-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.gui;\r
-\r
-import javax.swing.*;\r
-import java.awt.event.ActionListener;\r
-import java.awt.event.ActionEvent;\r
-import java.awt.BorderLayout;\r
-import java.awt.*;\r
-\r
-import jalview.schemes.*;\r
-\r
-public class AnnotationColourChooser\r
- extends JPanel\r
-{\r
- JInternalFrame frame;\r
- AlignViewport av;\r
- AlignmentPanel ap;\r
- ColourSchemeI oldcs;\r
-\r
- public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)\r
- {\r
- oldcs = av.getGlobalColourScheme();\r
- this.av = av;\r
- this.ap = ap;\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- Desktop.addInternalFrame(frame, "Colour by Annotation", 470, 110, false);\r
-\r
- try{\r
- jbInit();\r
- }catch(Exception ex){}\r
-\r
- if(av.alignment.getAlignmentAnnotation()==null)\r
- return;\r
-\r
- if(oldcs instanceof AnnotationColourGradient)\r
- {\r
- AnnotationColourGradient acg = (AnnotationColourGradient)oldcs;\r
- minColour.setBackground( acg.getMinColour() );\r
- maxColour.setBackground( acg.getMaxColour() );\r
- }\r
- else\r
- {\r
- minColour.setBackground(Color.orange);\r
- maxColour.setBackground(Color.red);\r
- }\r
-\r
- for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)\r
- {\r
- annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);\r
- }\r
-\r
- }\r
-\r
- public AnnotationColourChooser()\r
- {\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- minColour.setBounds(new Rectangle(145, 5, 85, 25));\r
- minColour.setToolTipText("");\r
- minColour.setMargin(new Insets(2, 2, 2, 2));\r
- minColour.setText("Min Colour");\r
- minColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- minColour_actionPerformed(e);\r
- }\r
- });\r
- maxColour.setBounds(new Rectangle(235, 5, 89, 25));\r
- maxColour.setMargin(new Insets(2, 2, 2, 2));\r
- maxColour.setText("Max Colour");\r
- maxColour.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- maxColour_actionPerformed(e);\r
- }\r
- });\r
- thresholdCheck.setOpaque(false);\r
- thresholdCheck.setHorizontalTextPosition(SwingConstants.LEADING);\r
- thresholdCheck.setSelectedIcon(null);\r
- thresholdCheck.setText("Above Threshold");\r
- thresholdCheck.setBounds(new Rectangle(329, 6, 109, 23));\r
- thresholdCheck.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- thresholdCheck_actionPerformed(e);\r
- }\r
- });\r
- ok.setOpaque(false);\r
- ok.setText("OK");\r
- ok.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- cancel.setOpaque(false);\r
- cancel.setText("Cancel");\r
- cancel.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cancel_actionPerformed(e);\r
- }\r
- });\r
- this.setLayout(borderLayout1);\r
- jPanel2.setLayout(null);\r
- annotations.setBounds(new Rectangle(5, 7, 135, 21));\r
- annotations.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- annotations_actionPerformed(e);\r
- }\r
- });\r
- jPanel1.setBackground(Color.white);\r
- jPanel2.setBackground(Color.white);\r
- jPanel1.add(ok);\r
- jPanel1.add(cancel);\r
- jPanel2.add(annotations);\r
- jPanel2.add(minColour);\r
- jPanel2.add(maxColour);\r
- jPanel2.add(thresholdCheck);\r
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
- this.add(jPanel2, java.awt.BorderLayout.CENTER);\r
- }\r
-\r
- JComboBox annotations = new JComboBox();\r
- JButton minColour = new JButton();\r
- JButton maxColour = new JButton();\r
- JCheckBox thresholdCheck = new JCheckBox();\r
- JButton ok = new JButton();\r
- JButton cancel = new JButton();\r
- JPanel jPanel1 = new JPanel();\r
- JPanel jPanel2 = new JPanel();\r
- BorderLayout borderLayout1 = new BorderLayout();\r
-\r
-\r
- public void minColour_actionPerformed(ActionEvent e)\r
- {\r
- Color col = JColorChooser.showDialog(this,\r
- "Select Colour for Minimum Value",\r
- minColour.getBackground());\r
- if (col != null)\r
- minColour.setBackground(col);\r
- minColour.repaint();\r
- changeColour();\r
- }\r
-\r
- public void maxColour_actionPerformed(ActionEvent e)\r
- {\r
- Color col = JColorChooser.showDialog(this,\r
- "Select Colour for Maximum Value",\r
- maxColour.getBackground());\r
- if (col != null)\r
- maxColour.setBackground(col);\r
- maxColour.repaint();\r
- changeColour();\r
- }\r
-\r
- void changeColour()\r
- {\r
- jalview.datamodel.AlignmentAnnotation aa = av.alignment.getAlignmentAnnotation()[annotations.getSelectedIndex()];\r
-\r
- AnnotationColourGradient acg = new AnnotationColourGradient(aa,\r
- minColour.getBackground(),\r
- maxColour.getBackground(),\r
- thresholdCheck.isSelected());\r
-\r
- if(thresholdCheck.isSelected() && aa.graphLines==null)\r
- {\r
- aa.addGraphLine(new jalview.datamodel.GraphLine((aa.graphMax-aa.graphMin)/2f, "Threshold", Color.black));\r
- }\r
-\r
- av.setGlobalColourScheme(acg);\r
- ap.repaint();\r
-\r
- }\r
-\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
- changeColour();\r
- try{\r
- frame.setClosed(true);\r
- }catch(Exception ex){}\r
- }\r
-\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- av.setGlobalColourScheme(oldcs);\r
- try{\r
- frame.setClosed(true);\r
