Merge branch 'develop' into feature/JAL-2422ChimeraX
[jalview.git] / src / jalview / gui / StructureViewerBase.java
index e9c1051..6dd7d50 100644 (file)
@@ -22,9 +22,7 @@ package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
-import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.StructureViewer.ViewerType;
@@ -53,6 +51,7 @@ import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Random;
 import java.util.Vector;
 
 import javax.swing.ButtonGroup;
@@ -90,13 +89,13 @@ public abstract class StructureViewerBase extends GStructureViewer
   /**
    * list of alignment panels to use for superposition
    */
-  protected Vector<AlignmentPanel> _alignwith = new Vector<>();
+  protected Vector<AlignmentViewPanel> _alignwith = new Vector<>();
 
   /**
    * list of alignment panels that are used for colouring structures by aligned
    * sequences
    */
-  protected Vector<AlignmentPanel> _colourwith = new Vector<>();
+  protected Vector<AlignmentViewPanel> _colourwith = new Vector<>();
 
   private String viewId = null;
 
@@ -121,6 +120,10 @@ public abstract class StructureViewerBase extends GStructureViewer
    */
   protected volatile boolean seqColoursApplied = false;
 
+  private IProgressIndicator progressBar = null;
+
+  private Random random = new Random();
+
   /**
    * Default constructor
    */
@@ -159,13 +162,14 @@ public abstract class StructureViewerBase extends GStructureViewer
     return _aps.contains(ap2.av.getSequenceSetId());
   }
 
-  public boolean isUsedforaligment(AlignmentPanel ap2)
+  public boolean isUsedforaligment(AlignmentViewPanel ap2)
   {
 
     return (_alignwith != null) && _alignwith.contains(ap2);
   }
 
-  public boolean isUsedforcolourby(AlignmentPanel ap2)
+  @Override
+  public boolean isUsedForColourBy(AlignmentViewPanel ap2)
   {
     return (_colourwith != null) && _colourwith.contains(ap2);
   }
@@ -215,6 +219,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
+  @Override
   public AlignmentPanel getAlignmentPanel()
   {
     return ap;
@@ -267,7 +272,8 @@ public abstract class StructureViewerBase extends GStructureViewer
    * 
    * @param nap
    */
-  public void removeAlignmentPanel(AlignmentPanel nap)
+  @Override
+  public void removeAlignmentPanel(AlignmentViewPanel nap)
   {
     try
     {
@@ -339,8 +345,6 @@ public abstract class StructureViewerBase extends GStructureViewer
 
   public abstract ViewerType getViewerType();
 
-  protected abstract IProgressIndicator getIProgressIndicator();
-
   /**
    * add a new structure (with associated sequences and chains) to this viewer,
    * retrieving it if necessary first.
@@ -449,7 +453,7 @@ public abstract class StructureViewerBase extends GStructureViewer
      * create the mappings
      */
     apanel.getStructureSelectionManager().setMapping(seq, chains,
-            pdbFilename, DataSourceType.FILE, getIProgressIndicator());
+            pdbFilename, DataSourceType.FILE, getProgressIndicator());
 
     /*
      * alert the FeatureRenderer to show new (PDB RESNUM) features
@@ -554,8 +558,6 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
-  abstract void showSelectedChains();
-
   /**
    * Action on selecting one of Jalview's registered colour schemes
    */
@@ -564,8 +566,9 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     AlignmentI al = getAlignmentPanel().av.getAlignment();
     ColourSchemeI cs = ColourSchemes.getInstance()
-            .getColourScheme(colourSchemeName, al, null);
-    getBinding().setJalviewColourScheme(cs);
+            .getColourScheme(colourSchemeName, getAlignmentPanel().av, al,
+                    null);
+    getBinding().colourByJalviewColourScheme(cs);
   }
 
   /**
@@ -599,7 +602,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        viewerColour_actionPerformed(actionEvent);
+        viewerColour_actionPerformed();
       }
     });
     colourMenu.add(viewerColour);
@@ -615,7 +618,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        background_actionPerformed(actionEvent);
+        background_actionPerformed();
       }
     });
     colourMenu.add(backGround);
@@ -646,7 +649,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        seqColour_actionPerformed(actionEvent);
+        seqColour_actionPerformed();
       }
     });
 
@@ -658,7 +661,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        chainColour_actionPerformed(actionEvent);
+        chainColour_actionPerformed();
       }
     });
 
@@ -670,7 +673,7 @@ public abstract class StructureViewerBase extends GStructureViewer
       @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
-        chargeColour_actionPerformed(actionEvent);
+        chargeColour_actionPerformed();
       }
     });
 
@@ -702,7 +705,7 @@ public abstract class StructureViewerBase extends GStructureViewer
                 else
                 {
                   // update the Chimera display now.
-                  seqColour_actionPerformed(null);
+                  seqColour_actionPerformed();
                 }
               }
             });
@@ -746,24 +749,13 @@ public abstract class StructureViewerBase extends GStructureViewer
     buildColourMenu();
   }
 
