X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=c8bd69c8389cd2f3a97f41205b16379de47990a6;hb=eed52865f3bf3e1d4d8c7f08fba483ecce6d83e6;hp=ed59ef60188711fd1fd5442fd04112ccc88d1705;hpb=c03d2649512cdc491a46dda1d1370273241b5253;p=jalview.git
diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index ed59ef6..c8bd69c 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -1,22 +1,36 @@
+/*
+ * 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 .
+ * 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.AnnotationFilterParameter;
-import jalview.datamodel.AnnotationFilterParameter.SearchableAnnotationField;
-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.List;
import java.util.Vector;
+import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JInternalFrame;
@@ -27,8 +41,7 @@ import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
@SuppressWarnings("serial")
-public abstract class AnnotationRowFilter extends JPanel implements
- AnnotationRowFilterI
+public abstract class AnnotationRowFilter extends JPanel
{
protected AlignViewport av;
@@ -38,7 +51,7 @@ public abstract class AnnotationRowFilter extends JPanel implements
protected boolean enableSeqAss = false;
- private jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ private AlignmentAnnotation currentAnnotation;
protected boolean adjusting = false;
@@ -57,6 +70,11 @@ public abstract class AnnotationRowFilter extends JPanel implements
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
@@ -112,7 +130,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
});
}
-
public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
{
this.av = av;
@@ -124,7 +141,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
}
- @Override
public Vector getAnnotationItems(boolean isSeqAssociated)
{
Vector list = new Vector();
@@ -144,11 +160,20 @@ public abstract class AnnotationRowFilter extends JPanel implements
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
{
@@ -183,9 +208,8 @@ public abstract class AnnotationRowFilter extends JPanel implements
seqAssociated.setEnabled(enableSeqAss);
}
- public void ok_actionPerformed(ActionEvent e)
+ public void ok_actionPerformed()
{
- updateView();
try
{
frame.setClosed(true);
@@ -194,7 +218,7 @@ public abstract class AnnotationRowFilter extends JPanel implements
}
}
- public void cancel_actionPerformed(ActionEvent e)
+ public void cancel_actionPerformed()
{
reset();
ap.paintAlignment(true);
@@ -206,22 +230,22 @@ public abstract class AnnotationRowFilter extends JPanel implements
}
}
- 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
{
@@ -233,7 +257,7 @@ public abstract class AnnotationRowFilter extends JPanel implements
}
}
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ public void thresholdIsMin_actionPerformed()
{
updateView();
}
@@ -241,15 +265,14 @@ public abstract class AnnotationRowFilter extends JPanel implements
protected void populateThresholdComboBox(JComboBox 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 annotations, JCheckBox seqAssociated)
+ protected void seqAssociated_actionPerformed(JComboBox annotations)
{
adjusting = true;
String cursel = (String) annotations.getSelectedItem();
@@ -306,26 +329,25 @@ public abstract class AnnotationRowFilter extends JPanel implements
}
}
- 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);
}
@@ -346,17 +368,17 @@ public abstract class AnnotationRowFilter extends JPanel implements
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());
}
@@ -366,89 +388,6 @@ public abstract class AnnotationRowFilter extends JPanel implements
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 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;
@@ -460,4 +399,9 @@ public abstract class AnnotationRowFilter extends JPanel implements
this.currentAnnotation = currentAnnotation;
}
+ public abstract void valueChanged(boolean updateAllAnnotation);
+
+ public abstract void updateView();
+
+ public abstract void reset();
}