JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java
index 20f5c1f..418a84d 100644 (file)
--- a/src/jalview/gui/StructureViewerBase.java
+++ b/src/jalview/gui/StructureViewerBase.java
@@ -27,6 +27,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
 import jalview.io.DataSourceType;
@@ -57,7 +58,6 @@ import java.util.Vector;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JColorChooser;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.JRadioButtonMenuItem;
@@ -410,35 +410,23 @@ public abstract class StructureViewerBase extends GStructureViewer
     return Desktop.instance.getStructureViewers(alp, this.getClass());
   }
 
-
-  /**
-   * Check for any existing views involving this alignment and give user the
-   * option to add and align this molecule to one of them
-   * 
-   * @param pdbentry
-   * @param seq
-   * @param chains
-   * @param apanel
-   * @param pdbId
-   * @return true if user adds to a view, or cancels entirely, else false
-   */
   @Override
-  public boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+  public void addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
           String[] chains, final AlignmentViewPanel apanel, String pdbId)
   {
     /*
      * JAL-1742 exclude view with this structure already mapped (don't offer
-     * to align chain B to chain A of the same structure)
+     * to align chain B to chain A of the same structure); code may defend
+     * against this possibility before we reach here
      */
     if (hasPdbId(pdbId))
     {
-      return false;
+      return;
     }
-    AlignmentPanel ap = (AlignmentPanel) apanel; // Implementation error if this
+    AlignmentPanel alignPanel = (AlignmentPanel) apanel; // Implementation error if this
                                                  // cast fails
-    useAlignmentPanelForSuperposition(ap);
-    addStructure(pdbentry, seq, chains, ap.alignFrame);
-    return true;
+    useAlignmentPanelForSuperposition(alignPanel);
+    addStructure(pdbentry, seq, chains, alignPanel.alignFrame);
   }
 
   /**
@@ -502,33 +490,20 @@ public abstract class StructureViewerBase extends GStructureViewer
     }
   }
 
-  /**
-   * Check if the PDB file is already loaded, if so offer to add it to the
-   * existing viewer
-   * 
-   * @param seq
-   * @param chains
-   * @param apanel
-   * @param pdbId
-   * @return true if the user chooses to add to a viewer, or to cancel entirely
-   */
   @Override
   public boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
           final AlignmentViewPanel apanel, String pdbId)
   {
-    boolean finished = false;
     String alreadyMapped = apanel.getStructureSelectionManager()
             .alreadyMappedToFile(pdbId);
 
-    if (alreadyMapped != null)
+    if (alreadyMapped == null)
     {
-      /*
-       * the PDB file is already loaded
-       */
-      addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
-      finished = true;
+      return false;
     }
-    return finished;
+
+    addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+    return true;
   }
 
   void setChainMenuItems(List<String> chainNames)
@@ -589,7 +564,8 @@ public abstract class StructureViewerBase extends GStructureViewer
   {
     AlignmentI al = getAlignmentPanel().av.getAlignment();
     ColourSchemeI cs = ColourSchemes.getInstance()
-            .getColourScheme(colourSchemeName, al, null);
+            .getColourScheme(colourSchemeName, getAlignmentPanel().av, al,
+                    null);
     getBinding().setJalviewColourScheme(cs);
   }
 
@@ -808,11 +784,11 @@ public abstract class StructureViewerBase extends GStructureViewer
       int[] alm = new int[_alignwith.size()];
       int a = 0;
 
-      for (AlignmentPanel ap : _alignwith)
+      for (AlignmentPanel alignPanel : _alignwith)
       {
-        als[a] = ap.av.getAlignment();
+        als[a] = alignPanel.av.getAlignment();
         alm[a] = -1;
-        alc[a++] = ap.av.getAlignment().getHiddenColumns();
+        alc[a++] = alignPanel.av.getAlignment().getHiddenColumns();
       }
       reply = getBinding().superposeStructures(als, alm, alc);
       if (reply != null)
@@ -824,9 +800,9 @@ public abstract class StructureViewerBase extends GStructureViewer
     } catch (Exception e)
     {
       StringBuffer sp = new StringBuffer();
-      for (AlignmentPanel ap : _alignwith)
+      for (AlignmentPanel alignPanel : _alignwith)
       {
-        sp.append("'" + ap.alignFrame.getTitle() + "' ");
+        sp.append("'" + alignPanel.alignFrame.getTitle() + "' ");
       }
       Cache.log.info("Couldn't align structures with the " + sp.toString()
               + "associated alignment panels.", e);
@@ -834,16 +810,23 @@ public abstract class StructureViewerBase extends GStructureViewer
     return reply;
   }
 
+  /**
+   * Opens a colour chooser dialog, and applies the chosen colour to the
+   * background of the structure viewer
+   */
   @Override
   public void background_actionPerformed(ActionEvent actionEvent)
   {
-    Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_background_colour"),
-            null);
-    if (col != null)
+    String ttl = MessageManager.getString("label.select_background_colour");
+    ColourChooserListener listener = new ColourChooserListener()
     {
-      getBinding().setBackgroundColour(col);
-    }
+      @Override
+      public void colourSelected(Color c)
+      {
+        getBinding().setBackgroundColour(c);
+      }
+    };
+    JalviewColourChooser.showColourChooser(this, ttl, null, listener);
   }
 
   @Override
@@ -890,9 +873,9 @@ public abstract class StructureViewerBase extends GStructureViewer
         }
       }
       // Set the colour using the current view for the associated alignframe
-      for (AlignmentPanel ap : _colourwith)
+      for (AlignmentPanel alignPanel : _colourwith)
       {
-        binding.colourBySequence(ap);
+        binding.colourBySequence(alignPanel);
       }
       seqColoursApplied = true;
     }
@@ -901,6 +884,7 @@ public abstract class StructureViewerBase extends GStructureViewer
   @Override
   public void pdbFile_actionPerformed(ActionEvent actionEvent)
   {
+    // TODO: JAL-3048 not needed for Jalview-JS - save PDB file
     JalviewFileChooser chooser = new JalviewFileChooser(
             Cache.getProperty("LAST_DIRECTORY"));
 
@@ -1059,4 +1043,10 @@ public abstract class StructureViewerBase extends GStructureViewer
     return seqColoursApplied;
   }
 
+  @Override
+  public void raiseViewer()
+  {
+    toFront();
+  }
+
 }