X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=599cf0b201ad6d885b49a7df079011139e45636f;hb=d83db1c05bf39e076ce0cd53635bedf7e89afed1;hp=83a8a12b0cb1733abe1abc44c00fe9b14d483ccc;hpb=b35507f7bb2af382a19ba88a005ccbb27ffaa802;p=jalview.git
diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 83a8a12..599cf0b 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,517 +1,665 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-import javax.swing.event.*;
-
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import java.awt.Dimension;
-
-public class AnnotationColourChooser
- extends JPanel
-{
- JInternalFrame frame;
- AlignViewport av;
- AlignmentPanel ap;
- ColourSchemeI oldcs;
- Hashtable oldgroupColours;
- jalview.datamodel.AlignmentAnnotation currentAnnotation;
- boolean adjusting = false;
-
- public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
- {
- oldcs = av.getGlobalColourScheme();
- if (av.alignment.getGroups() != null)
- {
- oldgroupColours = new Hashtable();
- Vector allGroups = ap.av.alignment.getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
- {
- sg = (SequenceGroup) allGroups.get(g);
- if (sg.cs != null)
- {
- oldgroupColours.put(sg, sg.cs);
- }
- }
- }
- this.av = av;
- this.ap = ap;
- frame = new JInternalFrame();
- frame.setContentPane(this);
- frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145);
-
-
- slider.addChangeListener(new ChangeListener()
- {
- public void stateChanged(ChangeEvent evt)
- {
- if (!adjusting)
- {
- thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
- valueChanged();
- }
- }
- });
- slider.addMouseListener(new MouseAdapter()
- {
- public void mouseReleased(MouseEvent evt)
- {
- ap.paintAlignment(true);
- }
- });
-
- if (av.alignment.getAlignmentAnnotation() == null)
- {
- return;
- }
-
- if (oldcs instanceof AnnotationColourGradient)
- {
- AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
- minColour.setBackground(acg.getMinColour());
- maxColour.setBackground(acg.getMaxColour());
- }
- else
- {
- minColour.setBackground(Color.orange);
- maxColour.setBackground(Color.red);
- }
-
- adjusting = true;
- Vector list = new Vector();
- int index = 1;
- for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
- {
- String label = av.alignment.getAlignmentAnnotation()[i].label;
- if (!list.contains(label))
- list.addElement(label);
- else
- list.addElement(label+"_"+(index++));
- }
-
- annotations = new JComboBox(list);
-
- threshold.addItem("No Threshold");
- threshold.addItem("Above Threshold");
- threshold.addItem("Below Threshold");
-
- try
- {
- jbInit();
- }
- catch (Exception ex)
- {}
-
- adjusting = false;
-
- changeColour();
-
- }
-
- public AnnotationColourChooser()
- {
- try
- {
- jbInit();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- private void jbInit()
- throws Exception
- {
- minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- minColour.setBorder(BorderFactory.createEtchedBorder());
- minColour.setPreferredSize(new Dimension(40, 20));
- minColour.setToolTipText("Minimum Colour");
- minColour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent e)
- {
- if (minColour.isEnabled())
- {
- minColour_actionPerformed();
- }
- }
- });
- maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- maxColour.setBorder(BorderFactory.createEtchedBorder());
- maxColour.setPreferredSize(new Dimension(40, 20));
- maxColour.setToolTipText("Maximum Colour");
- maxColour.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent e)
- {
- if (maxColour.isEnabled())
- {
- maxColour_actionPerformed();
- }
- }
- });
- ok.setOpaque(false);
- ok.setText("OK");
- ok.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- ok_actionPerformed(e);
- }
- });
- cancel.setOpaque(false);
- cancel.setText("Cancel");
- cancel.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- cancel_actionPerformed(e);
- }
- });
- this.setLayout(borderLayout1);
- jPanel2.setLayout(flowLayout1);
- annotations.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- annotations_actionPerformed(e);
- }
- });
- jPanel1.setBackground(Color.white);
- jPanel2.setBackground(Color.white);
