From b879c4a2d32d3489e63ac06917e81637e6bb4068 Mon Sep 17 00:00:00 2001 From: hansonr Date: Mon, 20 Aug 2018 21:10:41 -0500 Subject: [PATCH] mc_view references were MCview --- src/jalview/appletgui/APopupMenu.java | 2 +- src/jalview/appletgui/AlignFrame.java | 2 +- src/jalview/appletgui/AppletJmol.java | 2 +- src/jalview/appletgui/CutAndPasteTransfer.java | 2 +- src/jalview/appletgui/UserDefinedColours.java | 4 ++-- src/jalview/bin/JalviewLite.java | 6 +++--- src/jalview/ext/jmol/JalviewJmolBinding.java | 2 +- src/jalview/ext/jmol/JmolParser.java | 6 +++--- src/jalview/io/AppletFormatAdapter.java | 6 +++--- src/jalview/io/FileFormat.java | 2 +- src/jalview/io/PDBFeatureSettings.java | 2 +- src/jalview/io/StructureFile.java | 2 +- src/jalview/structure/StructureSelectionManager.java | 6 +++--- src/jalview/ws/sifts/SiftsClient.java | 4 ++-- 14 files changed, 24 insertions(+), 24 deletions(-) diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 76f2705..3aed7ec 100644 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 --- 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 { -- 1.7.10.2