/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
{
oldcs = av.getGlobalColourScheme();
- if (av.alignment.getGroups() != null)
+ if (av.getAlignment().getGroups() != null)
{
oldgroupColours = new Hashtable();
- Vector allGroups = ap.av.alignment.getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+ for (SequenceGroup sg:ap.av.getAlignment().getGroups())
{
- sg = (SequenceGroup) allGroups.get(g);
if (sg.cs != null)
{
oldgroupColours.put(sg, sg.cs);
}
});
- if (av.alignment.getAlignmentAnnotation() == null)
+ if (av.getAlignment().getAlignmentAnnotation() == null)
{
return;
}
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
}
+ seqAssociated.setSelected(acg.isSeqAssociated());
}
-
adjusting = true;
- Vector list = new Vector();
- int index = 1;
- for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
- {
- String label = av.alignment.getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
- list.addElement(label);
- else
- list.addElement(label + "_" + (index++));
- }
-
- annotations = new JComboBox(list);
+ annotations = new JComboBox(getAnnotationItems(seqAssociated.isSelected()));
threshold.addItem("No Threshold");
threshold.addItem("Above Threshold");
adjusting = false;
changeColour();
- validate();
+ frame.invalidate();
+ frame.pack();
}
+ private Vector<String> getAnnotationItems(boolean isSeqAssociated) {
+ Vector<String> list = new Vector<String>();
+ int index = 1;
+ int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+ boolean enableSeqAss=false;
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ {
+ if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef==null)
+ {
+ if (isSeqAssociated)
+ {
+ continue;
+ }
+ } else {
+ enableSeqAss=true;
+ }
+ String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ if (!list.contains(label))
+ {anmap[list.size()] = i;
+ list.addElement(label);
+
+ }else {
+ if (!isSeqAssociated) {
+ anmap[list.size()] = i;
+ list.addElement(label + "_" + (index++));
+ }
+ }
+ }
+ seqAssociated.setEnabled(enableSeqAss);
+ annmap = new int[list.size()];
+ System.arraycopy(anmap, 0, annmap, 0, annmap.length);
+ return list;
+ }
private void setDefaultMinMax()
{
minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
thresholdIsMin_actionPerformed(actionEvent);
}
});
+ seqAssociated.setBackground(Color.white);
+ seqAssociated.setFont(JvSwingUtils.getLabelFont());
+ seqAssociated.setText("Per-sequence only");
+ seqAssociated.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ seqAssociated_actionPerformed(arg0);
+ }
+ });
+
this.setLayout(borderLayout1);
jPanel2.setLayout(new MigLayout("","[left][center][right]","[][][]"));
jPanel1.setBackground(Color.white);
jPanel1.add(ok);
jPanel1.add(cancel);
- jPanel2.add(annotations);
+ jPanel2.add(annotations, "grow, wrap");
+ jPanel2.add(seqAssociated);
jPanel2.add(currentColours);
JPanel colpanel = new JPanel(new FlowLayout());
colpanel.setBackground(Color.white);
colpanel.add(minColour);
colpanel.add(maxColour);
jPanel2.add(colpanel, "wrap");
-
jPanel2.add(threshold);
jPanel2.add(defColours,"skip 1, wrap");
jPanel2.add(thresholdIsMin);
jPanel2.add(thresholdValue, "grow");
this.add(jPanel1, java.awt.BorderLayout.SOUTH);
this.add(jPanel2, java.awt.BorderLayout.CENTER);
+ this.validate();
+ }
+
+ protected void seqAssociated_actionPerformed(ActionEvent arg0)
+ {
+ adjusting=true;
+ String cursel = (String) annotations.getSelectedItem();
+ boolean isvalid=false,isseqs=seqAssociated.isSelected();
+ this.annotations.removeAllItems();
+ for (String anitem:getAnnotationItems(seqAssociated.isSelected()))
+ {
+ if (anitem.equals( cursel) || (isseqs && cursel.startsWith(anitem)))
+ {
+ isvalid=true;
+ cursel=anitem;
+ }
+ this.annotations.addItem(anitem);
+ }
+ adjusting=false;
+ if (isvalid) { this.annotations.setSelectedItem(cursel); } else {
+ if (annotations.getItemCount()>0) {
+ annotations.setSelectedIndex(0);
+ }
+ }
}
protected void resetColours_actionPerformed(ActionEvent arg0)
}
JComboBox annotations;
-
+ int[] annmap;
JPanel minColour = new JPanel();
JPanel maxColour = new JPanel();
JCheckBox currentColours = new JCheckBox();
JCheckBox thresholdIsMin = new JCheckBox();
+
+ JCheckBox seqAssociated = new JCheckBox();
public void minColour_actionPerformed()
{
return;
}
- currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
- .getSelectedIndex()];
+ currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .getSelectedIndex()]];
int aboveThreshold = -1;
if (threshold.getSelectedItem().equals("Above Threshold"))
minColour.getBackground(), maxColour.getBackground(),
aboveThreshold);
}
+ acg.setSeqAssociated(seqAssociated.isSelected());
if (currentAnnotation.graphMin == 0f
&& currentAnnotation.graphMax == 0f)
av.setGlobalColourScheme(acg);
- if (av.alignment.getGroups() != null)
+ if (av.getAlignment().getGroups() != null)
{
- Vector allGroups = ap.av.alignment.getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+
+ for (SequenceGroup sg:ap.av.getAlignment().getGroups())
{
- sg = (SequenceGroup) allGroups.get(g);
-
if (sg.cs == null)
{
continue;
{
sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
aboveThreshold);
+ ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected());
+
}
else
{
sg.cs = new AnnotationColourGradient(currentAnnotation,
minColour.getBackground(), maxColour.getBackground(),
aboveThreshold);
+ ((AnnotationColourGradient)sg.cs).setSeqAssociated(seqAssociated.isSelected());
}
}
}
+ ap.alignmentChanged();
// ensure all associated views (overviews, structures, etc) are notified of updated colours.
ap.paintAlignment(true);
}
void reset()
{
av.setGlobalColourScheme(oldcs);
- if (av.alignment.getGroups() != null)
+ if (av.getAlignment().getGroups() != null)
{
- Vector allGroups = ap.av.alignment.getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
+
+ for (SequenceGroup sg:ap.av.getAlignment().getGroups())
{
- sg = (SequenceGroup) allGroups.get(g);
sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
}
}