X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=79d2f1f986468d365b34d5987abfc887139dbc32;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=db928b7f305cadef4db2bdc13badec0180dc8acc;hpb=cb5d856b1304448cae13a333cbd9017f81520d90;p=jalview.git
diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java
index db928b7..79d2f1f 100644
--- a/src/jalview/appletgui/AnnotationColourChooser.java
+++ b/src/jalview/appletgui/AnnotationColourChooser.java
@@ -1,32 +1,54 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * 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.
+ * 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 .
+ * 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.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
import jalview.util.MessageManager;
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Choice;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.Hashtable;
+import java.util.Vector;
+
public class AnnotationColourChooser extends Panel implements
ActionListener, AdjustmentListener, ItemListener, MouseListener
{
@@ -75,7 +97,8 @@ public class AnnotationColourChooser extends Panel implements
slider.addAdjustmentListener(this);
slider.addMouseListener(this);
- if (av.getAlignment().getAlignmentAnnotation() == null)
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns == null)
{
return;
}
@@ -86,8 +109,9 @@ public class AnnotationColourChooser extends Panel implements
if (oldcs instanceof AnnotationColourGradient)
{
AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- currentColours.setState(acg.isPredefinedColours() || acg.getBaseColour()!=null);
- if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+ currentColours.setState(acg.isPredefinedColours()
+ || acg.getBaseColour() != null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
{
minColour.setBackground(acg.getMinColour());
maxColour.setBackground(acg.getMaxColour());
@@ -95,16 +119,23 @@ public class AnnotationColourChooser extends Panel implements
// seqAssociated.setState(acg.isSeqAssociated());
}
-
- Vector list = new Vector();
+ Vector list = new Vector();
int index = 1;
- for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ for (int i = 0; i < anns.length; i++)
{
- String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ String label = anns[i].label;
+ if (anns[i].sequenceRef != null)
+ {
+ label = label + "_" + anns[i].sequenceRef.getName();
+ }
if (!list.contains(label))
+ {
list.addElement(label);
+ }
else
+ {
list.addElement(label + "_" + (index++));
+ }
}
for (int i = 0; i < list.size(); i++)
@@ -112,9 +143,12 @@ public class AnnotationColourChooser extends Panel implements
annotations.addItem(list.elementAt(i).toString());
}
- threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
- threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
- threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_no_threshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_above_threshold"));
+ threshold.addItem(MessageManager
+ .getString("label.threshold_feature_below_threshold"));
if (oldcs instanceof AnnotationColourGradient)
{
@@ -133,7 +167,8 @@ public class AnnotationColourChooser extends Panel implements
break;
default:
throw new Error(
- "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+ MessageManager
+ .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient"));
}
thresholdIsMin.setState(acg.thresholdIsMinMax);
thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -145,7 +180,8 @@ public class AnnotationColourChooser extends Panel implements
frame = new Frame();
frame.add(this);
- jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.colour_by_annotation"), 560,
+ jalview.bin.JalviewLite.addFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 560,
175);
validate();
}
@@ -200,11 +236,13 @@ public class AnnotationColourChooser extends Panel implements
thresholdValue.setEnabled(false);
thresholdValue.setColumns(5);
currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- currentColours.setLabel(MessageManager.getString("label.use_original_colours"));
+ currentColours.setLabel(MessageManager
+ .getString("label.use_original_colours"));
currentColours.addItemListener(this);
thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setLabel(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.setLabel(MessageManager
+ .getString("label.threshold_minmax"));
this.setLayout(borderLayout1);
@@ -277,6 +315,7 @@ public class AnnotationColourChooser extends Panel implements
Checkbox thresholdIsMin = new Checkbox();
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == thresholdValue)
@@ -304,7 +343,6 @@ public class AnnotationColourChooser extends Panel implements
}
else if (evt.getSource() == ok)
{
- changeColour();
frame.setVisible(false);
}
else if (evt.getSource() == cancel)
@@ -320,6 +358,7 @@ public class AnnotationColourChooser extends Panel implements
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == currentColours)
@@ -337,18 +376,19 @@ public class AnnotationColourChooser extends Panel implements
changeColour();
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
if (!adjusting)
{
- thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+ thresholdValue.setText((slider.getValue() / 1000f) + "");
if (currentColours.getState()
&& !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
{
changeColour();
}
- currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+ currentAnnotation.threshold.value = slider.getValue() / 1000f;
ap.paintAlignment(false);
}
}
@@ -402,11 +442,11 @@ public class AnnotationColourChooser extends Panel implements
.getSelectedIndex()];
int aboveThreshold = -1;
- if (threshold.getSelectedIndex()==1)
+ if (threshold.getSelectedIndex() == 1)
{
aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
}
- else if (threshold.getSelectedIndex()==2)
+ else if (threshold.getSelectedIndex() == 2)
{
aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
}
@@ -521,23 +561,28 @@ public class AnnotationColourChooser extends Panel implements
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
ap.paintAlignment(true);
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}