- threshold.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- threshold_actionPerformed(e);
- }
- });
- jPanel3.setLayout(flowLayout2);
- thresholdValue.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- thresholdValue_actionPerformed(e);
- }
- });
- slider.setPaintLabels(false);
- slider.setPaintTicks(true);
- slider.setBackground(Color.white);
- slider.setEnabled(false);
- slider.setOpaque(false);
- slider.setPreferredSize(new Dimension(100, 32));
- thresholdValue.setEnabled(false);
- thresholdValue.setColumns(7);
- jPanel3.setBackground(Color.white);
- currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
- currentColours.setOpaque(false);
- currentColours.setText("Use Original Colours");
- currentColours.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- currentColours_actionPerformed(e);
- }
- });
- thresholdIsMin.setBackground(Color.white);
- thresholdIsMin.setText("Threshold is Min/Max");
- thresholdIsMin.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent actionEvent)
- {
- thresholdIsMin_actionPerformed(actionEvent);
- }
- });
- jPanel1.add(ok);
- jPanel1.add(cancel);
- jPanel2.add(annotations);
- jPanel2.add(currentColours);
- jPanel2.add(minColour);
- jPanel2.add(maxColour);
- this.add(jPanel3, java.awt.BorderLayout.CENTER);
- jPanel3.add(threshold);
- jPanel3.add(slider);
- jPanel3.add(thresholdValue);
- jPanel3.add(thresholdIsMin);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel2, java.awt.BorderLayout.NORTH);
- }
-
- JComboBox annotations;
- JPanel minColour = new JPanel();
- JPanel maxColour = new JPanel();
- JButton ok = new JButton();
- JButton cancel = new JButton();
- JPanel jPanel1 = new JPanel();
- JPanel jPanel2 = new JPanel();
- BorderLayout borderLayout1 = new BorderLayout();
- JComboBox threshold = new JComboBox();
- FlowLayout flowLayout1 = new FlowLayout();
- JPanel jPanel3 = new JPanel();
- FlowLayout flowLayout2 = new FlowLayout();
- JSlider slider = new JSlider();
- JTextField thresholdValue = new JTextField(20);
- JCheckBox currentColours = new JCheckBox();
- JCheckBox thresholdIsMin = new JCheckBox();
-
- public void minColour_actionPerformed()
- {
- Color col = JColorChooser.showDialog(this,
- "Select Colour for Minimum Value",
- minColour.getBackground());
- if (col != null)
- {
- minColour.setBackground(col);
- }
- minColour.repaint();
- changeColour();
- }
-
- public void maxColour_actionPerformed()
- {
- Color col = JColorChooser.showDialog(this,
- "Select Colour for Maximum Value",
- maxColour.getBackground());
- if (col != null)
- {
- maxColour.setBackground(col);
- }
- maxColour.repaint();
- changeColour();
- }
-
- void changeColour()
- {
- // Check if combobox is still adjusting
- if (adjusting)
- {
- return;
- }
-
-
- currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];
-
- int aboveThreshold = -1;
- if (threshold.getSelectedItem().equals("Above Threshold"))
- {
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
- }
- else if (threshold.getSelectedItem().equals("Below Threshold"))
- {
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
- }
-
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
-
- if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
- {
- slider.setEnabled(false);
- thresholdValue.setEnabled(false);
- thresholdValue.setText("");
- }
- else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
- currentAnnotation.threshold == null)
- {
- currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
- ( (currentAnnotation.graphMax -
- currentAnnotation.graphMin) / 2f,
- "Threshold",
- Color.black));
- }
-
- if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
- {
- adjusting = true;
- float range = currentAnnotation.graphMax * 1000 -
- currentAnnotation.graphMin * 1000;
-
- slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));
- slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));
- slider.setValue( (int) (currentAnnotation.threshold.value * 1000));
- thresholdValue.setText(currentAnnotation.threshold.value + "");
- slider.setMajorTickSpacing( (int) (range / 10f));
- slider.setEnabled(true);
- thresholdValue.setEnabled(true);
- adjusting = false;
