import java.awt.event.ItemListener;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
-import java.util.Hashtable;
+import java.util.HashMap;
+import java.util.Map;
import java.util.Vector;
- import jalview.datamodel.AlignmentAnnotation;
- import jalview.datamodel.SequenceGroup;
- import jalview.schemes.AnnotationColourGradient;
- import jalview.schemes.ColourSchemeI;
- import jalview.util.MessageManager;
-
public class AnnotationColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
{
oldcs = av.getGlobalColourScheme();
if (av.getAlignment().getGroups() != null)
{
- oldgroupColours = new Hashtable();
+ oldgroupColours = new HashMap<SequenceGroup, ColourSchemeI>();
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs != null)
- {
- oldgroupColours.put(sg, sg.cs);
- }
- if (sg.getColourScheme() != null)
- {
- oldgroupColours.put(sg, sg.getColourScheme());
- }
- else
- {
- oldgroupColours.put(sg, "null");
- }
++ oldgroupColours.put(sg, sg.getColourScheme());
}
}
this.av = av;
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- if (sg.cs == null)
-
+ if (sg.getColourScheme() == null)
{
continue;
}
}
else
{
- sg.cs = new AnnotationColourGradient(currentAnnotation,
- minColour.getBackground(), maxColour.getBackground(),
- aboveThreshold);
+ sg.setColourScheme(new AnnotationColourGradient(
+ currentAnnotation, minColour.getBackground(), maxColour
+ .getBackground(), aboveThreshold));
}
-
}
}
{
for (SequenceGroup sg : ap.av.getAlignment().getGroups())
{
- sg.cs = oldgroupColours.get(sg);
- Object cs = oldgroupColours.get(sg);
- if (cs instanceof ColourSchemeI)
- {
- sg.setColourScheme((ColourSchemeI) cs);
- }
- else
- {
- // probably the "null" string we set it to if it was null originally.
- sg.setColourScheme(null);
- }
++ sg.setColourScheme(oldgroupColours.get(sg));
}
}
ap.paintAlignment(true);
--
}
@Override
ap.paintAlignment(true);
}
+ protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn, int selectedThresholdOption)
+ {
+
+ AnnotationColourGradient acg = null;
+ if (currentColours.isSelected())
+ {
+ acg = new AnnotationColourGradient(currentAnn,
+ av.getGlobalColourScheme(), selectedThresholdOption);
+ }
+ else
+ {
+ acg = new AnnotationColourGradient(currentAnn,
+ minColour.getBackground(), maxColour.getBackground(),
+ selectedThresholdOption);
+ }
+ acg.setSeqAssociated(seqAssociated.isSelected());
+
+ if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
+ {
+ acg.setPredefinedColours(true);
+ }
+
+ acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
+
+ av.setGlobalColourScheme(acg);
+
+ if (av.getAlignment().getGroups() != null)
+ {
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ if (currentColours.isSelected())
+ {
- sg.cs = new AnnotationColourGradient(currentAnn, sg.cs,
- selectedThresholdOption);
++ sg.setColourScheme(new AnnotationColourGradient(currentAnn, sg
++ .getColourScheme(), selectedThresholdOption));
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
+ }
+ else
+ {
- sg.cs = new AnnotationColourGradient(currentAnn,
++ sg.setColourScheme(new AnnotationColourGradient(currentAnn,
+ minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdOption);
++ selectedThresholdOption));
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
+ }
+ }
+ }
+ return false;
+ }
+
}
protected int[] annmap;
- protected boolean enableSeqAss = false;
-
- private AlignmentAnnotation currentAnnotation;
-
protected boolean adjusting = false;
-
++
+ protected JCheckBox currentColours = new JCheckBox();
+
+ protected JPanel minColour = new JPanel();
+
+ protected JPanel maxColour = new JPanel();
protected JCheckBox seqAssociated = new JCheckBox();
}
}
- protected AlignmentAnnotation getCurrentAnnotation()
- protected boolean colorAlignmContaining(AlignmentAnnotation currentAnn,
