mc_view references were MCview

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 76f2705..3aed7ec 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -945,7 +945,7 @@ public class APopupMenu extends java.awt.PopupMenu
       }
       else
       {
-        new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
+        new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
                 DataSourceType.URL);
       }
 

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 5ad212e..8740f51 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -4183,7 +4183,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     }
     else
     {
-      new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
+      new mc_view.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
     }
 
   }

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 3d1442d..7fda3c4 100644 (file)
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -335,7 +335,7 @@ public class AppletJmol extends EmbmenuFrame implements
             }
             FileParse fp = new FileParse(pdbentry.getFile(), protocol);
             fp.mark();
-            // reader = new MCview.PDBfile(fp);
+            // reader = new mc_view.PDBfile(fp);
             // could set ID, etc.
             // if (!reader.isValid())
             // {

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 22a49cd..f42686d 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -451,7 +451,7 @@ public class CutAndPasteTransfer extends Panel
     }
     else
     {
-      new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
+      new mc_view.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
               alignFrame.alignPanel, DataSourceType.PASTE);
     }
   }

diff --git a/src/jalview/appletgui/UserDefinedColours.java b/src/jalview/appletgui/UserDefinedColours.java
index 6831a73..febe5f8 100644 (file)
--- a/src/jalview/appletgui/UserDefinedColours.java
+++ b/src/jalview/appletgui/UserDefinedColours.java
@@ -70,7 +70,7 @@ public class UserDefinedColours extends Panel
 
   Frame frame;
 
-  MCview.AppletPDBCanvas pdbcanvas;
+  mc_view.AppletPDBCanvas pdbcanvas;
 
   AppletJmol jmol;
 
@@ -107,7 +107,7 @@ public class UserDefinedColours extends Panel
     init();
   }
 
-  public UserDefinedColours(MCview.AppletPDBCanvas pdb)
+  public UserDefinedColours(mc_view.AppletPDBCanvas pdb)
   {
     this.pdbcanvas = pdb;
     init();

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index a60496c..e483fce 100644 (file)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -1333,7 +1333,7 @@ public class JalviewLite extends Applet
   private boolean alignPdbStructures = false;
 
   /**
-   * use an external structure viewer exclusively (no jmols or MCViews will be
+   * use an external structure viewer exclusively (no jmols or mc_views will be
    * opened by JalviewLite itself)
    */
   public boolean useXtrnalSviewer = false;
@@ -1798,7 +1798,7 @@ public class JalviewLite extends Applet
           if (!jmolAvailable)
           {
             System.out.println(
-                    "Jmol not available - Using MCview for structures");
+                    "Jmol not available - Using mc_view for structures");
           }
         } catch (java.lang.ClassNotFoundException ex)
         {
@@ -1810,7 +1810,7 @@ public class JalviewLite extends Applet
         if (debug)
         {
           System.err.println(
-                  "Skipping Jmol check. Will use MCView (probably)");
+                  "Skipping Jmol check. Will use mc_view (probably)");
         }
       }
       checkedForJmol = true;

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 258d806..5afbc8e 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -935,7 +935,7 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
   {
     /**
      * this implements the toggle label behaviour copied from the original
-     * structure viewer, MCView
+     * structure viewer, mc_view
      */
     if (strData != null)
     {

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index fd483ad..e94da73 100644 (file)
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -45,9 +45,9 @@ import org.jmol.c.STR;
 import org.jmol.modelset.ModelSet;
 import org.jmol.viewer.Viewer;
 
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.Residue;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.Residue;
 
 /**
  * Import and process files with Jmol for file like PDB, mmCIF

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 95cbb61..8c376fc 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -178,9 +178,9 @@ public class AppletFormatAdapter
         }
         else
         {
-          // todo is MCview parsing obsolete yet? JAL-2120
+          // todo is mc_view parsing obsolete yet? JAL-2120
           StructureImportSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
+          alignFile = new mc_view.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   sourceType);
         }
@@ -265,7 +265,7 @@ public class AppletFormatAdapter
         else
         {
           StructureImportSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
+          alignFile = new mc_view.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, source);
         }
         ((StructureFile) alignFile).setDbRefType(Type.PDB);

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 4b33dbf..ff7475f 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -306,7 +306,7 @@ public enum FileFormat implements FileFormatI
       else
       {
         StructureImportSettings.setShowSeqFeatures(true);
-        return new MCview.PDBfile(
+        return new mc_view.PDBfile(
                 StructureImportSettings.isVisibleChainAnnotation(),
                 StructureImportSettings.isProcessSecondaryStructure(),
                 StructureImportSettings.isExternalSecondaryStructure(),

diff --git a/src/jalview/io/PDBFeatureSettings.java b/src/jalview/io/PDBFeatureSettings.java
index 0f2b0ac..01610a1 100644 (file)
--- a/src/jalview/io/PDBFeatureSettings.java
+++ b/src/jalview/io/PDBFeatureSettings.java
@@ -26,7 +26,7 @@ import jalview.schemes.FeatureSettingsAdapter;
 
 import java.awt.Color;
 
-import MCview.PDBChain;
+import mc_view.PDBChain;
 
 public class PDBFeatureSettings extends FeatureSettingsAdapter
 {

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 778c683..16ae0a1 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -38,7 +38,7 @@ import java.lang.reflect.Constructor;
 import java.util.List;
 import java.util.Vector;
 
-import MCview.PDBChain;
+import mc_view.PDBChain;
 
 public abstract class StructureFile extends AlignFile
 {

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index cd986c0..6261e74 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -56,9 +56,9 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.PDBfile;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.PDBfile;
 
 public class StructureSelectionManager
 {

diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index b5f9653..d065666 100644 (file)
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -71,8 +71,8 @@ import javax.xml.bind.Unmarshaller;
 import javax.xml.stream.XMLInputFactory;
 import javax.xml.stream.XMLStreamReader;
 
-import MCview.Atom;
-import MCview.PDBChain;
+import mc_view.Atom;
+import mc_view.PDBChain;
 
 public class SiftsClient implements SiftsClientI
 {