Merge branch 'develop' into features/JAL-653_gffalignments

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 1970388..cd9c533 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -78,6 +78,7 @@ import jalview.api.AlignViewControllerGuiI;
 import jalview.api.AlignViewControllerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsControllerI;
 import jalview.api.SplitContainerI;
 import jalview.api.ViewStyleI;
 import jalview.api.analysis.ScoreModelI;
@@ -107,7 +108,6 @@ 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;
@@ -240,6 +240,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     this(al, hiddenColumns, width, height, null);
   }
 
+
   /**
    * Create alignment frame for al with hiddenColumns, a specific width and
    * height, and specific sequenceId
@@ -289,6 +290,29 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     init();
   }
 
+  public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
+          ColumnSelection hiddenColumns, int width, int height)
+  {
+    setSize(width, height);
+
+    if (al.getDataset() == null)
+    {
+      al.setDataset(null);
+    }
+
+    viewport = new AlignViewport(al, hiddenColumns);
+
+    if (hiddenSeqs != null && hiddenSeqs.length > 0)
+    {
+      viewport.hideSequence(hiddenSeqs);
+      viewport.setHasHiddenRows(true);
+    }
+    alignPanel = new AlignmentPanel(this, viewport);
+    addAlignmentPanel(alignPanel, true);
+    init();
+  }
+
+
   /**
    * Make a new AlignFrame from existing alignmentPanels
    * 
@@ -1245,11 +1269,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         alignmentToExport = viewport.getAlignment();
         alignmentStartEnd = getStartEnd(alignmentStartEnd, viewport
                 .getColumnSelection().getHiddenColumns());
+        viewport.setIncludeHiddenRegion(false);
       }
       else
       {
         // export all region including visible
         alignmentToExport = hiddenSeqs.getFullAlignment();
+        viewport.setIncludeHiddenRegion(true);
       }
     }
 
@@ -3133,6 +3159,12 @@ 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)
@@ -4982,41 +5014,29 @@ 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)
   {
@@ -6106,29 +6126,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
   }
 
-  @Override
-  public void hideColumns(List<int[]> colsToHide)
-  {
-    for (int[] colRange : colsToHide)
-    {
-      viewport.hideColumns(colRange[0], colRange[1]);
-    }
-
-  }
-
-  @Override
-  public void syncHiddenSequences()
-  {
-    AlignmentI al = viewport.getAlignment();
-    HiddenSequences hiddenSeqs = al.getHiddenSequences();
-    for (SequenceI seq : al.getSequencesArray())
-      {
-        if (seq.isHidden())
-        {
-        hiddenSeqs.hideSequence(seq);
-        }
-      }
-  }
 }
 
 class PrintThread extends Thread