- int selectedThresholdOption)
++ public AlignmentAnnotation getCurrentAnnotation()
{
+ return currentAnnotation;
+ }
- AnnotationColourGradient acg = null;
- if (currentColours.isSelected())
- {
- acg = new AnnotationColourGradient(currentAnn,
- av.getGlobalColourScheme(), selectedThresholdOption);
- }
- else
- {
- acg = new AnnotationColourGradient(currentAnn,
- minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdOption);
- }
- acg.setSeqAssociated(seqAssociated.isSelected());
+ protected void setCurrentAnnotation(AlignmentAnnotation currentAnnotation)
+ {
+ this.currentAnnotation = currentAnnotation;
+ }
- if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
- {
- acg.setPredefinedColours(true);
- }
+ protected abstract void valueChanged(boolean updateAllAnnotation);
- acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+ protected abstract void updateView();
- av.setGlobalColourScheme(acg);
+ protected abstract void reset();
- if (av.getAlignment().getGroups() != null)
+ protected String getAnnotationMenuLabel(AlignmentAnnotation ann)
+ {
+ return annotationLabels.get(ann);
+ }
+
+ protected void jbInit()
+ {
+ ok.setOpaque(false);
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new ActionListener()
{
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed();
+ }
+ });
- for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ cancel.setOpaque(false);
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- if (sg.cs == null)
- {
- continue;
- }
+ cancel_actionPerformed();
+ }
+ });
- AnnotationColourGradient scheme = null;
- if (currentColours.isSelected())
- {
- scheme = new AnnotationColourGradient(currentAnn,
- sg.getColourScheme(), selectedThresholdOption);
- }
- else
- {
- scheme = new AnnotationColourGradient(currentAnn,
- minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdOption);
- }
- scheme.setSeqAssociated(seqAssociated.isSelected());
- sg.setColourScheme(scheme);
+ annotations.addItemListener(new ItemListener()
+ {
+ @Override
+ public void itemStateChanged(ItemEvent e)
+ {
+ selectedAnnotationChanged();
}
- }
- return false;
+ });
+ annotations.setToolTipText(MessageManager
+ .getString("info.select_annotation_row"));
+
+ threshold.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ threshold_actionPerformed();
+ }
+ });
+
+ thresholdValue.setEnabled(false);
+ thresholdValue.setColumns(7);
+ thresholdValue.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ thresholdValue_actionPerformed();
+ }
+ });
+
+ slider.setPaintLabels(false);
+ slider.setPaintTicks(true);
+ slider.setBackground(Color.white);
+ slider.setEnabled(false);
+ slider.setOpaque(false);
+ slider.setPreferredSize(new Dimension(100, 32));
}
- public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
+ public JComboBox<String> getThreshold()
{
- return currentAnnotation;
+ return threshold;
}
- public void setCurrentAnnotation(
- jalview.datamodel.AlignmentAnnotation currentAnnotation)
+ public void setThreshold(JComboBox<String> thresh)
{
- this.currentAnnotation = currentAnnotation;
+ this.threshold = thresh;
}
- public abstract void valueChanged(boolean updateAllAnnotation);
-
- public abstract void updateView();
+ public JComboBox<String> getAnnotations()
+ {
+ return annotations;
+ }
- public abstract void reset();
+ public void setAnnotations(JComboBox<String> anns)
+ {
+ this.annotations = anns;
+ }
}
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.FeatureColour;
--import jalview.schemes.ResidueColourScheme;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
import jalview.structure.StructureSelectionManager;
return matchedFile;
}
++ /**
++ * Populates the AnnotationColours xml for save. This captures the settings of
++ * the options in the 'Colour by Annotation' dialog.
