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Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh...
[jalview.git]
/
src
/
jalview
/
io
/
NewickFile.java
diff --git
a/src/jalview/io/NewickFile.java
b/src/jalview/io/NewickFile.java
index
4a30d73
..
a283691
100755
(executable)
--- a/
src/jalview/io/NewickFile.java
+++ b/
src/jalview/io/NewickFile.java
@@
-80,14
+80,14
@@
public class NewickFile extends FileParse
{
SequenceNode root;
{
SequenceNode root;
- private boolean HasBootstrap = false;
+ private boolean hasBootstrap = false;
- private boolean HasDistances = false;
+ private boolean hasDistances = false;
- private boolean RootHasDistance = false;
+ private boolean rootHasDistance = false;
// File IO Flags
// File IO Flags
- boolean ReplaceUnderscores = false;
+ boolean replaceUnderscores = false;
boolean printRootInfo = true;
boolean printRootInfo = true;
@@
-160,7
+160,7
@@
public class NewickFile extends FileParse
*/
public NewickFile(SequenceNode newtree, boolean bootstrap)
{
*/
public NewickFile(SequenceNode newtree, boolean bootstrap)
{
- HasBootstrap = bootstrap;
+ hasBootstrap = bootstrap;
root = newtree;
}
root = newtree;
}
@@
-178,8
+178,8
@@
public class NewickFile extends FileParse
boolean distances)
{
root = newtree;
boolean distances)
{
root = newtree;
- HasBootstrap = bootstrap;
- HasDistances = distances;
+ hasBootstrap = bootstrap;
+ hasDistances = distances;
}
/**
}
/**
@@
-198,9
+198,9
@@
public class NewickFile extends FileParse
boolean distances, boolean rootdistance)
{
root = newtree;
boolean distances, boolean rootdistance)
{
root = newtree;
- HasBootstrap = bootstrap;
- HasDistances = distances;
- RootHasDistance = rootdistance;
+ hasBootstrap = bootstrap;
+ hasDistances = distances;
+ rootHasDistance = rootdistance;
}
/**
}
/**
@@
-230,9
+230,9
@@
public class NewickFile extends FileParse
// @tree annotations
// These are set automatically by the reader
// @tree annotations
// These are set automatically by the reader
- public boolean HasBootstrap()
+ public boolean hasBootstrap()
{
{
- return HasBootstrap;
+ return hasBootstrap;
}
/**
}
/**
@@
-240,14
+240,14
@@
public class NewickFile extends FileParse
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public boolean HasDistances()
+ public boolean hasDistances()
{
{
- return HasDistances;
+ return hasDistances;
}
}
- public boolean HasRootDistance()
+ public boolean hasRootDistance()
{
{
- return RootHasDistance;
+ return rootHasDistance;
}
/**
}
/**
@@
-439,7
+439,7
@@
public class NewickFile extends FileParse
{
if (nodename == null)
{
{
if (nodename == null)
{
- if (ReplaceUnderscores)
+ if (replaceUnderscores)
{
nodename = uqnodename.stringMatched(1).replace('_', ' ');
}
{
nodename = uqnodename.stringMatched(1).replace('_', ' ');
}
@@
-472,7
+472,7
@@
public class NewickFile extends FileParse
{
bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
.intValue();
{
bootstrap = (Integer.valueOf(nbootstrap.stringMatched(1)))
.intValue();
- HasBootstrap = true;
+ hasBootstrap = true;
} catch (Exception e)
{
Error = ErrorStringrange(Error, "Can't parse bootstrap value",
} catch (Exception e)
{
Error = ErrorStringrange(Error, "Can't parse bootstrap value",
@@
-503,12
+503,12
@@
public class NewickFile extends FileParse
// Write node info here
c.setName(nodename);
// Trees without distances still need a render distance
// Write node info here
c.setName(nodename);
// Trees without distances still need a render distance
- c.dist = (HasDistances) ? distance : DefDistance;
+ c.dist = (hasDistances) ? distance : DefDistance;
// be consistent for internal bootstrap defaults too
// be consistent for internal bootstrap defaults too
- c.setBootstrap((HasBootstrap) ? bootstrap : DefBootstrap);
+ c.setBootstrap((hasBootstrap) ? bootstrap : DefBootstrap);
if (c == realroot)
{
if (c == realroot)
{
- RootHasDistance = nodehasdistance; // JBPNote This is really
+ rootHasDistance = nodehasdistance; // JBPNote This is really
// UGLY!!! Ensure root node gets
// its given distance
}
// UGLY!!! Ensure root node gets
// its given distance
}
@@
-519,8
+519,8
@@
public class NewickFile extends FileParse
{
// Find a place to put the leaf
SequenceNode newnode = new SequenceNode(null, c, nodename,
{
// Find a place to put the leaf
SequenceNode newnode = new SequenceNode(null, c, nodename,
- (HasDistances) ? distance : DefDistance,
- (HasBootstrap) ? bootstrap : DefBootstrap, false);
+ (hasDistances) ? distance : DefDistance,
+ (hasBootstrap) ? bootstrap : DefBootstrap, false);
parseNHXNodeProps(c, commentString2);
commentString2 = null;
parseNHXNodeProps(c, commentString2);
commentString2 = null;
@@
-539,7
+539,7
@@
public class NewickFile extends FileParse
// Insert a dummy node for polytomy
// dummy nodes have distances
SequenceNode newdummy = new SequenceNode(null, c, null,
// Insert a dummy node for polytomy
// dummy nodes have distances
SequenceNode newdummy = new SequenceNode(null, c, null,
- (HasDistances ? 0 : DefDistance), 0, true);
+ (hasDistances ? 0 : DefDistance), 0, true);
newdummy.SetChildren(c.left(), newnode);
c.setLeft(newdummy);
}
newdummy.SetChildren(c.left(), newnode);
c.setLeft(newdummy);
}
@@
-617,9
+617,9
@@
public class NewickFile extends FileParse
// (root.right()!=null && root.isDummy())
root = (SequenceNode) root.right().detach(); // remove the imaginary root.
