*/
package jalview.gui;
-import java.util.*;
-
-import java.awt.*;
-
-import jalview.analysis.*;
-import jalview.api.AlignCalcManagerI;
+import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.OOMHandlerI;
-
-import jalview.bin.*;
-
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.UserColourScheme;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
import jalview.viewmodel.AlignmentViewport;
-import jalview.workers.AlignCalcManager;
-import jalview.workers.ConsensusThread;
-import jalview.workers.ConservationThread;
-import jalview.workers.StrucConsensusThread;
+import jalview.ws.params.AutoCalcSetting;
+
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.Stack;
+import java.util.Vector;
/**
* DOCUMENT ME!
*/
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 Hashtable<String, AutoCalcSetting> calcIdParams=new Hashtable<String, AutoCalcSetting>();
+ public AutoCalcSetting getCalcIdSettingsFor(String calcId)
+ {
+ return calcIdParams.get(calcId);
+ }
+
+ public void setCalcIdSettingsFor(String calcId, AutoCalcSetting settings, boolean needsUpdate)
+ {
+ calcIdParams.put(calcId, settings);
+ // TODO: create a restart list to trigger any calculations that need to be restarted after load
+ // calculator.getRegisteredWorkersOfClass(settings.getWorkerClass())
+ if (needsUpdate)
+ {
+ Cache.log.debug("trigger update for "+calcId);
+ }
+ }
}