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JAL-1605 merge commit
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
91cc51e
..
497dad4
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-42,9
+42,8
@@
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
+import jalview.commands.CommandI;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
@@
-98,7
+97,7
@@
public class AlignViewport extends AlignmentViewport implements
boolean showSequenceFeatures = false;
boolean showSequenceFeatures = false;
- boolean showAnnotation = true;
+ private boolean showAnnotation = true;
SequenceAnnotationOrder sortAnnotationsBy = null;
SequenceAnnotationOrder sortAnnotationsBy = null;
@@
-140,9
+139,9
@@
public class AlignViewport extends AlignmentViewport implements
boolean gatherViewsHere = false;
boolean gatherViewsHere = false;
- Stack historyList = new Stack();
+ Stack<CommandI> historyList = new Stack<CommandI>();
- Stack redoList = new Stack();
+ Stack<CommandI> redoList = new Stack<CommandI>();
int thresholdTextColour = 0;
int thresholdTextColour = 0;
@@
-150,7
+149,7
@@
public class AlignViewport extends AlignmentViewport implements
Color textColour2 = Color.white;
Color textColour2 = Color.white;
- boolean rightAlignIds = false;
+ private boolean rightAlignIds = false;
/**
* Creates a new AlignViewport object.
/**
* Creates a new AlignViewport object.
@@
-287,9
+286,9
@@
public class AlignViewport extends AlignmentViewport implements
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
antiAlias = Cache.getDefault("ANTI_ALIAS", false);
showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);
- showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);
+ setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));
- rightAlignIds = Cache.getDefault("RIGHT_ALIGN_IDS", false);
+ setRightAlignIds(Cache.getDefault("RIGHT_ALIGN_IDS", false));
centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
centreColumnLabels = Cache.getDefault("CENTRE_COLUMN_LABELS", false);
autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);
@@
-337,10
+336,6
@@
public class AlignViewport extends AlignmentViewport implements
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
false);
showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false);
showConsensus = Cache.getDefault("SHOW_IDENTITY", true);
- consensus = new AlignmentAnnotation("Consensus", "PID",
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- consensus.hasText = true;
- consensus.autoCalculated = true;
}
initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
}
initAutoAnnotation();
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)
@@
-844,7
+839,7
@@
public class AlignViewport extends AlignmentViewport implements
*/
public boolean getShowAnnotation()
{
*/
public boolean getShowAnnotation()
{
- return showAnnotation;
+ return isShowAnnotation();
}
/**
}
/**
@@
-1308,4
+1303,19
@@
public class AlignViewport extends AlignmentViewport implements
{
this.showAutocalculatedAbove = showAutocalculatedAbove;
}
{
this.showAutocalculatedAbove = showAutocalculatedAbove;
}
+
+ public boolean isShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ public boolean isRightAlignIds()
+ {
+ return rightAlignIds;
+ }
+
+ public void setRightAlignIds(boolean rightAlignIds)
+ {
+ this.rightAlignIds = rightAlignIds;
+ }
}
}