++ *
++ * @param acg
++ * @param userColours
++ * @param jms
++ * @return
++ */
private AnnotationColours constructAnnotationColours(
AnnotationColourGradient acg, List<UserColourScheme> userColours,
JalviewModelSequence jms)
AnnotationColours ac = new AnnotationColours();
ac.setAboveThreshold(acg.getAboveThreshold());
ac.setThreshold(acg.getAnnotationThreshold());
- ac.setAnnotation(acg.getAnnotation());
- if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ // 2.10.2 save annotationId (unique) not annotation label
+ ac.setAnnotation(acg.getAnnotation().annotationId);
- if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
++ if (acg.getBaseColour() instanceof UserColourScheme)
{
ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
userColours, jms));
return af;
}
++ /**
++ * Reads saved data to restore Colour by Annotation settings
++ *
++ * @param viewAnnColour
++ * @param af
++ * @param al
++ * @param jms
++ * @param checkGroupAnnColour
++ * @return
++ */
private ColourSchemeI constructAnnotationColour(
AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
JalviewModelSequence jms, boolean checkGroupAnnColour)
{
boolean propagateAnnColour = false;
- AnnotationColourGradient cs = null;
- ColourSchemeI cs = null;
AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
if (checkGroupAnnColour && al.getGroups() != null
&& al.getGroups().size() > 0)
// pre 2.8.1 behaviour
// check to see if we should transfer annotation colours
propagateAnnColour = true;
- for (jalview.datamodel.SequenceGroup sg : al.getGroups())
+ for (SequenceGroup sg : al.getGroups())
{
- if (sg.cs instanceof AnnotationColourGradient)
+ if (sg.getColourScheme() instanceof AnnotationColourGradient)
{
propagateAnnColour = false;
}
}
}
- // int find annotation
- if (annAlignment.getAlignmentAnnotation() != null)
+
+ /*
- * pre 2.10.2: annotationId is AlignmentAnnotation.label
- * 2.10.2- : annotationId is AlignmentAnnotation.annotationId
++ * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
+ */
+ String annotationId = viewAnnColour.getAnnotation();
- AlignmentAnnotation annotation = annotationIds.get(annotationId);
++ AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
+
- if (annotation == null && annAlignment.getAlignmentAnnotation() != null)
++ /*
++ * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
++ */
++ if (matchedAnnotation == null && annAlignment.getAlignmentAnnotation() != null)
{
for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
{
- if (annAlignment.getAlignmentAnnotation()[i].label
- .equals(viewAnnColour.getAnnotation()))
+ if (annotationId
+ .equals(annAlignment.getAlignmentAnnotation()[i].label))
{
- annotation = annAlignment.getAlignmentAnnotation()[i];
- if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
- {
- annAlignment.getAlignmentAnnotation()[i]
- .setThreshold(new jalview.datamodel.GraphLine(
- viewAnnColour.getThreshold(), "Threshold",
- java.awt.Color.black)
-
- );
- }
-
- if (viewAnnColour.getColourScheme().equals(
- ResidueColourScheme.NONE))
- {
- cs = new AnnotationColourGradient(
- annAlignment.getAlignmentAnnotation()[i],
- new java.awt.Color(viewAnnColour.getMinColour()),
- new java.awt.Color(viewAnnColour.getMaxColour()),
- viewAnnColour.getAboveThreshold());
- }
- else if (viewAnnColour.getColourScheme().startsWith("ucs"))
- {
- cs = new AnnotationColourGradient(
- annAlignment.getAlignmentAnnotation()[i],
- getUserColourScheme(jms,
- viewAnnColour.getColourScheme()),
- viewAnnColour.getAboveThreshold());
- }
- else
- {
- cs = new AnnotationColourGradient(
- annAlignment.getAlignmentAnnotation()[i],
- ColourSchemeProperty.getColourScheme(al,
- viewAnnColour.getColourScheme()),
- viewAnnColour.getAboveThreshold());
- }
- if (viewAnnColour.hasPerSequence())
- {
- ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
- .isPerSequence());
- }
- if (viewAnnColour.hasPredefinedColours())
- {
- ((AnnotationColourGradient) cs)
