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mc_view references were MCview
author
hansonr
<hansonr@STO24954W.ad.stolaf.edu>
Tue, 21 Aug 2018 02:10:41 +0000
(21:10 -0500)
committer
hansonr
<hansonr@STO24954W.ad.stolaf.edu>
Tue, 21 Aug 2018 02:10:59 +0000
(21:10 -0500)
14 files changed:
src/jalview/appletgui/APopupMenu.java
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src/jalview/appletgui/AlignFrame.java
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src/jalview/appletgui/AppletJmol.java
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src/jalview/appletgui/CutAndPasteTransfer.java
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src/jalview/appletgui/UserDefinedColours.java
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src/jalview/bin/JalviewLite.java
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src/jalview/ext/jmol/JalviewJmolBinding.java
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src/jalview/ext/jmol/JmolParser.java
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src/jalview/io/AppletFormatAdapter.java
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src/jalview/io/FileFormat.java
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src/jalview/io/PDBFeatureSettings.java
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src/jalview/io/StructureFile.java
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src/jalview/structure/StructureSelectionManager.java
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src/jalview/ws/sifts/SiftsClient.java
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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
{
}
else
{
- new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
+ new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null, ap,
DataSourceType.URL);
}
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
{
}
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();
}
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())
// {
// 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
{
}
else
{
- new MCview.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
+ new mc_view.AppletPDBViewer(pdb, new SequenceI[] { seq }, null,
alignFrame.alignPanel, DataSourceType.PASTE);
}
}
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;
Frame frame;
- MCview.AppletPDBCanvas pdbcanvas;
+ mc_view.AppletPDBCanvas pdbcanvas;
AppletJmol jmol;
AppletJmol jmol;
@@
-107,7
+107,7
@@
public class UserDefinedColours extends Panel
init();
}
init();
}
- public UserDefinedColours(MCview.AppletPDBCanvas pdb)
+ public UserDefinedColours(mc_view.AppletPDBCanvas pdb)
{
this.pdbcanvas = pdb;
init();
{
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;
/**
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;
* opened by JalviewLite itself)
*/
public boolean useXtrnalSviewer = false;
@@
-1798,7
+1798,7
@@
public class JalviewLite extends Applet
if (!jmolAvailable)
{
System.out.println(
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)
{
}
} catch (java.lang.ClassNotFoundException ex)
{
@@
-1810,7
+1810,7
@@
public class JalviewLite extends Applet
if (debug)
{
System.err.println(
if (debug)
{
System.err.println(
- "Skipping Jmol check. Will use MCView (probably)");
+ "Skipping Jmol check. Will use mc_view (probably)");
}
}
checkedForJmol = true;
}
}
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
{
/**
* this implements the toggle label behaviour copied from the original
- * structure viewer, MCView
+ * structure viewer, mc_view
*/
if (strData != null)
{
*/
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 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
/**
* 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
{
}
else
{
- // todo is MCview parsing obsolete yet? JAL-2120
+ // todo is mc_view parsing obsolete yet? JAL-2120
StructureImportSettings.setShowSeqFeatures(true);
StructureImportSettings.setShowSeqFeatures(true);
- alignFile = new MCview.PDBfile(annotFromStructure,
+ alignFile = new mc_view.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, inFile,
sourceType);
}
localSecondaryStruct, serviceSecondaryStruct, inFile,
sourceType);
}
@@
-265,7
+265,7
@@
public class AppletFormatAdapter
else
{
StructureImportSettings.setShowSeqFeatures(true);
else
{
StructureImportSettings.setShowSeqFeatures(true);
- alignFile = new MCview.PDBfile(annotFromStructure,
+ alignFile = new mc_view.PDBfile(annotFromStructure,
localSecondaryStruct, serviceSecondaryStruct, source);
}
((StructureFile) alignFile).setDbRefType(Type.PDB);
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);
else
{
StructureImportSettings.setShowSeqFeatures(true);
- return new MCview.PDBfile(
+ return new mc_view.PDBfile(
StructureImportSettings.isVisibleChainAnnotation(),
StructureImportSettings.isProcessSecondaryStructure(),
StructureImportSettings.isExternalSecondaryStructure(),
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 java.awt.Color;
-import MCview.PDBChain;
+import mc_view.PDBChain;
public class PDBFeatureSettings extends FeatureSettingsAdapter
{
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 java.util.List;
import java.util.Vector;
-import MCview.PDBChain;
+import mc_view.PDBChain;
public abstract class StructureFile extends AlignFile
{
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 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
{
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 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
{
public class SiftsClient implements SiftsClientI
{