// (root.right()!=null && root.isDummy())
root = (SequenceNode) root.right().detach(); // remove the imaginary root.
- if (!RootHasDistance)
+ if (!rootHasDistance)
{
{
- root.dist = (HasDistances) ? 0 : DefDistance;
+ root.dist = (hasDistances) ? 0 : DefDistance;
}
}
}
}
@@
-658,7
+658,7
@@
public class NewickFile extends FileParse
v = iv.intValue(); // jalview only does integer bootstraps
// currently
c.setBootstrap(v);
v = iv.intValue(); // jalview only does integer bootstraps
// currently
c.setBootstrap(v);
- HasBootstrap = true;
+ hasBootstrap = true;
}
// more codes here.
} catch (Exception e)
}
// more codes here.
} catch (Exception e)
@@
-715,11
+715,11
@@
public class NewickFile extends FileParse
{
synchronized (this)
{
{
synchronized (this)
{
- boolean boots = this.HasBootstrap;
- this.HasBootstrap = withbootstraps;
+ boolean boots = this.hasBootstrap;
+ this.hasBootstrap = withbootstraps;
String rv = print();
String rv = print();
- this.HasBootstrap = boots;
+ this.hasBootstrap = boots;
return rv;
}
return rv;
}
@@
-741,11
+741,11
@@
public class NewickFile extends FileParse
{
synchronized (this)
{
{
synchronized (this)
{
- boolean dists = this.HasDistances;
- this.HasDistances = withdists;
+ boolean dists = this.hasDistances;
+ this.hasDistances = withdists;
String rv = print(withbootstraps);
String rv = print(withbootstraps);
- this.HasDistances = dists;
+ this.hasDistances = dists;
return rv;
}
return rv;
}
@@
-835,10
+835,10
@@
public class NewickFile extends FileParse
private String printNodeField(SequenceNode c)
{
return ((c.getName() == null) ? "" : nodeName(c.getName()))
private String printNodeField(SequenceNode c)
{
return ((c.getName() == null) ? "" : nodeName(c.getName()))
- + ((HasBootstrap) ? ((c.getBootstrap() > -1)
+ + ((hasBootstrap) ? ((c.getBootstrap() > -1)
? ((c.getName() != null ? " " : "") + c.getBootstrap())
: "") : "")
? ((c.getName() != null ? " " : "") + c.getBootstrap())
: "") : "")
- + ((HasDistances) ? (":" + c.dist) : "");
+ + ((hasDistances) ? (":" + c.dist) : "");
}
/**
}
/**
@@
-853,13
+853,13
@@
public class NewickFile extends FileParse
{
return (printRootInfo)
? (((root.getName() == null) ? "" : nodeName(root.getName()))
{
return (printRootInfo)
? (((root.getName() == null) ? "" : nodeName(root.getName()))
- + ((HasBootstrap)
+ + ((hasBootstrap)
? ((root.getBootstrap() > -1)
? ((root.getName() != null ? " " : "")
+ +root.getBootstrap())
: "")
: "")
? ((root.getBootstrap() > -1)
? ((root.getName() != null ? " " : "")
+ +root.getBootstrap())
: "")
: "")
- + ((RootHasDistance) ? (":" + root.dist) : ""))
+ + ((rootHasDistance) ? (":" + root.dist) : ""))
: "";
}
: "";
}