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License added to new files
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
2922f09
..
7f86753
100755
(executable)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-43,7
+43,7
@@
public class AlignViewport
int endRes;
\r
int startSeq;
\r
int endSeq;
\r
int endRes;
\r
int startSeq;
\r
int endSeq;
\r
- boolean showFullId = false;
\r
+ boolean showJVSuffix = true;
\r
boolean showText = true;
\r
boolean showColourText = false;
\r
boolean showBoxes = true;
\r
boolean showText = true;
\r
boolean showColourText = false;
\r
boolean showBoxes = true;
\r
@@
-86,6
+86,15
@@
public class AlignViewport
\r
boolean ignoreGapsInConsensusCalculation = false;
\r
\r
\r
boolean ignoreGapsInConsensusCalculation = false;
\r
\r
+ boolean isDataset = false;
\r
+
\r
+
\r
+ public AlignViewport(AlignmentI al, boolean dataset)
\r
+ {
\r
+ isDataset = dataset;
\r
+ setAlignment(al);
\r
+ init();
\r
+ }
\r
/**
\r
* Creates a new AlignViewport object.
\r
*
\r
/**
\r
* Creates a new AlignViewport object.
\r
*
\r
@@
-94,20
+103,17
@@
public class AlignViewport
public AlignViewport(AlignmentI al)
\r
{
\r
setAlignment(al);
\r
public AlignViewport(AlignmentI al)
\r
{
\r
setAlignment(al);
\r
- this.startRes = 0;
\r
- this.endRes = al.getWidth() - 1;
\r
- this.startSeq = 0;
\r
- this.endSeq = al.getHeight() - 1;
\r
-
\r
- updateFromPreferences();
\r
+ init();
\r
}
\r
\r
}
\r
\r
- /**
\r
- * DOCUMENT ME!
\r
- */
\r
- public void updateFromPreferences()
\r
+ void init()
\r
{
\r
{
\r
- showFullId = Cache.getDefault("SHOW_FULL_ID", true);
\r
+ this.startRes = 0;
\r
+ this.endRes = alignment.getWidth() - 1;
\r
+ this.startSeq = 0;
\r
+ this.endSeq = alignment.getHeight() - 1;
\r
+
\r
+ showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
\r
showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
\r
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
\r
\r
showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
\r
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);
\r
\r
@@
-137,9
+143,11
@@
public class AlignViewport
\r
// We must set conservation and consensus before setting colour,
\r
// as Blosum and Clustal require this to be done
\r
\r
// We must set conservation and consensus before setting colour,
\r
// as Blosum and Clustal require this to be done
\r
- updateConservation();
\r
-
\r
- updateConsensus();
\r
+ if(vconsensus==null && !isDataset)
\r
+ {
\r
+ updateConservation();
\r
+ updateConsensus();
\r
+ }
\r
\r
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
\r
{
\r
\r
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
\r
{
\r
@@
-914,9
+922,9
@@
public class AlignViewport
*
\r
* @return DOCUMENT ME!
\r
*/
\r
*
\r
* @return DOCUMENT ME!
\r
*/
\r
- public boolean getShowFullId()
\r
+ public boolean getShowJVSuffix()
\r
{
\r
{
\r
- return showFullId;
\r
+ return showJVSuffix;
\r
}
\r
\r
/**
\r
}
\r
\r
/**
\r
@@
-924,11
+932,12
@@
public class AlignViewport
*
\r
* @param b DOCUMENT ME!
\r
*/
\r
*
\r
* @param b DOCUMENT ME!
\r
*/
\r
- public void setShowFullId(boolean b)
\r
+ public void setShowJVSuffix(boolean b)
\r
{
\r
{
\r
- showFullId = b;
\r
+ showJVSuffix = b;
\r
}
\r
\r
}
\r
\r
+
\r
/**
\r
* DOCUMENT ME!
\r
*
\r
/**
\r
* DOCUMENT ME!
\r
*
\r
@@
-1058,4
+1067,14
@@
public class AlignViewport
{
\r
return ignoreGapsInConsensusCalculation;
\r
}
\r
{
\r
return ignoreGapsInConsensusCalculation;
\r
}
\r
+
\r
+ public void setDataset(boolean b)
\r
+ {
\r
+ isDataset = b;
\r
+ }
\r
+
\r
+ public boolean isDataset()
\r
+ {
\r
+ return isDataset;
\r
+ }
\r
}
\r
}
\r