JAL-3048 DialogRunnerI reduced to minimal implementation

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 14b7af0..62a3698 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -22,7 +22,6 @@ package jalview.gui;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
@@ -36,7 +35,6 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
@@ -58,10 +56,9 @@ import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.Rectangle;
-import java.util.ArrayList;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
-import java.util.Vector;
 
 import javax.swing.JInternalFrame;
 
@@ -76,15 +73,13 @@ public class AlignViewport extends AlignmentViewport
 {
   Font font;
 
-  TreeModel currentTree = null;
-
   boolean cursorMode = false;
 
   boolean antiAlias = false;
 
   private Rectangle explodedGeometry;
 
-  String viewName;
+  private String viewName;
 
   /*
    * Flag set true on the view that should 'gather' multiple views of the same
@@ -448,27 +443,6 @@ public class AlignViewport extends AlignmentViewport
   }
 
   /**
-   * DOCUMENT ME!
-   * 
-   * @param tree
-   *          DOCUMENT ME!
-   */
-  public void setCurrentTree(TreeModel tree)
-  {
-    currentTree = tree;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public TreeModel getCurrentTree()
-  {
-    return currentTree;
-  }
-
-  /**
    * returns the visible column regions of the alignment
    * 
    * @param selectedRegionOnly
@@ -476,10 +450,10 @@ public class AlignViewport extends AlignmentViewport
    *          area
    * @return
    */
-  public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
+  public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
   {
-    int[] viscontigs = null;
-    int start = 0, end = 0;
+    int start = 0;
+    int end = 0;
     if (selectedRegionOnly && selectionGroup != null)
     {
       start = selectionGroup.getStartRes();
@@ -489,8 +463,8 @@ public class AlignViewport extends AlignmentViewport
     {
       end = alignment.getWidth();
     }
-    viscontigs = alignment.getHiddenColumns().getVisibleContigs(start, end);
-    return viscontigs;
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
   }
 
   /**
@@ -627,7 +601,7 @@ public class AlignViewport extends AlignmentViewport
     return validCharWidth;
   }
 
-  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<String, AutoCalcSetting>();
+  private Hashtable<String, AutoCalcSetting> calcIdParams = new Hashtable<>();
 
   public AutoCalcSetting getCalcIdSettingsFor(String calcId)
   {
@@ -733,16 +707,20 @@ public class AlignViewport extends AlignmentViewport
     {
       if (AlignmentUtils.isMappable(toAdd, getAlignment()))
       {
-        if (openLinkedAlignment(toAdd, title))
-        {
-          return;
-        }
+        openLinkedAlignment(toAdd, title);
+        return;
       }
     }
+    addDataToAlignment(toAdd);
+  }
 
-    /*
-     * No mappings, or offer declined - add sequences to this alignment
-     */
+  /**
+   * adds sequences to this alignment
+   * 
+   * @param toAdd
+   */
+  void addDataToAlignment(AlignmentI toAdd)
+  {
     // TODO: JAL-407 regardless of above - identical sequences (based on ID and
     // provenance) should share the same dataset sequence
 
@@ -777,30 +755,58 @@ public class AlignViewport extends AlignmentViewport
    * @param al
    * @param title
    */
-  protected boolean openLinkedAlignment(AlignmentI al, String title)
+  protected void openLinkedAlignment(AlignmentI al, String title)
   {
     String[] options = new String[] { MessageManager.getString("action.no"),
         MessageManager.getString("label.split_window"),
         MessageManager.getString("label.new_window"), };
     final String question = JvSwingUtils.wrapTooltip(true,
             MessageManager.getString("label.open_split_window?"));
-    int response = JvOptionPane.showOptionDialog(Desktop.desktop, question,
+    final AlignViewport us = this;
+    
+    /*
+     * options No, Split Window, New Window correspond to
+     * dialog responses 0, 1, 2 (even though JOptionPane shows them
+     * in reverse order)
+     */
+    JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
+            .setResponseHandler(0, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                  addDataToAlignment(al);
+              }
+            }).setResponseHandler(1, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                us.openLinkedAlignmentAs(al, title, true);
+              }
+            }).setResponseHandler(2, new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                us.openLinkedAlignmentAs(al, title, false);
+              }
+            });
+       dialog.showDialog(question,
             MessageManager.getString("label.open_split_window"),
             JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
             options, options[0]);
+  }
 
-    if (response != 1 && response != 2)
+  protected void openLinkedAlignmentAs(AlignmentI al, String title,
+          boolean newWindowOrSplitPane)
     {
-      return false;
-    }
-    final boolean openSplitPane = (response == 1);
-    final boolean openInNewWindow = (response == 2);
-
     /*
      * Identify protein and dna alignments. Make a copy of this one if opening
      * in a new split pane.
      */
-    AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+    AlignmentI thisAlignment = newWindowOrSplitPane
+            ? new Alignment(getAlignment())
             : getAlignment();
     AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
     final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
@@ -821,7 +827,7 @@ public class AlignViewport extends AlignmentViewport
     AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
     newAlignFrame.setTitle(title);
-    newAlignFrame.statusBar.setText(MessageManager
+    newAlignFrame.setStatus(MessageManager
             .formatMessage("label.successfully_loaded_file", new Object[]
             { title }));
 
@@ -832,7 +838,7 @@ public class AlignViewport extends AlignmentViewport
     // alignFrame.setFileName(file, format);
     // }
 
-    if (openInNewWindow)
+    if (!newWindowOrSplitPane)
     {
       Desktop.addInternalFrame(newAlignFrame, title,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -846,13 +852,11 @@ public class AlignViewport extends AlignmentViewport
     {
     }
 
-    if (openSplitPane)
+    if (newWindowOrSplitPane)
     {
       al.alignAs(thisAlignment);
       protein = openSplitFrame(newAlignFrame, thisAlignment);
     }
-
-    return true;
   }
 
   /**
@@ -1059,4 +1063,13 @@ public class AlignViewport extends AlignmentViewport
     fr.setTransparency(featureSettings.getTransparency());
   }
 
+  public String getViewName()
+  {
+    return viewName;
+  }
+
+  public void setViewName(String viewName)
+  {
+    this.viewName = viewName;
+  }
 }