- }catch(Exception ex){}\r
- }\r
-\r
- public void thresholdCheck_actionPerformed(ActionEvent e)\r
- {\r
- changeColour();\r
- }\r
-\r
- public void annotations_actionPerformed(ActionEvent e)\r
- {\r
- changeColour();\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 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 jalview.util.MessageManager;
+
+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;
+ /**
+ * enabled if the user is dragging the slider - try to keep updates to a minimun
+ */
+ boolean sliderDragging = 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, MessageManager.getString("label.colour_by_annotation"), 520, 215);
+
+ slider.addChangeListener(new ChangeListener()
+ {
+ public void stateChanged(ChangeEvent evt)
+ {
+ if (!adjusting)
+ {
+ thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+ valueChanged(!sliderDragging);
+ }
+ }
+ });
+ slider.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ sliderDragging=true;
+ super.mousePressed(e);
+ }
+
+ @Override
+ public void mouseDragged(MouseEvent e)
+ {
+ sliderDragging=true;
+ super.mouseDragged(e);
+ }
+ public void mouseReleased(MouseEvent evt)
+ {
+ if (sliderDragging)
+ {
+ sliderDragging=false;
+ valueChanged(true);
+ }
+ ap.paintAlignment(true);
+ }
+ });
+
+ if (av.getAlignment().getAlignmentAnnotation() == null)
+ {
+ return;
+ }
+
+ // Always get default shading from preferences.
+ setDefaultMinMax();
+
+ adjusting = true;
+ if (oldcs instanceof AnnotationColourGradient)
+ {
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+ currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+ {
+ minColour.setBackground(acg.getMinColour());
+ maxColour.setBackground(acg.getMaxColour());
+ }
+ seqAssociated.setSelected(acg.isSeqAssociated());
+
+ }
+ annotations = new JComboBox(
+ getAnnotationItems(seqAssociated.isSelected()));
+
+ 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"));
+
+ if (oldcs instanceof AnnotationColourGradient)
+ {
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+ annotations.setSelectedItem(acg.getAnnotation());
+ switch (acg.getAboveThreshold())
+ {
+ case AnnotationColourGradient.NO_THRESHOLD:
+ threshold.setSelectedIndex(0);
+ break;
+ case AnnotationColourGradient.ABOVE_THRESHOLD:
+ threshold.setSelectedIndex(1);
+ break;
+ case AnnotationColourGradient.BELOW_THRESHOLD:
+ threshold.setSelectedIndex(2);
+ 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<String> getAnnotationItems(boolean isSeqAssociated)
+ {
+ Vector<String> list = new Vector<String>();
+ 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(MessageManager.getString("label.min_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(MessageManager.getString("label.max_colour"));
+ maxColour.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ if (maxColour.isEnabled())
+ {
+ maxColour_actionPerformed();
+ }
+ }
+ });
+ ok.setOpaque(false);
+ ok.setText(MessageManager.getString("action.ok"));
+ ok.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ cancel.setOpaque(false);
+ cancel.setText(MessageManager.getString("action.cancel"));
+ cancel.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ cancel_actionPerformed(e);
+ }
+ });
+ defColours.setOpaque(false);
+ defColours.setText(MessageManager.getString("action.set_defaults"));
+ defColours
+ .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
+ 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(MessageManager.getString("label.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(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ thresholdIsMin_actionPerformed(actionEvent);
+ }
+ });
+ seqAssociated.setBackground(Color.white);
+ seqAssociated.setFont(JvSwingUtils.getLabelFont());
+ seqAssociated.setText(MessageManager.getString("label.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.getSelectedIndex()==1)
+ {
+ aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+ }
+ else if (threshold.getSelectedIndex()==2)
+ {
+ 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.setPredefinedColours(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(boolean updateAllAnnotation)
+ {
+ if (currentColours.isSelected()
+ && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+ {
+ changeColour();
+ }
+ currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+ propagateSeqAssociatedThreshold(updateAllAnnotation);
+ ap.paintAlignment(false);
+ }
+
+ private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+ {
+ if (currentAnnotation.sequenceRef == null
+ || currentAnnotation.threshold == null)
+ {
+ return;
+ }
+ // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
+
+ float thr = currentAnnotation.threshold.value;
+ for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+ {
+ AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+ if (aa.label.equals(currentAnnotation.label))
+ {
+ aa.threshold.value = thr;
+ }
+ }
+ }
+
+ 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();
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff