git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
removed some uncheck warnings
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
msa_compactor
/
MsaCompactor.java
diff --git
a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java
index
6209da1
..
b4d2fe7
100644
(file)
--- a/
forester/java/src/org/forester/msa_compactor/MsaCompactor.java
+++ b/
forester/java/src/org/forester/msa_compactor/MsaCompactor.java
@@
-179,6
+179,7
@@
public class MsaCompactor {
}
++i;
}
}
++i;
}
+
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, true );
displayTree( phy );
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, true );
displayTree( phy );
@@
-350,7
+351,14
@@
public class MsaCompactor {
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, false );
displayTree( phy );
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, false );
displayTree( phy );
- }
+ System.out.println( "calculating phylogentic tree..." );
+ System.out.println();
+ final Phylogeny phy2 = calcTree();
+ addSeqs2Tree( _msa, phy2 );
+ displayTree( phy2 );
+ }
+
+
return msa_props;
}
return msa_props;
}
@@
-401,7
+409,13
@@
public class MsaCompactor {
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, false );
displayTree( phy );
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, false );
displayTree( phy );
- }
+ System.out.println( "calculating phylogentic tree..." );
+ System.out.println();
+ final Phylogeny phy2 = calcTree();
+ addSeqs2Tree( _msa, phy2 );
+ displayTree( phy2 );
+ }
+
return msa_props;
}
return msa_props;
}
@@
-456,7
+470,8
@@
public class MsaCompactor {
final Phylogeny phy2 = calcTree();
addSeqs2Tree( _msa, phy2 );
displayTree( phy2 );
final Phylogeny phy2 = calcTree();
addSeqs2Tree( _msa, phy2 );
displayTree( phy2 );
- }
+ }
+
return msa_props;
}
return msa_props;
}