X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=9df3b731e4cc30af7cdef33e1f3155e780570bc4;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=2853b6b949f5a665ca7f07a74664908c62f4e0d4;hpb=136cfe6c2bede95a91ee16bd4093e71848a97be5;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java old mode 100755 new mode 100644 index 2853b6b..9df3b73 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,446 +1,576 @@ -/* - * 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.appletgui; - -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; -import jalview.schemes.*; -import java.awt.Rectangle; - -public class AnnotationColourChooser - extends Panel implements ActionListener, - AdjustmentListener, ItemListener, MouseListener -{ - Frame frame; - AlignViewport av; - AlignmentPanel ap; - ColourSchemeI oldcs; - Hashtable oldgroupColours; - jalview.datamodel.AlignmentAnnotation currentAnnotation; - boolean adjusting = false; - - public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap) - { - try - { - jbInit(); - } - catch (Exception ex) - {} - - 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.elementAt(g); - oldgroupColours.put(sg, sg.cs); - } - } - this.av = av; - this.ap = ap; - - slider.addAdjustmentListener(this); - slider.addMouseListener(this); - - 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++)); - } - - for (int i = 0; i < list.size(); i++) - { - annotations.addItem(list.elementAt(i).toString()); - } - - threshold.addItem("No Threshold"); - threshold.addItem("Above Threshold"); - threshold.addItem("Below Threshold"); - - adjusting = false; - - changeColour(); - - frame = new Frame(); - frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, 145); - validate(); - } - - 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.setLabel("Min Colour"); - minColour.addActionListener(this); - - maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - maxColour.setLabel("Max Colour"); - maxColour.addActionListener(this); - - thresholdIsMin.addItemListener(this); - ok.setLabel("OK"); - ok.addActionListener(this); - - cancel.setLabel("Cancel"); - cancel.addActionListener(this); - - this.setLayout(borderLayout1); - jPanel2.setLayout(flowLayout1); - annotations.addItemListener(this); - - jPanel1.setBackground(Color.white); - jPanel2.setBackground(Color.white); - threshold.addItemListener(this); - jPanel3.setLayout(null); - thresholdValue.addActionListener(this); - - slider.setBackground(Color.white); - slider.setEnabled(false); - slider.setBounds(new Rectangle(125, 6, 82, 16)); - thresholdValue.setEnabled(false); - thresholdValue.setBounds(new Rectangle(211, 4, 56, 22)); - thresholdValue.setColumns(5); - jPanel3.setBackground(Color.white); - currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); - currentColours.setLabel("Use Original Colours"); - currentColours.addItemListener(this); - - threshold.setBounds(new Rectangle(11, 3, 113, 22)); - thresholdIsMin.setBackground(Color.white); - thresholdIsMin.setLabel("Threshold is min/max"); - thresholdIsMin.setBounds(new Rectangle(270, 3, 135, 23)); - jPanel1.add(ok); - jPanel1.add(cancel); - jPanel2.add(annotations); - jPanel2.add(currentColours); - jPanel2.add(minColour); - jPanel2.add(maxColour); - jPanel3.add(threshold); - jPanel3.add(slider); - jPanel3.add(thresholdValue); - jPanel3.add(thresholdIsMin); - this.add(jPanel2, java.awt.BorderLayout.NORTH); - this.add(jPanel3, java.awt.BorderLayout.CENTER); - this.add(jPanel1, java.awt.BorderLayout.SOUTH); - } - - Choice annotations = new Choice(); - Button minColour = new Button(); - Button maxColour = new Button(); - Button ok = new Button(); - Button cancel = new Button(); - Panel jPanel1 = new Panel(); - Panel jPanel2 = new Panel(); - Choice threshold = new Choice(); - FlowLayout flowLayout1 = new FlowLayout(); - Panel jPanel3 = new Panel(); - Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL); - TextField thresholdValue = new TextField(20); - Checkbox currentColours = new Checkbox(); - BorderLayout borderLayout1 = new BorderLayout(); - Checkbox thresholdIsMin = new Checkbox(); - - public void actionPerformed(ActionEvent evt) - { - if (evt.getSource() == thresholdValue) - { - try - { - float f = new Float(thresholdValue.getText()).floatValue(); - slider.setValue( (int) (f * 1000)); - adjustmentValueChanged(null); - } - catch (NumberFormatException ex) - {} - } - else if (evt.getSource() == minColour) - { - minColour_actionPerformed(null); - } - else if (evt.getSource() == maxColour) - { - maxColour_actionPerformed(null); - } - - else if (evt.getSource() == ok) - { - changeColour(); - frame.setVisible(false); - } - else if (evt.getSource() == cancel) - { - reset(); - ap.paintAlignment(true); - frame.setVisible(false); - } - - else - { - changeColour(); - } - } - - public void itemStateChanged(ItemEvent evt) - { - if (evt.getSource() == currentColours) - { - if (currentColours.getState()) - { - reset(); - } - - maxColour.setEnabled(!currentColours.getState()); - minColour.setEnabled(!currentColours.getState()); - - } - - changeColour(); - } - - public