- .setPredefinedColours(viewAnnColour
- .isPredefinedColours());
- }
- if (propagateAnnColour && al.getGroups() != null)
- {
- // Also use these settings for all the groups
- for (int g = 0; g < al.getGroups().size(); g++)
- {
- jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
-
- if (sg.cs == null)
- {
- continue;
- }
++ matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
+ break;
+ }
+ }
+ }
- if (annotation == null)
++ if (matchedAnnotation == null)
+ {
+ System.err.println("Failed to match annotation colour scheme for "
+ + annotationId);
+ return null;
+ }
- if (annotation.getThreshold() == null)
++ if (matchedAnnotation.getThreshold() == null)
+ {
- annotation.setThreshold(new GraphLine(viewAnnColour.getThreshold(),
++ matchedAnnotation.setThreshold(new GraphLine(viewAnnColour.getThreshold(),
+ "Threshold", Color.black));
+ }
- /*
- * if (viewAnnColour.getColourScheme().equals(ResidueColourScheme.NONE)) { sg.cs =
- * new AnnotationColourGradient(
- * annAlignment.getAlignmentAnnotation()[i], new
- * java.awt.Color(viewAnnColour. getMinColour()), new
- * java.awt.Color(viewAnnColour. getMaxColour()),
- * viewAnnColour.getAboveThreshold()); } else
- */
- {
- sg.setColourScheme(new AnnotationColourGradient(
- annAlignment.getAlignmentAnnotation()[i], sg
- .getColourScheme(), viewAnnColour
- .getAboveThreshold()));
- if (cs instanceof AnnotationColourGradient)
- {
- if (viewAnnColour.hasPerSequence())
- {
- ((AnnotationColourGradient) cs)
- .setSeqAssociated(viewAnnColour.isPerSequence());
- }
- if (viewAnnColour.hasPredefinedColours())
- {
- ((AnnotationColourGradient) cs)
- .setPredefinedColours(viewAnnColour
- .isPredefinedColours());
- }
- }
- }
++ AnnotationColourGradient cs = null;
+ if (viewAnnColour.getColourScheme().equals("None"))
+ {
- cs = new AnnotationColourGradient(annotation, new Color(
++ cs = new AnnotationColourGradient(matchedAnnotation, new Color(
+ viewAnnColour.getMinColour()), new Color(
+ viewAnnColour.getMaxColour()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+ {
- cs = new AnnotationColourGradient(annotation, getUserColourScheme(
++ cs = new AnnotationColourGradient(matchedAnnotation, getUserColourScheme(
+ jms, viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else
+ {
- cs = new AnnotationColourGradient(annotation,
- ColourSchemeProperty.getColour(al,
++ cs = new AnnotationColourGradient(matchedAnnotation,
++ ColourSchemeProperty.getColourScheme(al,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
- if (viewAnnColour.hasPerSequence())
- {
- cs.setSeqAssociated(viewAnnColour.isPerSequence());
- }
- if (viewAnnColour.hasPredefinedColours())
- {
- cs.setPredefinedColours(viewAnnColour.isPredefinedColours());
- }
+
- }
- }
++ boolean perSequenceOnly = viewAnnColour.isPerSequence();
++ boolean useOriginalColours = viewAnnColour.isPredefinedColours();
++ cs.setSeqAssociated(perSequenceOnly);
++ cs.setPredefinedColours(useOriginalColours);
+
- break;
+ if (propagateAnnColour && al.getGroups() != null)
+ {
+ // Also use these settings for all the groups
+ for (int g = 0; g < al.getGroups().size(); g++)
+ {
+ SequenceGroup sg = al.getGroups().get(g);
-
- if (sg.cs == null)
++ if (sg.getGroupColourScheme() == null)
+ {
+ continue;
}
- /*
- * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
- * new AnnotationColourGradient(
- * annAlignment.getAlignmentAnnotation()[i], new
- * java.awt.Color(viewAnnColour. getMinColour()), new
- * java.awt.Color(viewAnnColour. getMaxColour()),
- * viewAnnColour.getAboveThreshold()); } else
- *
- {*/
- sg.cs = new AnnotationColourGradient(annotation, sg.cs,
++ AnnotationColourGradient groupScheme = new AnnotationColourGradient(
++ matchedAnnotation, sg.getColourScheme(),
+ viewAnnColour.getAboveThreshold());
- if (cs instanceof AnnotationColourGradient)
- {
- if (viewAnnColour.hasPerSequence())
- {
- cs.setSeqAssociated(viewAnnColour.isPerSequence());
