JAL-2422 pull up refactoring in preparation for ChimeraX subclasses

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 35a5475..c9607c6 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -53,6 +53,7 @@ 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 +91,13 @@ 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 +122,10 @@ public abstract class StructureViewerBase extends GStructureViewer
    */
   protected volatile boolean seqColoursApplied = false;
 
+  private IProgressIndicator progressBar = null;
+
+  private Random random = new Random();
+
   /**
    * Default constructor
    */
@@ -159,13 +164,14 @@ 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 +221,7 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
+  @Override
   public AlignmentPanel getAlignmentPanel()
   {
     return ap;
@@ -267,7 +274,8 @@ public abstract class StructureViewerBase extends GStructureViewer
    * 
    * @param nap
    */
-  public void removeAlignmentPanel(AlignmentPanel nap)
+  @Override
+  public void removeAlignmentPanel(AlignmentViewPanel nap)
   {
     try
     {
@@ -339,8 +347,6 @@ 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 +455,7 @@ 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
@@ -784,11 +790,11 @@ public abstract class StructureViewerBase extends GStructureViewer
       int[] alm = new int[_alignwith.size()];
       int a = 0;
 
-      for (AlignmentPanel alignPanel : _alignwith)
+      for (AlignmentViewPanel alignPanel : _alignwith)
       {
-        als[a] = alignPanel.av.getAlignment();
+        als[a] = alignPanel.getAlignment();
         alm[a] = -1;
-        alc[a++] = alignPanel.av.getAlignment().getHiddenColumns();
+        alc[a++] = alignPanel.getAlignment().getHiddenColumns();
       }
       reply = getBinding().superposeStructures(als, alm, alc);
       if (reply != null)
@@ -800,9 +806,9 @@ 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);
@@ -866,7 +872,7 @@ 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);
       }
@@ -1041,4 +1047,61 @@ public abstract class StructureViewerBase extends GStructureViewer
     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;
+  }
+
+  /**
+   * End the progress bar with the specified handle, leaving a message (if not
+   * null) on the status bar
+   * 
+   * @param msg
+   * @param handle
+   */
+  public void stopProgressBar(String msg, long handle)
+  {
+    if (progressBar != null)
+    {
+      progressBar.setProgressBar(msg, handle);
+    }
+  }
+
+  @Override
+  public void stopProgressBar(Object object, long 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
+  }
+
 }