+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
-import jalview.api.AnnotationRowFilterI;
import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceGroup;
import jalview.schemes.AnnotationColourGradient;
import jalview.util.MessageManager;
-import java.awt.event.ActionEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.util.Vector;
+import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
import javax.swing.event.ChangeListener;
@SuppressWarnings("serial")
-public abstract class AnnotationRowFilter extends JPanel implements
- AnnotationRowFilterI
+public abstract class AnnotationRowFilter extends JPanel
{
protected AlignViewport av;
protected boolean enableSeqAss = false;
- private jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ private AlignmentAnnotation currentAnnotation;
protected boolean adjusting = false;
protected JTextField thresholdValue = new JTextField(20);
protected JInternalFrame frame;
+
+ protected JButton ok = new JButton();
+
+ protected JButton cancel = new JButton();
+
/**
* enabled if the user is dragging the slider - try to keep updates to a
* minimun
});
}
-
public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
{
this.av = av;
}
- @Override
public Vector<String> getAnnotationItems(boolean isSeqAssociated)
{
Vector<String> list = new Vector<String>();
enableSeqAss = true;
}
String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ // add associated sequence ID if available
+ if (!isSeqAssociated
+ && av.getAlignment().getAlignmentAnnotation()[i].sequenceRef != null)
+ {
+ label = label
+ + "_"
+ + av.getAlignment().getAlignmentAnnotation()[i].sequenceRef
+ .getName();
+ }
+ // make label unique
if (!list.contains(label))
{
anmap[list.size()] = i;
list.add(label);
-
}
else
{
}
}
}
- // seqAssociated.setEnabled(enableSeqAss);
this.annmap = new int[list.size()];
System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
return list;
seqAssociated.setEnabled(enableSeqAss);
}
- public void ok_actionPerformed(ActionEvent e)
+ public void ok_actionPerformed()
{
- updateView();
try
{
frame.setClosed(true);
}
}
- public void cancel_actionPerformed(ActionEvent e)
+ public void cancel_actionPerformed()
{
reset();
ap.paintAlignment(true);
}
}
- public void thresholdCheck_actionPerformed(ActionEvent e)
+ public void thresholdCheck_actionPerformed()
{
updateView();
}
- public void annotations_actionPerformed(ActionEvent e)
+ public void annotations_actionPerformed()
{
updateView();
}
- public void threshold_actionPerformed(ActionEvent e)
+ public void threshold_actionPerformed()
{
updateView();
}
- public void thresholdValue_actionPerformed(ActionEvent e)
+ public void thresholdValue_actionPerformed()
{
try
{
}
}
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ public void thresholdIsMin_actionPerformed()
{
updateView();
}
protected void populateThresholdComboBox(JComboBox<String> threshold)
{
threshold.addItem(MessageManager
- .getString("label.threshold_feature_no_thereshold"));
+ .getString("label.threshold_feature_no_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_above_thereshold"));
+ .getString("label.threshold_feature_above_threshold"));
threshold.addItem(MessageManager
- .getString("label.threshold_feature_below_thereshold"));
+ .getString("label.threshold_feature_below_threshold"));
}
- protected void seqAssociated_actionPerformed(ActionEvent arg0,
- JComboBox<String> annotations, JCheckBox seqAssociated)
+ protected void seqAssociated_actionPerformed(JComboBox<String> annotations)
{
adjusting = true;
String cursel = (String) annotations.getSelectedItem();
}
}
- protected boolean colorAlignmContaining(
- AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
+ protected boolean colorAlignmContaining(AlignmentAnnotation currentAnn,
+ int selectedThresholdOption)
{
AnnotationColourGradient acg = null;
if (currentColours.isSelected())
{
- acg = new AnnotationColourGradient(currentAnnotation,
- av.getGlobalColourScheme(), selectedThresholdItem);
+ acg = new AnnotationColourGradient(currentAnn,
+ av.getGlobalColourScheme(), selectedThresholdOption);
}
else
{
- acg = new AnnotationColourGradient(currentAnnotation,
+ acg = new AnnotationColourGradient(currentAnn,
minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdItem);
+ selectedThresholdOption);
}
acg.setSeqAssociated(seqAssociated.isSelected());
- if (currentAnnotation.graphMin == 0f
- && currentAnnotation.graphMax == 0f)
+ if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
{
acg.setPredefinedColours(true);
}
if (currentColours.isSelected())
{
- sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
- selectedThresholdItem);
+ sg.cs = new AnnotationColourGradient(currentAnn, sg.cs,
+ selectedThresholdOption);
((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
.isSelected());
}
else
{
- sg.cs = new AnnotationColourGradient(currentAnnotation,
+ sg.cs = new AnnotationColourGradient(currentAnn,
minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdItem);
+ selectedThresholdOption);
((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
.isSelected());
}
return false;
}
- protected boolean markColumnsContaining(
- AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
- {
- try
- {
- if (currentAnnotation != null)
- {
- Annotation[] annotations = currentAnnotation.annotations;
- ColumnSelection cs = av.getColumnSelection();
- cs.clear();
- if (thresholdComparisonType == AnnotationColourGradient.NO_THRESHOLD)
- {
- int count = 0;
- do
- {
- if (annotations[count] != null)
- {
- if (currentAnnotation.label.equals("Secondary Structure")
- && annotations[count].secondaryStructure != ' ')
- {
- cs.addElement(count);
- }
- else if (currentAnnotation.label
- .equals("Iron Sulphur Contacts"))
- {
- cs.addElement(count);
- }
- else if (annotations[count].value != 0.0)
- {
- cs.addElement(count);
- }
-
- }
- count++;
- } while (count < annotations.length);
- }
- else
- {
- int count = 0;
- do
- {
- if (annotations[count] != null)
- {
- if (thresholdComparisonType == AnnotationColourGradient.ABOVE_THRESHOLD)
- {
- if (annotations[count].value > currentAnnotation.threshold.value)
- {
- cs.addElement(count);
- }
- }
- else if (thresholdComparisonType == AnnotationColourGradient.BELOW_THRESHOLD)
- {
- if (annotations[count].value < currentAnnotation.threshold.value)
- {
- cs.addElement(count);
- }
- }
-
- }
- count++;
- } while (count < annotations.length);
- }
- }
-
- return true;
- } catch (Exception e)
- {
- e.printStackTrace();
- return false;
- }
- }
-
public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
{
return currentAnnotation;
this.currentAnnotation = currentAnnotation;
}
+ public abstract void valueChanged(boolean updateAllAnnotation);
+
+ public abstract void updateView();
+
+ public abstract void reset();
}
git://source.jalview.org / jalview.git / blobdiff