*/
public class AlignViewport extends AlignmentViewport implements SelectionSource, VamsasSource, AlignViewportI
{
- private static final int RIGHT_JUSTIFY = 1;
-
int startRes;
int endRes;
boolean showAnnotation = true;
- boolean colourAppliesToAllGroups = true;
-
- boolean conservationColourSelected = false;
-
- boolean abovePIDThreshold = false;
-
int charHeight;
int charWidth;
boolean seqNameItalics;
- int threshold;
-
- int increment;
NJTree currentTree = null;
return sq;
}
-
- /**
- * GUI state
- *
- * @return true if conservation based shading is enabled
- */
- public boolean getConservationSelected()
- {
- return conservationColourSelected;
- }
-
- /**
- * GUI state
- *
- * @param b
- * enable conservation based shading
- */
- public void setConservationSelected(boolean b)
- {
- conservationColourSelected = b;
- }
-
- /**
- * GUI state
- *
- * @return true if percent identity threshold is applied to shading
- */
- public boolean getAbovePIDThreshold()
- {
- return abovePIDThreshold;
- }
-
- /**
- * GUI state
- *
- *
- * @param b
- * indicate if percent identity threshold is applied to shading
- */
- public void setAbovePIDThreshold(boolean b)
- {
- abovePIDThreshold = b;
- }
-
/**
* DOCUMENT ME!
*
/**
* DOCUMENT ME!
*
- * @param thresh
- * DOCUMENT ME!
- */
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getThreshold()
- {
- return threshold;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param inc
- * DOCUMENT ME!
- */
- public void setIncrement(int inc)
- {
- increment = inc;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getIncrement()
- {
- return increment;
- }
-
- /**
- * DOCUMENT ME!
- *
* @return DOCUMENT ME!
*/
public ColumnSelection getColumnSelection()
/**
* DOCUMENT ME!
*
- * @param b
- * DOCUMENT ME!
- */
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean getColourAppliesToAllGroups()
- {
- return colourAppliesToAllGroups;
- }
-
- /**
- * DOCUMENT ME!
- *
* @return DOCUMENT ME!
*/
public boolean getShowJVSuffix()
*/
public long[] getUndoRedoHash()
{
+ // TODO: JAL-1126
if (historyList == null || redoList == null)
return new long[]
{ -1, -1 };
public void updateSequenceIdColours()
{
- Vector groups = alignment.getGroups();
if (sequenceColours == null)
{
sequenceColours = new Hashtable();
}
- for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
+ for (SequenceGroup sg:alignment.getGroups())
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
if (sg.idColour != null)
{
- Vector sqs = sg.getSequences(getHiddenRepSequences());
- for (int s = 0, sSize = sqs.size(); s < sSize; s++)
+ for (SequenceI s:sg.getSequences(getHiddenRepSequences()))
{
- sequenceColours.put(sqs.elementAt(s), sg.idColour);
+ sequenceColours.put(s, sg.idColour);
}
}
}
{
return validCharWidth;
}
+ private jalview.ws.jws2.dm.AAConsSettings preferredAAConsSettings;
+
+ public jalview.ws.jws2.dm.AAConsSettings getPreferredAAConsSettings()
+ {
+ return preferredAAConsSettings;
+ }
+ public void setPreferredAAConsSettings(jalview.ws.jws2.dm.AAConsSettings aaConsSettings)
+ {
+ preferredAAConsSettings=aaConsSettings;
+ }
+
}