JAL-3048 openLinkedAlignment refactor to use dialogRunner plus a conditional callback...

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 86dcbca..35a0cd3 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;
@@ -50,6 +48,7 @@ import jalview.structure.SelectionSource;
 import jalview.structure.StructureSelectionManager;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
+import jalview.util.dialogrunner.RunResponse;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.params.AutoCalcSetting;
 
@@ -58,11 +57,9 @@ 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;
 
@@ -77,8 +74,6 @@ public class AlignViewport extends AlignmentViewport
 {
   Font font;
 
-  TreeModel currentTree = null;
-
   boolean cursorMode = false;
 
   boolean antiAlias = false;
@@ -449,27 +444,6 @@ 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
@@ -490,7 +464,8 @@ public class AlignViewport extends AlignmentViewport
     {
       end = alignment.getWidth();
     }
-    return (alignment.getHiddenColumns().getVisContigsIterator(start, end));
+    return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
+            false));
   }
 
   /**
@@ -606,58 +581,6 @@ public class AlignViewport extends AlignmentViewport
             .getStructureSelectionManager(Desktop.instance);
   }
 
-  /**
-   * 
-   * @param pdbEntries
-   * @return an array of SequenceI arrays, one for each PDBEntry, listing which
-   *         sequences in the alignment hold a reference to it
-   */
-  public SequenceI[][] collateForPDB(PDBEntry[] pdbEntries)
-  {
-    List<SequenceI[]> seqvectors = new ArrayList<>();
-    for (PDBEntry pdb : pdbEntries)
-    {
-      List<SequenceI> choosenSeqs = new ArrayList<>();
-      for (SequenceI sq : alignment.getSequences())
-      {
-        Vector<PDBEntry> pdbRefEntries = sq.getDatasetSequence()
-                .getAllPDBEntries();
-        if (pdbRefEntries == null)
-        {
-          continue;
-        }
-        for (PDBEntry pdbRefEntry : pdbRefEntries)
-        {
-          if (pdbRefEntry.getId().equals(pdb.getId()))
-          {
-            if (pdbRefEntry.getChainCode() != null
-                    && pdb.getChainCode() != null)
-            {
-              if (pdbRefEntry.getChainCode().equalsIgnoreCase(
-                      pdb.getChainCode()) && !choosenSeqs.contains(sq))
-              {
-                choosenSeqs.add(sq);
-                continue;
-              }
-            }
-            else
-            {
-              if (!choosenSeqs.contains(sq))
-              {
-                choosenSeqs.add(sq);
-                continue;
-              }
-            }
-
-          }
-        }
-      }
-      seqvectors
-              .add(choosenSeqs.toArray(new SequenceI[choosenSeqs.size()]));
-    }
-    return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
-  }
-
   @Override
   public boolean isNormaliseSequenceLogo()
   {
@@ -785,13 +708,15 @@ public class AlignViewport extends AlignmentViewport
     {
       if (AlignmentUtils.isMappable(toAdd, getAlignment()))
       {
-        if (openLinkedAlignment(toAdd, title))
-        {
-          return;
-        }
+        openLinkedAlignment(toAdd, title);
+        return;
       }
     }
+    alignmentDataAdded(toAdd);
+  }
 
+  private void alignmentDataAdded(AlignmentI toAdd)
+  {
     /*
      * No mappings, or offer declined - add sequences to this alignment
      */
@@ -829,30 +754,51 @@ 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;
+    JvOptionPane.newOptionDialog(Desktop.desktop)
+            .response(new RunResponse(1)
+            {
+              @Override
+              public void run()
+              {
+                us.openLinkedAlignmentAs(al, title, true);
+              }
+            }).response(new RunResponse(2)
+            {
+              @Override
+              public void run()
+              {
+                us.openLinkedAlignmentAs(al, title, false);
+              }
+            }).defaultResponse(new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                alignmentDataAdded(al);
+              }
+            }).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;
@@ -884,7 +830,7 @@ public class AlignViewport extends AlignmentViewport
     // alignFrame.setFileName(file, format);
     // }
 
-    if (openInNewWindow)
+    if (!newWindowOrSplitPane)
     {
       Desktop.addInternalFrame(newAlignFrame, title,
               AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -898,13 +844,11 @@ public class AlignViewport extends AlignmentViewport
     {
     }
 
-    if (openSplitPane)
+    if (newWindowOrSplitPane)
     {
       al.alignAs(thisAlignment);
       protein = openSplitFrame(newAlignFrame, thisAlignment);
     }
-
-    return true;
   }
 
   /**
@@ -1110,5 +1054,4 @@ public class AlignViewport extends AlignmentViewport
     }
     fr.setTransparency(featureSettings.getTransparency());
   }
-
 }