- }
- if (viewAnnColour.hasPredefinedColours())
- {
- cs.setPredefinedColours(viewAnnColour.isPredefinedColours());
- }
- }
++ sg.setColourScheme(groupScheme);
++ groupScheme.setSeqAssociated(perSequenceOnly);
++ groupScheme.setPredefinedColours(useOriginalColours);
}
}
return cs;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
- import jalview.io.FileFormat;
+ import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.io.FileFormatI;
+ import jalview.io.FileFormats;
import jalview.io.FormatAdapter;
import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.AnnotationColourGradient;
import jalview.schemes.Blosum62ColourScheme;
- import jalview.schemes.BuriedColourScheme;
- import jalview.schemes.ClustalxColourScheme;
- import jalview.schemes.HelixColourScheme;
- import jalview.schemes.HydrophobicColourScheme;
- import jalview.schemes.NucleotideColourScheme;
+ import jalview.schemes.ColourSchemeI;
+ import jalview.schemes.ColourSchemes;
import jalview.schemes.PIDColourScheme;
- import jalview.schemes.PurinePyrimidineColourScheme;
- import jalview.schemes.StrandColourScheme;
- import jalview.schemes.TaylorColourScheme;
- import jalview.schemes.TurnColourScheme;
- import jalview.schemes.UserColourScheme;
- import jalview.schemes.ZappoColourScheme;
+ import jalview.schemes.ResidueColourScheme;
import jalview.util.GroupUrlLink;
import jalview.util.GroupUrlLink.UrlStringTooLongException;
import jalview.util.MessageManager;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
++import jalview.renderer.AnnotationRenderer;
++import jalview.util.Comparison;
+
+ import java.awt.Color;
+ import java.util.IdentityHashMap;
+ import java.util.Map;
public class AnnotationColourGradient extends FollowerColourScheme
{
public static final int ABOVE_THRESHOLD = 1;
- public AlignmentAnnotation annotation;
+ private final AlignmentAnnotation annotation;
- int aboveAnnotationThreshold = -1;
+ private final int aboveAnnotationThreshold;
- private boolean thresholdIsMinMax = false;
+ public boolean thresholdIsMinMax = false;
- GraphLine annotationThreshold;
+ private GraphLine annotationThreshold;
- float r1, g1, b1, rr, gg, bb;
+ private int redMin;
+
+ private int greenMin;
+
+ private int blueMin;
+
+ private int redRange;
+
+ private int greenRange;
+
+ private int blueRange;
private boolean predefinedColours = false;
*/
private boolean noGradient = false;
- IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
+ private IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
@Override
- public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ public ColourSchemeI getInstance(AnnotatedCollectionI sg,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
AnnotationColourGradient acg = new AnnotationColourGradient(annotation,
}
/**
-- * DOCUMENT ME!
++ * Returns the colour for a given character and position in a sequence
*
-- * @param n
-- * DOCUMENT ME!
++ * @param c
++ * the residue character
* @param j
-- * DOCUMENT ME!
-- *
-- * @return DOCUMENT ME!
++ * the aligned position
++ * @param seq
++ * the sequence
++ * @return
*/
@Override
public Color findColour(char c, int j, SequenceI seq)
{
-- Color currentColour = Color.white;
- AlignmentAnnotation annotation = (seqAssociated && seqannot != null ? seqannot
++ /*
++ * locate the annotation we are configured to colour by
++ */
+ AlignmentAnnotation ann = (seqAssociated && seqannot != null ? seqannot
.get(seq) : this.annotation);
- if (ann == null)
- if (annotation == null)
++
++ /*
++ * if gap or no annotation at position, no colour (White)
++ */
++ if (ann == null || ann.annotations == null
++ || j >= ann.annotations.length || ann.annotations[j] == null
++ || Comparison.isGap(c))
{
-- return currentColour;
++ return Color.white;
}
- if ((threshold == 0) || aboveThreshold(c, j))
- // if ((threshold == 0) || aboveThreshold(c, j))
- // {
- if (annotation.annotations != null && j < annotation.annotations.length