-  @Override
-  public void setJalviewColourScheme(ColourSchemeI cs)
-  {
-    getBinding().setJalviewColourScheme(cs);
-  }
-
   /**
    * Sends commands to the structure viewer to superimpose structures based on
    * currently associated alignments. May optionally return an error message for
    * the operation.
    */
   @Override
-  protected String alignStructs_actionPerformed(ActionEvent actionEvent)
-  {
-    return alignStructs_withAllAlignPanels();
-  }
-
-  protected String alignStructs_withAllAlignPanels()
+  protected String alignStructsWithAllAlignPanels()
   {
     if (getAlignmentPanel() == null)
     {
@@ -778,19 +770,8 @@ public abstract class StructureViewerBase extends GStructureViewer
     String reply = null;
     try
     {
-      AlignmentI[] als = new Alignment[_alignwith.size()];
-      HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
-      int[] alm = new int[_alignwith.size()];
-      int a = 0;
-
-      for (AlignmentPanel alignPanel : _alignwith)
-      {
-        als[a] = alignPanel.av.getAlignment();
-        alm[a] = -1;
-        alc[a++] = alignPanel.av.getAlignment().getHiddenColumns();
-      }
-      reply = getBinding().superposeStructures(als, alm, alc);
-      if (reply != null)
+      reply = getBinding().superposeStructures(_alignwith);
+      if (reply != null && !reply.isEmpty())
       {
         String text = MessageManager
                 .formatMessage("error.superposition_failed", reply);
@@ -799,9 +780,9 @@ public abstract class StructureViewerBase extends GStructureViewer
     } catch (Exception e)
     {
       StringBuffer sp = new StringBuffer();
-      for (AlignmentPanel alignPanel : _alignwith)
+      for (AlignmentViewPanel alignPanel : _alignwith)
       {
-        sp.append("'" + alignPanel.alignFrame.getTitle() + "' ");
+        sp.append("'" + alignPanel.getViewName() + "' ");
       }
       Cache.log.info("Couldn't align structures with the " + sp.toString()
               + "associated alignment panels.", e);
@@ -810,7 +791,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void background_actionPerformed(ActionEvent actionEvent)
+  public void background_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
             MessageManager.getString("label.select_background_colour"),
@@ -822,7 +803,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void viewerColour_actionPerformed(ActionEvent actionEvent)
+  public void viewerColour_actionPerformed()
   {
     if (viewerColour.isSelected())
     {
@@ -832,21 +813,21 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void chainColour_actionPerformed(ActionEvent actionEvent)
+  public void chainColour_actionPerformed()
   {
     chainColour.setSelected(true);
     getBinding().colourByChain();
   }
 
   @Override
-  public void chargeColour_actionPerformed(ActionEvent actionEvent)
+  public void chargeColour_actionPerformed()
   {
     chargeColour.setSelected(true);
     getBinding().colourByCharge();
   }
 
   @Override
-  public void seqColour_actionPerformed(ActionEvent actionEvent)
+  public void seqColour_actionPerformed()
   {
     AAStructureBindingModel binding = getBinding();
     binding.setColourBySequence(seqColour.isSelected());
@@ -865,7 +846,7 @@ public abstract class StructureViewerBase extends GStructureViewer
         }
       }
       // Set the colour using the current view for the associated alignframe
-      for (AlignmentPanel alignPanel : _colourwith)
+      for (AlignmentViewPanel alignPanel : _colourwith)
       {
         binding.colourBySequence(alignPanel);
       }
@@ -874,7 +855,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void pdbFile_actionPerformed(ActionEvent actionEvent)
+  public void pdbFile_actionPerformed()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"));
@@ -925,7 +906,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void viewMapping_actionPerformed(ActionEvent actionEvent)
+  public void viewMapping_actionPerformed()
   {
     CutAndPasteTransfer cap = new CutAndPasteTransfer();
     try
@@ -987,7 +968,7 @@ public abstract class StructureViewerBase extends GStructureViewer
 
     if (!binding.isLoadingFromArchive())
     {
-      seqColour_actionPerformed(null);
+      seqColour_actionPerformed();
     }
   }
 
@@ -1035,9 +1016,75 @@ public abstract class StructureViewerBase extends GStructureViewer
   }
 
   @Override
-  public void toFront()
+  public void raiseViewer()
   {
     toFront();
   }
 
+  @Override
+  public long startProgressBar(String msg)
+  {
+    // TODO would rather have startProgress/stopProgress as the
+    // IProgressIndicator interface
+    long tm = random.nextLong();
+    if (progressBar != null)
+    {
+      progressBar.setProgressBar(msg, tm);
+    }
+    return tm;
+  }
+
+  @Override
+  public void stopProgressBar(String msg, long handle)
+  {
+    if (progressBar != null)
+    {
+      progressBar.setProgressBar(msg, handle);
+    }
+  }
+
+  protected IProgressIndicator getProgressIndicator()
+  {
+    return progressBar;
+  }
+
+  protected void setProgressIndicator(IProgressIndicator pi)
+  {
+    progressBar = pi;
+  }
+
+  protected void setProgressMessage(String message, long id)
+  {
+    if (progressBar != null)
+    {
+      progressBar.setProgressBar(message, id);
+    }
+  }
+
+  @Override
+  public void showConsole(boolean show)
+  {
+    // default does nothing
+  }
+
+  /**
+   * Show only the selected chain(s) in the viewer
+   */
+  protected void showSelectedChains()
+  {
+    List<String> toshow = new ArrayList<>();
+    for (int i = 0; i < chainMenu.getItemCount(); i++)
+    {
+      if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
+      {
+        JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
+        if (item.isSelected())
+        {
+          toshow.add(item.getText());
+        }
+      }
+    }
+    getBinding().showChains(toshow);
+  }
+
 }