-/*\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", 480, 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
- if(av.alignment.getAlignmentAnnotation()[i].graph>0)\r
- annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);\r
- }\r
-\r
- threshold.addItem("No Threshold");\r
- threshold.addItem("Above Threshold");\r
- threshold.addItem("Below Threshold");\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
- 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
- threshold.setBounds(new Rectangle(328, 6, 125, 22));\r
- threshold.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- threshold_actionPerformed(e);\r
- }\r
- });\r
- jPanel1.add(ok);\r
- jPanel1.add(cancel);\r
- jPanel2.add(annotations);\r
- jPanel2.add(minColour);\r
- jPanel2.add(maxColour);\r
- jPanel2.add(threshold);\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
- 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
- JComboBox threshold = new JComboBox();\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
- // Check if combobox is still adjusting\r
- if(threshold.getSelectedIndex()==-1)\r
- return;\r
-\r
- // We removed the non-graph annotations when filling the combobox\r
- // so allow for them again here\r
- int nograph = 0, graph = -1;\r
- for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)\r
- {\r
- if (av.alignment.getAlignmentAnnotation()[i].graph == 0)\r
- nograph ++;\r
- else\r
- graph ++;\r
-\r
- if(graph==annotations.getSelectedIndex())\r
- break;\r
- }\r
-\r
- jalview.datamodel.AlignmentAnnotation aa\r
- = av.alignment.getAlignmentAnnotation()[graph+nograph];\r
-\r
-\r
- int aboveThreshold = -1;\r
- if(threshold.getSelectedItem().equals("Above Threshold"))\r
- aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;\r
- else if(threshold.getSelectedItem().equals("Below Threshold"))\r
- aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;\r
-\r
- if(aboveThreshold!=AnnotationColourGradient.NO_THRESHOLD && aa.threshold==null)\r
- {\r
- aa.setThreshold(new jalview.datamodel.GraphLine((aa.graphMax-aa.graphMin)/2f, "Threshold", Color.black));\r
- }\r
-\r
- AnnotationColourGradient acg = new AnnotationColourGradient(aa,\r
- minColour.getBackground(),\r
- maxColour.getBackground(),\r
- aboveThreshold );\r
-\r
-\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
- public void threshold_actionPerformed(ActionEvent e)\r
- {\r
- changeColour();\r
- }\r
-\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
+
+import net.miginfocom.swing.MigLayout;
+
+@SuppressWarnings("serial")
+public class AnnotationColourChooser extends AnnotationRowFilter
+{
+ private ColourSchemeI oldcs;
+
+ private JButton defColours;
+
+ private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
+
+ private JCheckBox useOriginalColours = new JCheckBox();
+
+ JPanel minColour = new JPanel();
+
+ JPanel maxColour = new JPanel();
+
+ private JCheckBox thresholdIsMin = new JCheckBox();
+
+ protected static final int MIN_WIDTH = 500;
+
+ protected static final int MIN_HEIGHT = 240;
+
+ public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
+ {
+ super(av, ap);
+ oldcs = av.getGlobalColourScheme();
+ if (av.getAlignment().getGroups() != null)
+ {
+ oldgroupColours = new Hashtable<>();
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.getColourScheme() != null)
+ {
+ oldgroupColours.put(sg, sg.getColourScheme());
+ }
+ }
+ }
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.colour_by_annotation"), 520,
+ 215);
+ frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
+ addSliderChangeListener();
+ addSliderMouseListeners();
+
+ if (av.getAlignment().getAlignmentAnnotation() == null)
+ {
+ return;
+ }
+
+ // Always get default shading from preferences.
+ setDefaultMinMax();
+
+ adjusting = true;
+ if (oldcs instanceof AnnotationColourGradient)
+ {
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+ useOriginalColours.setSelected(
+ acg.isPredefinedColours() || acg.getBaseColour() != null);
+ if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
+ {
+ minColour.setBackground(acg.getMinColour());
+ maxColour.setBackground(acg.getMaxColour());
+ }
+ seqAssociated.setSelected(acg.isSeqAssociated());
+
+ }
+ Vector<String> annotItems = getAnnotationItems(
+ seqAssociated.isSelected());
+ annotations = new JComboBox<>(annotItems);
+
+ populateThresholdComboBox(threshold);
+
+ if (oldcs instanceof AnnotationColourGradient)
+ {
+ AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+ String label = getAnnotationMenuLabel(acg.getAnnotation());
+ annotations.setSelectedItem(label);
+ switch (acg.getAboveThreshold())
+ {
+ case AnnotationColourGradient.NO_THRESHOLD:
+ getThreshold().setSelectedIndex(0);
+ break;
+ case AnnotationColourGradient.ABOVE_THRESHOLD:
+ getThreshold().setSelectedIndex(1);
+ break;
+ case AnnotationColourGradient.BELOW_THRESHOLD:
+ getThreshold().setSelectedIndex(2);
+ break;
+ default:
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_dont_know_about_threshold_setting"));
+ }
+ thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
+ thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
+ }
+
+ jbInit();
+ adjusting = false;
+
+ updateView();
+ frame.invalidate();
+ frame.pack();
+ }
+
+ @Override
+ protected void jbInit()
+ {
+ super.jbInit();
+
+ 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()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ if (minColour.isEnabled())
+ {
+ showColourChooser(minColour, "label.select_colour_minimum_value");
+ }
+ }
+ });
