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
JAL-1683 replace year/version strings with tokens in source
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
d6df385
..
b088e08
100644
(file)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-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;
@@
-96,8
+95,6
@@
public class AlignViewport extends AlignmentViewport implements
boolean renderGaps = true;
boolean renderGaps = true;
- boolean showAnnotation = true;
-
SequenceAnnotationOrder sortAnnotationsBy = null;
int charHeight;
SequenceAnnotationOrder sortAnnotationsBy = null;
int charHeight;
@@
-132,9
+129,9
@@
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;
@@
-142,8
+139,7
@@
public class AlignViewport extends AlignmentViewport implements
Color textColour2 = Color.white;
Color textColour2 = Color.white;
- boolean rightAlignIds = false;
-
+ private AnnotationColumnChooser annotationColumnSelectionState;
/**
* Creates a new AlignViewport object.
*
/**
* Creates a new AlignViewport object.
*
@@
-199,16
+195,7
@@
public class AlignViewport extends AlignmentViewport implements
setAlignment(al);
if (hiddenColumns != null)
{
setAlignment(al);
if (hiddenColumns != null)
{
- this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null
- && hiddenColumns.getHiddenColumns().size() > 0)
- {
- hasHiddenColumns = true;
- }
- else
- {
- hasHiddenColumns = false;
- }
+ colSel = hiddenColumns;
}
init();
}
}
init();
}
@@
-255,16
+242,7
@@
public class AlignViewport extends AlignmentViewport implements
setAlignment(al);
if (hiddenColumns != null)
{
setAlignment(al);
if (hiddenColumns != null)
{
- this.colSel = hiddenColumns;
- if (hiddenColumns.getHiddenColumns() != null
- && hiddenColumns.getHiddenColumns().size() > 0)
- {
- hasHiddenColumns = true;
- }
- else
- {
- hasHiddenColumns = false;
- }
+ colSel = hiddenColumns;
}
init();
}
}
init();
}
@@
-279,9
+257,9
@@
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);
@@
-329,10
+307,6
@@
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)
@@
-818,27
+792,6
@@
public class AlignViewport extends AlignmentViewport implements
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param b
- * DOCUMENT ME!
- */
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
public boolean getScaleAboveWrapped()
{
return scaleAboveWrapped;
public boolean getScaleAboveWrapped()
{
return scaleAboveWrapped;
@@
-1038,23
+991,6
@@
public class AlignViewport extends AlignmentViewport implements
shownpfeats = show;
}
shownpfeats = show;
}
- /**
- *
- * @return true if view has hidden rows
- */
- public boolean hasHiddenRows()
- {
- return hasHiddenRows;
- }
-
- /**
- *
- * @return true if view has hidden columns
- */
- public boolean hasHiddenColumns()
- {
- return hasHiddenColumns;
- }
/**
* when set, view will scroll to show the highlighted position
/**
* when set, view will scroll to show the highlighted position
@@
-1262,4
+1198,15
@@
public class AlignViewport extends AlignmentViewport implements
{
this.showAutocalculatedAbove = showAutocalculatedAbove;
}
{
this.showAutocalculatedAbove = showAutocalculatedAbove;
}
+
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
+ {
+ return annotationColumnSelectionState;
+ }
+
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser currentAnnotationColumnSelectionState)
+ {
+ this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
+ }
}
}