- && annotation.annotations[j] != null
- && !jalview.util.Comparison.isGap(c))
++
++ Annotation aj = ann.annotations[j];
++ // 'use original colours' => colourScheme != null
++ // -> look up colour to be used
++ // predefined colours => preconfigured shading
++ // -> only use original colours reference if thresholding enabled &
++ // minmax exists
++ // annotation.hasIcons => null or black colours replaced with glyph
++ // colours
++ // -> reuse original colours if present
++ // -> if thresholding enabled then return colour on non-whitespace glyph
++
++ /*
++ * if threshold applies, and annotation fails the test - no colour (white)
++ */
++ if (annotationThreshold != null)
{
- if (ann.annotations != null && j < ann.annotations.length
- && ann.annotations[j] != null
- && !jalview.util.Comparison.isGap(c))
- Annotation aj = annotation.annotations[j];
- // 'use original colours' => colourScheme != null
- // -> look up colour to be used
- // predefined colours => preconfigured shading
- // -> only use original colours reference if thresholding enabled &
- // minmax exists
- // annotation.hasIcons => null or black colours replaced with glyph
- // colours
- // -> reuse original colours if present
- // -> if thresholding enabled then return colour on non-whitespace glyph
-
- if (aboveAnnotationThreshold == NO_THRESHOLD
- || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
- : aj.value <= annotationThreshold.value)))
++ if ((aboveAnnotationThreshold == ABOVE_THRESHOLD && aj.value >= annotationThreshold.value)
++ || (aboveAnnotationThreshold == BELOW_THRESHOLD && aj.value > annotationThreshold.value))
{
- Annotation aj = ann.annotations[j];
- // 'use original colours' => colourScheme != null
- // -> look up colour to be used
- // predefined colours => preconfigured shading
- // -> only use original colours reference if thresholding enabled &
- // minmax exists
- // annotation.hasIcons => null or black colours replaced with glyph
- // colours
- // -> reuse original colours if present
- // -> if thresholding enabled then return colour on non-whitespace glyph
-
- if (aboveAnnotationThreshold == NO_THRESHOLD
- || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
- : aj.value <= annotationThreshold.value)))
- if (predefinedColours && aj.colour != null
- && !aj.colour.equals(Color.black))
- {
- currentColour = aj.colour;
- }
- else if (annotation.hasIcons
- && annotation.graph == AlignmentAnnotation.NO_GRAPH)
++ return Color.white;
++ }
++ }
++
++ /*
++ * If 'use original colours' then return the colour of the annotation
++ * at the aligned position - computed using the background colour scheme
++ */
++ if (predefinedColours && aj.colour != null
++ && !aj.colour.equals(Color.black))
++ {
++ return aj.colour;
++ }
++
++ Color result = Color.white;
++ if (ann.hasIcons && ann.graph == AlignmentAnnotation.NO_GRAPH)
++ {
++ /*
++ * secondary structure symbol colouring
++ */
++ if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
++ && aj.secondaryStructure != '-')
++ {
++ if (getColourScheme() != null)
{
- if (predefinedColours && aj.colour != null
- && !aj.colour.equals(Color.black))
- {
- currentColour = aj.colour;
- }
- else if (ann.hasIcons
- && ann.graph == AlignmentAnnotation.NO_GRAPH)
- {
- if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
- && aj.secondaryStructure != '-')
- {
- if (colourScheme != null)
- {
- currentColour = colourScheme.findColour(c, j, seq);
- }
- else
- {
- if (ann.isRNA())
- {
- currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
- }
- else
- {
- currentColour = ann.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
- : ann.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
- : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
- }
- }
- }
- else
- {
- //
- return Color.white;
- }
- }
- else if (noGradient)
- if (aj.secondaryStructure > ' ' && aj.secondaryStructure != '.'
