From 887c89bb3a626a8c5ec91ba742e3f7743f5255eb Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 17 Mar 2009 16:59:45 +0000 Subject: [PATCH] prototype dialog for setting feature display shading and threshold --- src/jalview/gui/FeatureColourChooser.java | 450 +++++++++++++++++++++++++++++ 1 file changed, 450 insertions(+) create mode 100644 src/jalview/gui/FeatureColourChooser.java diff --git a/src/jalview/gui/FeatureColourChooser.java b/src/jalview/gui/FeatureColourChooser.java new file mode 100644 index 0000000..993cd2e --- /dev/null +++ b/src/jalview/gui/FeatureColourChooser.java @@ -0,0 +1,450 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 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 FeatureColourChooser extends JPanel +{ + JInternalFrame frame; + + FeatureRenderer fr; + + FeatureSettings fs; + + GraduatedColor cs; + Object oldcs; + + Hashtable oldgroupColours; + + AlignmentPanel ap; + + + boolean adjusting = false; + + private float min; + + private float max; + String type = null; + public FeatureColourChooser(FeatureSettings fsettings, String type) + { + this.fs = fsettings; + this.type = type; + fr = fsettings.fr; + ap = fr.ap; + frame = new JInternalFrame(); + frame.setContentPane(this); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type, 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) + { + if (fr.ap!=null) { fr.ap.paintAlignment(true); }; + } + }); + + float mm[] = ((float[][]) fr.minmax.get(type))[0]; + min = mm[0]; + max = mm[1]; + oldcs = fr.featureColours.get(type); + if (oldcs instanceof GraduatedColor) + { + cs = new GraduatedColor((GraduatedColor) oldcs, min, max); + } else { + // promote original color to a graduated color + Color bl = Color.black; + if (oldcs instanceof Color) + { + bl = (Color) oldcs; + } + // original colour becomes the maximum colour + cs = new GraduatedColor(Color.white,bl,mm[0],mm[1]); + } + minColour.setBackground(cs.getMinColor()); + maxColour.setBackground(cs.getMaxColor()); + adjusting = true; + + try + { + jbInit(); + } catch (Exception ex) + { + } + + adjusting = false; + + changeColour(); + + } + + public FeatureColourChooser() + { + 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); + jPanel1.setBackground(Color.white); + jPanel2.setBackground(Color.white); + threshold.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + threshold_actionPerformed(e); + } + }); + threshold.addItem("No Threshold"); + threshold.addItem("Above Threshold"); + threshold.addItem("Below Threshold"); + 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(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); + } + + + 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); + // TODO refactor to tolower flag + JCheckBox currentColours = new JCheckBox(); + + JCheckBox thresholdIsMin = new JCheckBox(); + + private GraphLine threshline; + + 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; + } + + + int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD; + 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); + GraduatedColor acg = new GraduatedColor(minColour.getBackground(), maxColour.getBackground(), min, max); + + if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD) + { + slider.setEnabled(false); + thresholdValue.setEnabled(false); + thresholdValue.setText(""); + } + else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD + && threshline == null) + { + // todo visual indication of feature threshold + threshline = new jalview.datamodel.GraphLine( + (max - min) / 2f, + "Threshold", Color.black); + } + + if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) + { + adjusting = true; + acg.setThresh(threshline.value); + + float range = max * 1000f + - min * 1000f; + + slider.setMinimum((int) (min * 1000)); + slider.setMaximum((int) (max * 1000)); + slider.setValue((int) (threshline.value * 1000)); + thresholdValue.setText(threshline.value + ""); + slider.setMajorTickSpacing((int) (range / 10f)); + slider.setEnabled(true); + thresholdValue.setEnabled(true); + adjusting = false; + } + + acg.setThreshType(aboveThreshold); + if (thresholdIsMin.isSelected() && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD) + { + if (aboveThreshold==AnnotationColourGradient.ABOVE_THRESHOLD) + { + acg = new GraduatedColor(acg, threshline.value, max); + } else { + acg = new GraduatedColor(acg, min,threshline.value); + } + } + + fr.featureColours.put(type,acg); + cs = acg; + 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() + { + fr.featureColours.put(type, oldcs); + } + + 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)); + threshline.value = f; + } catch (NumberFormatException ex) + { + } + } + + public void valueChanged() + { + threshline.value = (float) slider.getValue() / 1000f; + cs.setThresh(threshline.value); + changeColour(); + 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(); + } + +} -- 1.7.10.2