+ 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()
+ {
+ @Override
+ public void mousePressed(MouseEvent e)
+ {
+ if (maxColour.isEnabled())
+ {
+ showColourChooser(maxColour, "label.select_colour_maximum_value");
+ }
+ }
+ });
+
+ defColours = new JButton();
+ 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();
+ }
+ });
+
+ useOriginalColours.setFont(JvSwingUtils.getLabelFont());
+ useOriginalColours.setOpaque(false);
+ useOriginalColours.setText(
+ MessageManager.getString("label.use_original_colours"));
+ useOriginalColours.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ originalColours_actionPerformed();
+ }
+ });
+ thresholdIsMin.setBackground(Color.white);
+ thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
+ thresholdIsMin
+ .setText(MessageManager.getString("label.threshold_minmax"));
+ thresholdIsMin.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ thresholdIsMin_actionPerformed();
+ }
+ });
+ 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(annotations);
+ }
+ });
+
+ this.setLayout(new BorderLayout());
+ JPanel jPanel1 = new JPanel();
+ JPanel jPanel2 = new JPanel();
+ 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(useOriginalColours);
+ JPanel colpanel = new JPanel(new FlowLayout());
+ colpanel.setBackground(Color.white);
+ colpanel.add(minColour);
+ colpanel.add(maxColour);
+ jPanel2.add(colpanel, "wrap");
+ jPanel2.add(getThreshold());
+ 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 resetColours_actionPerformed()
+ {
+ setDefaultMinMax();
+ updateView();
+ }
+
+ private void setDefaultMinMax()
+ {
+ minColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+ maxColour.setBackground(
+ Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+ }
+
+ protected void showColourChooser(JPanel colourPanel, String titleKey)
+ {
+ String ttl = MessageManager.getString(titleKey);
+ ColourChooserListener listener = new ColourChooserListener()
+ {
+ @Override
+ public void colourSelected(Color c)
+ {
+ colourPanel.setBackground(c);
+ colourPanel.repaint();
+ updateView();
+ }
+ };
+ JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl,
+ colourPanel.getBackground(), listener);
+ }
+
+ @Override
+ public void reset()
+ {
+ this.ap.alignFrame.changeColour(oldcs);
+ if (av.getAlignment().getGroups() != null)
+ {
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ sg.setColourScheme(oldgroupColours.get(sg));
+ }
+ }
+ }
+
+ @Override
+ public void valueChanged(boolean updateAllAnnotation)
+ {
+ if (slider.isEnabled())
+ {
+ if (useOriginalColours.isSelected() && !(av
+ .getGlobalColourScheme() instanceof AnnotationColourGradient))
+ {
+ updateView();
+ }
+ getCurrentAnnotation().threshold.value = getSliderValue();
+ propagateSeqAssociatedThreshold(updateAllAnnotation,
+ getCurrentAnnotation());
+ ap.paintAlignment(false, false);
+ }
+ }
+
+ public void originalColours_actionPerformed()
+ {
+ boolean selected = useOriginalColours.isSelected();
+ if (selected)
+ {
+ reset();
+ }
+ maxColour.setEnabled(!selected);
+ minColour.setEnabled(!selected);
+ thresholdIsMin.setEnabled(!selected);
+ updateView();
+ }
+
+ @Override
+ public void updateView()
+ {
+ // Check if combobox is still adjusting
+ if (adjusting)
+ {
+ return;
+ }
+
+ setCurrentAnnotation(
+ av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+ .getSelectedIndex()]]);
+
+ int selectedThresholdItem = getSelectedThresholdItem(
+ getThreshold().getSelectedIndex());
+
+ slider.setEnabled(true);
+ thresholdValue.setEnabled(true);
+ thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
+
+ final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
+ if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
+ {
+ slider.setEnabled(false);
+ thresholdValue.setEnabled(false);
+ thresholdValue.setText("");
+ thresholdIsMin.setEnabled(false);
+ }
+ else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
+ && currentAnnotation.threshold == null)
+ {
+ currentAnnotation.setThreshold(new GraphLine(
+ (currentAnnotation.graphMax - currentAnnotation.graphMin)
+ / 2f,
+ "Threshold", Color.black));
+ }
+
+ if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ adjusting = true;
+ setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
+ currentAnnotation.threshold.value);
+ slider.setEnabled(true);
+
+ setThresholdValueText();
+ thresholdValue.setEnabled(true);
+ adjusting = false;
+ }
+ colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
+
+ ap.alignmentChanged();
+ }
+
+ protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
+ int selectedThresholdOption)
+ {
+
+ AnnotationColourGradient acg = null;
+ if (useOriginalColours.isSelected())
+ {
+ acg = new AnnotationColourGradient(currentAnn,
+ av.getGlobalColourScheme(), selectedThresholdOption);
+ }
+ else
+ {
+ acg = new AnnotationColourGradient(currentAnn,
+ minColour.getBackground(), maxColour.getBackground(),
+ selectedThresholdOption);
+ }
+ acg.setSeqAssociated(seqAssociated.isSelected());
+
+ if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
+ {
+ acg.setPredefinedColours(true);
+ }
+
+ acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
+
+ this.ap.alignFrame.changeColour(acg);
+
+ if (av.getAlignment().getGroups() != null)
+ {
+
+ for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+ {
+ if (sg.cs == null)
+ {
+ continue;
+ }
+ sg.setColourScheme(acg.getInstance(av, sg));
+ }
+ }
+ }
+
+ @Override
+ protected void sliderDragReleased()
+ {
+ super.sliderDragReleased();
+ ap.paintAlignment(true, true);
+ }
+}
git://source.jalview.org / jalview.git / blobdiff