+/*
+ * 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.analysis.AnnotationFilterParameter;
-import jalview.api.analysis.AnnotationFilterParameter.SearchableAnnotationField;
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 java.awt.event.ActionEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
-import java.util.List;
import java.util.Vector;
+import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
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;
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;
public void ok_actionPerformed(ActionEvent e)
{
- updateView();
try
{
frame.setClosed(true);
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,
return false;
}
- protected boolean filterAnnotations(Annotation[] annotations,
- AnnotationFilterParameter filterParams, ColumnSelection cs)
- {
- av.showAllHiddenColumns();
- cs.clear();
- int count = 0;
- do
- {
- if (annotations[count] != null)
- {
-
- boolean itemMatched = false;
-
- if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
- && annotations[count].value > currentAnnotation.threshold.value)
- {
- itemMatched = true;
- }
- if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
- && annotations[count].value < currentAnnotation.threshold.value)
- {
- itemMatched = true;
- }
-
- if (filterParams.isFilterAlphaHelix()
- && annotations[count].secondaryStructure == 'H')
- {
- itemMatched = true;
- }
-
- if (filterParams.isFilterBetaSheet()
- && annotations[count].secondaryStructure == 'E')
- {
- itemMatched = true;
- }
-
- if (filterParams.isFilterTurn()
- && annotations[count].secondaryStructure == 'S')
- {
- itemMatched = true;
- }
-
- String regexSearchString = filterParams.getRegexString();
- if (regexSearchString != null
- && !filterParams.getRegexSearchFields().isEmpty())
- {
- List<SearchableAnnotationField> fields = filterParams
- .getRegexSearchFields();
- try
- {
- if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
- && annotations[count].displayCharacter
- .matches(regexSearchString))
- {
- itemMatched = true;
- }
- } catch (java.util.regex.PatternSyntaxException pse)
- {
- if (annotations[count].displayCharacter
- .equals(regexSearchString))
- {
- itemMatched = true;
- }
- }
- if (fields.contains(SearchableAnnotationField.DESCRIPTION)
- && annotations[count].description != null
- && annotations[count].description
- .matches(regexSearchString))
- {
- itemMatched = true;
- }
- }
-
- if (itemMatched)
- {
- cs.addElement(count);
- }
- }
- count++;
- } while (count < annotations.length);
- return false;
- }
-
public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
{
return currentAnnotation;