- }
-
- AnnotationColourGradient acg = null;
- if (currentColours.isSelected())
- {
- acg = new AnnotationColourGradient(
- currentAnnotation,
- av.getGlobalColourScheme(), aboveThreshold);
- }
- else
- {
- acg =
- new AnnotationColourGradient(
- currentAnnotation,
- minColour.getBackground(),
- maxColour.getBackground(),
- aboveThreshold);
- }
-
- if(currentAnnotation.graphMin==0f&& currentAnnotation.graphMax==0f)
- {
- acg.predefinedColours = true;
- }
-
- acg.thresholdIsMinMax = thresholdIsMin.isSelected();
-
- av.setGlobalColourScheme(acg);
-
- if (av.alignment.getGroups() != null)
- {
- Vector allGroups = ap.av.alignment.getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
- {
- sg = (SequenceGroup) allGroups.get(g);
-
- if (sg.cs == null)
- {
- continue;
- }
-
- if (currentColours.isSelected())
- {
- sg.cs = new AnnotationColourGradient(
- currentAnnotation,
- sg.cs, aboveThreshold);
- }
- else
- {
- sg.cs = new AnnotationColourGradient(
- currentAnnotation,
- minColour.getBackground(),
- maxColour.getBackground(),
- aboveThreshold);
- }
-
- }
- }
-
- ap.paintAlignment(false);
- }
-
- public void ok_actionPerformed(ActionEvent e)
- {
- changeColour();
- try
- {
- frame.setClosed(true);
- }
- catch (Exception ex)
- {}
- }
-
- public void cancel_actionPerformed(ActionEvent e)
- {
- reset();
- try
- {
- frame.setClosed(true);
- }
- catch (Exception ex)
- {}
- }
-
- void reset()
- {
- av.setGlobalColourScheme(oldcs);
- if (av.alignment.getGroups() != null)
- {
- Vector allGroups = ap.av.alignment.getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
- {
- sg = (SequenceGroup) allGroups.get(g);
- sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
- }
- }
- }
-
- public void thresholdCheck_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void annotations_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void threshold_actionPerformed(ActionEvent e)
- {
- changeColour();
- }
-
- public void thresholdValue_actionPerformed(ActionEvent e)
- {
- try
- {
- float f = Float.parseFloat(thresholdValue.getText());
- slider.setValue( (int) (f * 1000));
- }
- catch (NumberFormatException ex)
- {}
- }
-
- public void valueChanged()
- {
- if (currentColours.isSelected()
- && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
- {
- changeColour();
- }
-
- currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
- ap.paintAlignment(false);
- }
-
- public void currentColours_actionPerformed(ActionEvent e)
- {
- if (currentColours.isSelected())
- {
- reset();
- }
-
- maxColour.setEnabled(!currentColours.isSelected());
- minColour.setEnabled(!currentColours.isSelected());
-
- changeColour();
- }
-
- public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
- {
- changeColour();
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+import net.miginfocom.swing.MigLayout;
+
+import jalview.bin.Cache;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import java.awt.Dimension;
+
+public class AnnotationColourChooser extends JPanel
+{
+ JInternalFrame frame;
+
+ AlignViewport av;
+
+ AlignmentPanel ap;
+
+ ColourSchemeI oldcs;
+
+ Hashtable oldgroupColours;
+
+ jalview.datamodel.AlignmentAnnotation currentAnnotation;
+
+ boolean adjusting = false;
+
+ public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
+ {
+ oldcs = av.getGlobalColourScheme();
+ if (av.getAlignment().getGroups() != null)
+ {
+ oldgroupColours = new Hashtable();
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.cs != null)
+ {
+ oldgroupColours.put(sg, sg.cs);
+ }
+ }
+ }
+ this.av = av;
+ this.ap = ap;
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame, "Colour by Annotation", 520, 215);
+
+ slider.addChangeListener(new ChangeListener()
+ {
+ public void stateChanged(ChangeEvent evt)
+ {
+ if (!adjusting)
+ {
+ thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+ valueChanged();
+ }
+ }
+ });
+ slider.addMouseListener(new MouseAdapter()
+ {
+ public void mouseReleased(MouseEvent evt)
+ {
+ ap.paintAlignment(true);
+ }
+ });
+
+ if (av.getAlignment().getAlignmentAnnotation() == null)
+ {
+ return;
+ }
+
+ // Always get default shading from preferences.
