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JAL-3210 Barebones gradle/buildship/eclipse. See README
[jalview.git]
/
src
/
jalview
/
viewmodel
/
AlignmentViewport.java
diff --git
a/src/jalview/viewmodel/AlignmentViewport.java
b/src/jalview/viewmodel/AlignmentViewport.java
index
e74f2e0
..
536f767
100644
(file)
--- a/
src/jalview/viewmodel/AlignmentViewport.java
+++ b/
src/jalview/viewmodel/AlignmentViewport.java
@@
-711,13
+711,13
@@
public abstract class AlignmentViewport
/**
* results of cDNA complement consensus visible portion of view
*/
/**
* results of cDNA complement consensus visible portion of view
*/
- protected Hashtable[] hcomplementConsensus = null;
+ protected Hashtable<String, Object>[] hcomplementConsensus = null;
/**
* results of secondary structure base pair consensus for visible portion of
* view
*/
/**
* results of secondary structure base pair consensus for visible portion of
* view
*/
- protected Hashtable[] hStrucConsensus = null;
+ protected Hashtable<String, Object>[] hStrucConsensus = null;
protected Conservation hconservation = null;
protected Conservation hconservation = null;
@@
-746,7
+746,8
@@
public abstract class AlignmentViewport
}
@Override
}
@Override
- public void setComplementConsensusHash(Hashtable[] hconsensus)
+ public void setComplementConsensusHash(
+ Hashtable<String, Object>[] hconsensus)
{
this.hcomplementConsensus = hconsensus;
}
{
this.hcomplementConsensus = hconsensus;
}
@@
-758,19
+759,20
@@
public abstract class AlignmentViewport
}
@Override
}
@Override
- public Hashtable[] getComplementConsensusHash()
+ public Hashtable<String, Object>[] getComplementConsensusHash()
{
return hcomplementConsensus;
}
@Override
{
return hcomplementConsensus;
}
@Override
- public Hashtable[] getRnaStructureConsensusHash()
+ public Hashtable<String, Object>[] getRnaStructureConsensusHash()
{
return hStrucConsensus;
}
@Override
{
return hStrucConsensus;
}
@Override
- public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+ public void setRnaStructureConsensusHash(
+ Hashtable<String, Object>[] hStrucConsensus)
{
this.hStrucConsensus = hStrucConsensus;
{
this.hStrucConsensus = hStrucConsensus;
@@
-1800,7
+1802,7
@@
public abstract class AlignmentViewport
}
} while (end < max);
}
} while (end < max);
- int[][] startEnd = new int[regions.size()][2];
+ // int[][] startEnd = new int[regions.size()][2];
return regions;
}
return regions;
}
@@
-2155,7
+2157,7
@@
public abstract class AlignmentViewport
* TODO reorder the annotation rows according to group/sequence ordering on
* alignment
*/
* TODO reorder the annotation rows according to group/sequence ordering on
* alignment
*/
- boolean sortg = true;
+ // boolean sortg = true;
// remove old automatic annotation
// add any new annotation
// remove old automatic annotation
// add any new annotation
@@
-2265,7
+2267,7
@@
public abstract class AlignmentViewport
public void clearSequenceColours()
{
sequenceColours.clear();
public void clearSequenceColours()
{
sequenceColours.clear();
- };
+ }
@Override
public AlignViewportI getCodingComplement()
@Override
public AlignViewportI getCodingComplement()