X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationRowFilter.java;h=166e1ade7cea64dad28db756c90f646123be1fc3;hb=6129931bfa23eec90e6556a4d0412ef34aff5759;hp=21c91d85a014989a050443abe2591df8e30fff16;hpb=1d4b37e9bd54c095aa00e643b741c931eb61c58b;p=jalview.git
diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 21c91d8..166e1ad 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -1,3 +1,23 @@
+/*
+ * 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.datamodel.AlignmentAnnotation;
@@ -6,7 +26,6 @@ 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;
@@ -32,7 +51,7 @@ public abstract class AnnotationRowFilter extends JPanel
protected boolean enableSeqAss = false;
- private jalview.datamodel.AlignmentAnnotation currentAnnotation;
+ private AlignmentAnnotation currentAnnotation;
protected boolean adjusting = false;
@@ -111,7 +130,6 @@ public abstract class AnnotationRowFilter extends JPanel
});
}
-
public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
{
this.av = av;
@@ -142,11 +160,20 @@ public abstract class AnnotationRowFilter extends JPanel
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
{
@@ -181,9 +208,8 @@ public abstract class AnnotationRowFilter extends JPanel
seqAssociated.setEnabled(enableSeqAss);
}
- public void ok_actionPerformed(ActionEvent e)
+ public void ok_actionPerformed()
{
- updateView();
try
{
frame.setClosed(true);
@@ -192,7 +218,7 @@ public abstract class AnnotationRowFilter extends JPanel
}
}
- public void cancel_actionPerformed(ActionEvent e)
+ public void cancel_actionPerformed()
{
reset();
ap.paintAlignment(true);
@@ -204,22 +230,22 @@ public abstract class AnnotationRowFilter extends JPanel
}
}
- 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
{
@@ -231,7 +257,7 @@ public abstract class AnnotationRowFilter extends JPanel
}
}
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ public void thresholdIsMin_actionPerformed()
{
updateView();
}
@@ -239,15 +265,14 @@ public abstract class AnnotationRowFilter extends JPanel
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();
@@ -304,26 +329,25 @@ public abstract class AnnotationRowFilter extends JPanel
}
}
- 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);
}
@@ -342,29 +366,25 @@ public abstract class AnnotationRowFilter extends JPanel
continue;
}
+ AnnotationColourGradient scheme = null;
if (currentColours.isSelected())
{
- sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
- selectedThresholdItem);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
-
+ scheme = new AnnotationColourGradient(currentAnn,
+ sg.getColourScheme(), selectedThresholdOption);
}
else
{
- sg.cs = new AnnotationColourGradient(currentAnnotation,
+ scheme = new AnnotationColourGradient(currentAnn,
minColour.getBackground(), maxColour.getBackground(),
- selectedThresholdItem);
- ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
- .isSelected());
+ selectedThresholdOption);
}
-
+ scheme.setSeqAssociated(seqAssociated.isSelected());
+ sg.setColourScheme(scheme);
}
}
return false;
}
-
public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
{
return currentAnnotation;