+ setDefaultMinMax();
+
+ if (oldcs instanceof AnnotationColourGradient)
+ {
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+ currentColours.setSelected(acg.predefinedColours);
+ if (!acg.predefinedColours)
+ {
+ minColour.setBackground(acg.getMinColour());
+ maxColour.setBackground(acg.getMaxColour());
+ }
+ seqAssociated.setSelected(acg.isSeqAssociated());
+ }
+ adjusting = true;
+ annotations = new JComboBox(
+ getAnnotationItems(seqAssociated.isSelected()));
+
+ threshold.addItem("No Threshold");
+ threshold.addItem("Above Threshold");
+ threshold.addItem("Below Threshold");
+
+ if (oldcs instanceof AnnotationColourGradient)
+ {
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+ annotations.setSelectedItem(acg.getAnnotation());
+ switch (acg.getAboveThreshold())
+ {
+ case AnnotationColourGradient.NO_THRESHOLD:
+ threshold.setSelectedItem("No Threshold");
+ break;
+ case AnnotationColourGradient.ABOVE_THRESHOLD:
+ threshold.setSelectedItem("Above Threshold");
+ break;
+ case AnnotationColourGradient.BELOW_THRESHOLD:
+ threshold.setSelectedItem("Below Threshold");
+ break;
+ default:
+ throw new Error(
+ "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+ }
+ thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+ thresholdValue.setText("" + acg.getAnnotationThreshold());
+ }
+
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ }
+
+ adjusting = false;
+
+ changeColour();
+ frame.invalidate();
+ frame.pack();
+
+ }
+
+ private Vector getAnnotationItems(boolean isSeqAssociated)
+ {
+ Vector list = new Vector();
+ int index = 1;
+ int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+ boolean enableSeqAss = false;
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ {
+ if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
+ {
+ if (isSeqAssociated)
+ {
+ continue;
+ }
+ }
+ else
+ {
+ enableSeqAss = true;
+ }
+ String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+ if (!list.contains(label))
+ {
+ anmap[list.size()] = i;
+ list.addElement(label);
+
+ }
+ else
+ {
+ if (!isSeqAssociated)
+ {
+ anmap[list.size()] = i;
+ list.addElement(label + "_" + (index++));
+ }
+ }
+ }
+ seqAssociated.setEnabled(enableSeqAss);
+ annmap = new int[list.size()];
+ System.arraycopy(anmap, 0, annmap, 0, annmap.length);
+ return list;
+ }
+
+ private void setDefaultMinMax()
+ {
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
+ }
+
+ public AnnotationColourChooser()
+ {
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ minColour.setFont(JvSwingUtils.getLabelFont());
+ minColour.setBorder(BorderFactory.createEtchedBorder());
+ minColour.setPreferredSize(new Dimension(40, 20));
+ minColour.setToolTipText("Minimum Colour");
+ minColour.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ if (minColour.isEnabled())
+ {
+ minColour_actionPerformed();
+ }
+ }
+ });
+ maxColour.setFont(JvSwingUtils.getLabelFont());
+ maxColour.setBorder(BorderFactory.createEtchedBorder());
+ maxColour.setPreferredSize(new Dimension(40, 20));
+ maxColour.setToolTipText("Maximum Colour");
+ maxColour.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ if (maxColour.isEnabled())
+ {
+ maxColour_actionPerformed();
+ }
+ }
+ });
+ ok.setOpaque(false);
+ ok.setText("OK");
+ ok.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ cancel.setOpaque(false);
+ cancel.setText("Cancel");
+ cancel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+ defColours.setOpaque(false);
+ defColours.setText("Defaults");
+ defColours
+ .setToolTipText("Reset min and max colours to defaults from user preferences.");
+ defColours.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ resetColours_actionPerformed(arg0);
+ }
+ });
+
+ annotations.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ annotations_actionPerformed(e);
+ }
+ });
+ threshold.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ threshold_actionPerformed(e);
+ }
+ });
+ thresholdValue.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ thresholdValue_actionPerformed(e);
+ }
+ });
