 @@ import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.AlignmentProperties;
 import jalview.io.AnnotationFile;
 import jalview.io.BioJsHTMLOutput;
-import jalview.io.FeaturesFile;
 import jalview.io.FileLoader;
 import jalview.io.FormatAdapter;
 import jalview.io.HtmlSvgOutput;
@@ -3067,6 +3065,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public FeatureSettings featureSettings;
 
   @Override
+  public FeatureSettingsControllerI getFeatureSettingsUI()
+  {
+    return featureSettings;
+  }
+
+  @Override
   public void featureSettings_actionPerformed(ActionEvent e)
   {
     if (featureSettings != null)
@@ -4916,41 +4920,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    *          contents or path to retrieve file
    * @param type
    *          access mode of file (see jalview.io.AlignFile)
-   * @return true if features file was parsed corectly.
+   * @return true if features file was parsed correctly.
    */
   public boolean parseFeaturesFile(String file, String type)
   {
-    boolean featuresFile = false;
-    try
-    {
-      featuresFile = new FeaturesFile(file, type).parse(viewport
-              .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
-              .getFeatureRenderer().getFeatureColours(), false,
-              jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
+    return avc.parseFeaturesFile(file, type,
+            jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
+    
+  }
 
-    if (featuresFile)
+  @Override
+  public void refreshFeatureUI(boolean enableIfNecessary)
+  {
+    // note - currently this is only still here rather than in the controller
+    // because of the featureSettings hard reference that is yet to be
+    // abstracted
+    if (enableIfNecessary)
     {
       viewport.setShowSequenceFeatures(true);
       showSeqFeatures.setSelected(true);
-      if (alignPanel.getSeqPanel().seqCanvas.fr != null)
-      {
-        // update the min/max ranges where necessary
-        alignPanel.getSeqPanel().seqCanvas.fr.findAllFeatures(true);
-      }
-      if (featureSettings != null)
-      {
-        featureSettings.setTableData();
-      }
-      alignPanel.paintAlignment(true);
     }
 
-    return featuresFile;
-  }
 
+  }
   @Override
   public void dragEnter(DropTargetDragEvent evt)
   {

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureSettingsModel.java b/src/jalview/viewmodel/seqfeatures/FeatureSettingsModel.java
index 57d57da..15d1da7 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureSettingsModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureSettingsModel.java
@@ -2,7 +2,7 @@ package jalview.viewmodel.seqfeatures;
 
 import jalview.api.FeatureSettingsModelI;
 
-public class FeatureSettingsModel implements FeatureSettingsModelI
+public abstract class FeatureSettingsModel implements FeatureSettingsModelI
 {
 
 }