- && aj.secondaryStructure != '-')
- {
- if (getColourScheme() != null)
- {
- currentColour = getColourScheme().findColour(c, j, seq, null,
- 0f);
- }
- else
- {
- if (annotation.isRNA())
- {
- currentColour = ColourSchemeProperty.rnaHelices[(int) aj.value];
- }
- else
- {
- currentColour = annotation.annotations[j].secondaryStructure == 'H' ? jalview.renderer.AnnotationRenderer.HELIX_COLOUR
- : annotation.annotations[j].secondaryStructure == 'E' ? jalview.renderer.AnnotationRenderer.SHEET_COLOUR
- : jalview.renderer.AnnotationRenderer.STEM_COLOUR;
- }
- }
- }
- else
- {
- //
- return Color.white;
- }
++ result = getColourScheme().findColour(c, j, seq, null, 0f);
+ }
- else if (noGradient)
++ else
+ {
- if (getColourScheme() != null)
++ if (ann.isRNA())
{
- if (colourScheme != null)
- {
- currentColour = colourScheme.findColour(c, j, seq);
- }
- else
- {
- if (aj.colour != null)
- {
- currentColour = aj.colour;
- }
- }
- currentColour = getColourScheme().findColour(c, j, seq, null,
- 0f);
++ result = ColourSchemeProperty.rnaHelices[(int) aj.value];
}
else
{
- currentColour = shadeCalculation(ann, j);
- if (aj.colour != null)
- {
- currentColour = aj.colour;
- }
++ result = ann.annotations[j].secondaryStructure == 'H' ? AnnotationRenderer.HELIX_COLOUR
++ : ann.annotations[j].secondaryStructure == 'E' ? AnnotationRenderer.SHEET_COLOUR
++ : AnnotationRenderer.STEM_COLOUR;
}
}
- if (conservationColouring)
- else
++ }
++ else
++ {
++ return Color.white;
++ }
++ }
++ else if (noGradient)
++ {
++ if (getColourScheme() != null)
++ {
++ result = getColourScheme().findColour(c, j, seq, null, 0f);
++ }
++ else
++ {
++ if (aj.colour != null)
{
- currentColour = applyConservation(currentColour, j);
- currentColour = shadeCalculation(annotation, j);
++ result = aj.colour;
}
}
- // if (conservationColouring)
- // {
- // currentColour = applyConservation(currentColour, j);
- // }
}
- return currentColour;
- // }
- return currentColour;
++ else
++ {
++ result = shadeCalculation(ann, j);
++ }
++
++ return result;
}
- private Color shadeCalculation(AlignmentAnnotation annotation, int j)
+ /**
+ * Returns a graduated colour for the annotation at the given column. If there
+ * is a threshold value, and it is used as the top/bottom of the colour range,
+ * and the value satisfies the threshold condition, then a colour
+ * proportionate to the range from the threshold is calculated. For all other
+ * cases, a colour proportionate to the annotation's min-max range is
+ * calulated. Note that thresholding is _not_ done here (a colour is computed
+ * even if threshold is not passed).
+ *
+ * @param ann
+ * @param col
+ * @return
+ */
+ Color shadeCalculation(AlignmentAnnotation ann, int col)
{
-
- // calculate a shade
float range = 1f;
- if (thresholdIsMinMax
- && annotation.threshold != null
+ float value = ann.annotations[col].value;
+ if (thresholdIsMinMax && ann.threshold != null
&& aboveAnnotationThreshold == ABOVE_THRESHOLD
- && annotation.annotations[j].value >= annotation.threshold.value)
+ && value >= ann.threshold.value)
{
- range = (annotation.annotations[j].value - annotation.threshold.value)
- / (annotation.graphMax - annotation.threshold.value);
+ range = (value - ann.threshold.value)
+ / (ann.graphMax - ann.threshold.value);
}
- else if (thresholdIsMinMax && annotation.threshold != null
+ else if (thresholdIsMinMax && ann.threshold != null
&& aboveAnnotationThreshold == BELOW_THRESHOLD
- && annotation.annotations[j].value >= annotation.graphMin)
+ && value <= ann.threshold.value)
{
- range = (annotation.annotations[j].value - annotation.graphMin)
- / (annotation.threshold.value - annotation.graphMin);
+ range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
}
else
{
seqAssociated = sassoc;
}
+ public boolean isThresholdIsMinMax()
+ {
+ return thresholdIsMinMax;
+ }
+
- public void setThresholdIsMinMax(boolean thresholdIsMinMax)
++ public void setThresholdIsMinMax(boolean minMax)
++ {
++ this.thresholdIsMinMax = minMax;
++ }
++
+ @Override
+ public String getSchemeName()
+ {
+ return "Annotation";
+ }
+
+ @Override
+ public boolean isSimple()
{
- this.thresholdIsMinMax = thresholdIsMinMax;
+ return false;
}
}
git://source.jalview.org / jalview.git / commitdiff