+ slider.setPaintLabels(false);
+ slider.setPaintTicks(true);
+ slider.setBackground(Color.white);
+ slider.setEnabled(false);
+ slider.setOpaque(false);
+ slider.setPreferredSize(new Dimension(100, 32));
+ thresholdValue.setEnabled(false);
+ thresholdValue.setColumns(7);
+ currentColours.setFont(JvSwingUtils.getLabelFont());
+ currentColours.setOpaque(false);
+ currentColours.setText("Use Original Colours");
+ currentColours.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ currentColours_actionPerformed(e);
+ }
+ });
+ thresholdIsMin.setBackground(Color.white);
+ thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
+ thresholdIsMin.setText("Threshold is Min/Max");
+ thresholdIsMin.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ thresholdIsMin_actionPerformed(actionEvent);
+ }
+ });
+ seqAssociated.setBackground(Color.white);
+ seqAssociated.setFont(JvSwingUtils.getLabelFont());
+ seqAssociated.setText("Per-sequence only");
+ seqAssociated.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent arg0)
+ {
+ seqAssociated_actionPerformed(arg0);
+ }
+ });
+
+ this.setLayout(borderLayout1);
+ jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
+ jPanel1.setBackground(Color.white);
+ jPanel2.setBackground(Color.white);
+
+ jPanel1.add(ok);
+ jPanel1.add(cancel);
+ jPanel2.add(annotations, "grow, wrap");
+ jPanel2.add(seqAssociated);
+ jPanel2.add(currentColours);
+ JPanel colpanel = new JPanel(new FlowLayout());
+ colpanel.setBackground(Color.white);
+ colpanel.add(minColour);
+ colpanel.add(maxColour);
+ jPanel2.add(colpanel, "wrap");
+ jPanel2.add(threshold);
+ jPanel2.add(defColours, "skip 1, wrap");
+ jPanel2.add(thresholdIsMin);
+ jPanel2.add(slider, "grow");
+ jPanel2.add(thresholdValue, "grow");
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ this.add(jPanel2, java.awt.BorderLayout.CENTER);
+ this.validate();
+ }
+
+ protected void seqAssociated_actionPerformed(ActionEvent arg0)
+ {
+ adjusting = true;
+ String cursel = (String) annotations.getSelectedItem();
+ boolean isvalid = false, isseqs = seqAssociated.isSelected();
+ this.annotations.removeAllItems();
+ for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
+ {
+ if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
+ {
+ isvalid = true;
+ cursel = anitem;
+ }
+ this.annotations.addItem(anitem);
+ }
+ adjusting = false;
+ if (isvalid)
+ {
+ this.annotations.setSelectedItem(cursel);
+ }
+ else
+ {
+ if (annotations.getItemCount() > 0)
+ {
+ annotations.setSelectedIndex(0);
+ }
+ }
+ }
+
+ protected void resetColours_actionPerformed(ActionEvent arg0)
+ {
+ setDefaultMinMax();
+ changeColour();
+ }
+
+ JComboBox annotations;
+
+ int[] annmap;
+
+ JPanel minColour = new JPanel();
+
+ JPanel maxColour = new JPanel();
+
+ JButton defColours = new JButton();
+
+ JButton ok = new JButton();
+
+ JButton cancel = new JButton();
+
+ JPanel jPanel1 = new JPanel();
+
+ JPanel jPanel2 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ JComboBox threshold = new JComboBox();
+
+ JSlider slider = new JSlider();
+
+ JTextField thresholdValue = new JTextField(20);
+
+ JCheckBox currentColours = new JCheckBox();
+
+ JCheckBox thresholdIsMin = new JCheckBox();
+
+ JCheckBox seqAssociated = new JCheckBox();
+
+ public void minColour_actionPerformed()
+ {
+ Color col = JColorChooser.showDialog(this,
+ "Select Colour for Minimum Value", minColour.getBackground());
+ if (col != null)
+ {
+ minColour.setBackground(col);
+ }
+ minColour.repaint();
+ changeColour();
+ }
+
+ public void maxColour_actionPerformed()
+ {
+ Color col = JColorChooser.showDialog(this,
+ "Select Colour for Maximum Value", maxColour.getBackground());
+ if (col != null)
+ {
+ maxColour.setBackground(col);
+ }
+ maxColour.repaint();
+ changeColour();
+ }
+
+ void changeColour()
+ {
+ // Check if combobox is still adjusting
+ if (adjusting)
+ {
+ return;
+ }
+
+ currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .getSelectedIndex()]];
+
+ int aboveThreshold = -1;
+ if (threshold.getSelectedItem().equals("Above Threshold"))
+ {
+ aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+ }
+ else if (threshold.getSelectedItem().equals("Below Threshold"))
+ {
+ aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+ }
+
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ thresholdIsMin.setEnabled(true);
+
+ if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+ {
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdValue.setText("");
+ thresholdIsMin.setEnabled(false);
+ }
+ else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
+ && currentAnnotation.threshold == null)
+ {
+ currentAnnotation
+ .setThreshold(new jalview.datamodel.GraphLine(
+ (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
+ "Threshold", Color.black));
+ }
+
+ if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ adjusting = true;
+ float range = currentAnnotation.graphMax * 1000
+ - currentAnnotation.graphMin * 1000;
+
+ slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
+ slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
+ slider.setValue((int) (currentAnnotation.threshold.value * 1000));
+ thresholdValue.setText(currentAnnotation.threshold.value + "");
+ slider.setMajorTickSpacing((int) (range / 10f));
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ adjusting = false;
+ }
+
+ AnnotationColourGradient acg = null;
+ if (currentColours.isSelected())
+ {
+ acg = new AnnotationColourGradient(currentAnnotation,
+ av.getGlobalColourScheme(), aboveThreshold);
+ }
+ else
+ {
+ acg = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
+ aboveThreshold);
+ }
+ acg.setSeqAssociated(seqAssociated.isSelected());
+
+ if (currentAnnotation.graphMin == 0f
+ && currentAnnotation.graphMax == 0f)
+ {
+ acg.predefinedColours = true;
+ }
+
+ acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+
+ av.setGlobalColourScheme(acg);
+
+ if (av.getAlignment().getGroups() != null)
+ {
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ if (currentColours.isSelected())
+ {
+ sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
+ aboveThreshold);
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
+
+ }
+ else
+ {
+ sg.cs = new AnnotationColourGradient(currentAnnotation,
+ minColour.getBackground(), maxColour.getBackground(),
+ aboveThreshold);
+ ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+ .isSelected());
+ }
+
+ }
+ }
+ ap.alignmentChanged();
+ // ensure all associated views (overviews, structures, etc) are notified of
+ // updated colours.
+ ap.paintAlignment(true);
+ }
+
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ changeColour();
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ reset();
+ // ensure all original colouring is propagated to listeners.
+ ap.paintAlignment(true);
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ void reset()
+ {
+ av.setGlobalColourScheme(oldcs);
+ if (av.getAlignment().getGroups() != null)
+ {
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
+ }
+ }
+ }
+
+ public void thresholdCheck_actionPerformed(ActionEvent e)
+ {
+ changeColour();
+ }
+
+ public void annotations_actionPerformed(ActionEvent e)
+ {
+ changeColour();
+ }
+
+ public void threshold_actionPerformed(ActionEvent e)
+ {
+ changeColour();
+ }
+
+ public void thresholdValue_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ float f = Float.parseFloat(thresholdValue.getText());
+ slider.setValue((int) (f * 1000));
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+
+ public void valueChanged()
+ {
+ if (currentColours.isSelected()
+ && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ {
+ changeColour();
+ }
+
+ currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+ ap.paintAlignment(false);
+ }
+
+ public void currentColours_actionPerformed(ActionEvent e)
+ {
+ if (currentColours.isSelected())
+ {
+ reset();
+ }
+
+ maxColour.setEnabled(!currentColours.isSelected());
+ minColour.setEnabled(!currentColours.isSelected());
+
+ changeColour();
+ }
+
+ public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+ {
+ changeColour();
+ }
+
+}