void adjustmentValueChanged(AdjustmentEvent evt) - { - if (!adjusting) - { - thresholdValue.setText( ( (float) slider.getValue() / 1000f) + ""); - if (currentColours.getState() - && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient)) - { - changeColour(); - } - - currentAnnotation.threshold.value = (float) slider.getValue() / 1000f; - ap.paintAlignment(false); - } - } - - public void minColour_actionPerformed(Color newCol) - { - if (newCol != null) - { - minColour.setBackground(newCol); - minColour.repaint(); - changeColour(); - } - else - { - new UserDefinedColours(this, "Min Colour", - minColour.getBackground()); - } - - } - - public void maxColour_actionPerformed(Color newCol) - { - if (newCol != null) - { - maxColour.setBackground(newCol); - maxColour.repaint(); - changeColour(); - } - else - { - new UserDefinedColours(this, "Max Colour", - maxColour.getBackground()); - } - } - - 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; - - 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.setEnabled(true); - thresholdValue.setEnabled(true); - adjusting = false; - } - - AnnotationColourGradient acg = null; - if (currentColours.getState()) - { - 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.getState(); - - 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.elementAt(g); - - if (sg.cs == null) - { - continue; - } - - if (currentColours.getState()) - { - sg.cs = new AnnotationColourGradient( - currentAnnotation, - sg.cs, aboveThreshold); - } - else - { - sg.cs = new AnnotationColourGradient( - currentAnnotation, - minColour.getBackground(), - maxColour.getBackground(), - aboveThreshold); - } - - } - } - - ap.paintAlignment(false); - } - - 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.elementAt(g); - sg.cs = (ColourSchemeI) oldgroupColours.get(sg); - } - } - ap.paintAlignment(true); - - } - - public void mouseClicked(MouseEvent evt){} - public void mousePressed(MouseEvent evt){} - public void mouseReleased(MouseEvent evt){ ap.paintAlignment(true);} - public void mouseEntered(MouseEvent evt){} - public void mouseExited(MouseEvent evt){} - - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.appletgui; + +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 +{ + Frame frame; + + AlignViewport av; + + AlignmentPanel ap; + + ColourSchemeI oldcs; + + Hashtable oldgroupColours; + + jalview.datamodel.AlignmentAnnotation currentAnnotation; + + boolean adjusting = false; + + public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap) + { + try + { + jbInit(); + } catch (Exception ex) + { + } + + 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); + } + else + { + oldgroupColours.put(sg, "null"); + } + } + } + this.av = av; + this.ap = ap; + + slider.addAdjustmentListener(this); + slider.addMouseListener(this); + + if (av.getAlignment().getAlignmentAnnotation() == null) + { + return; + } + + setDefaultMinMax(); + + adjusting = true; + if (oldcs instanceof AnnotationColourGradient) + { + AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; + currentColours.setState(acg.isPredefinedColours() + || acg.getBaseColour() != null); + if (!acg.isPredefinedColours() && acg.getBaseColour() == null) + { + minColour.setBackground(acg.getMinColour()); + maxColour.setBackground(acg.getMaxColour()); + } + // seqAssociated.setState(acg.isSeqAssociated()); + } + + Vector list = new Vector(); + int index = 1; + for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) + { + String label = av.getAlignment().getAlignmentAnnotation()[i].label; + if (!list.contains(label)) + { + list.addElement(label); + } + else + { + list.addElement(label + "_" + (index++)); + } + } + + for (int i = 0; i < list.size(); i++) + { + 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")); + + if (oldcs instanceof AnnotationColourGradient) + { + AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; + annotations.select(acg.getAnnotation()); + switch (acg.getAboveThreshold()) + { + case AnnotationColourGradient.NO_THRESHOLD: + threshold.select(0); + break; + case AnnotationColourGradient.ABOVE_THRESHOLD: + threshold.select(1); + break; + case AnnotationColourGradient.BELOW_THRESHOLD: + threshold.select(1); + break; + default: + throw new Error( + MessageManager + .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient")); + } + thresholdIsMin.setState(acg.thresholdIsMinMax); + thresholdValue.setText("" + acg.getAnnotationThreshold()); + } + + adjusting = false; + + changeColour(); + + frame = new Frame(); + frame.add(this); + jalview.bin.JalviewLite.addFrame(frame, + MessageManager.getString("label.colour_by_annotation"), 560, + 175); + validate(); + } + + private void setDefaultMinMax() + { + minColour.setBackground(av.applet.getDefaultColourParameter( + "ANNOTATIONCOLOUR_MIN", Color.orange)); + maxColour.setBackground(av.applet.getDefaultColourParameter( + "ANNOTATIONCOLOUR_MAX", Color.red)); + + } + + 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.setLabel(MessageManager.getString("label.min_colour")); + minColour.addActionListener(this); + + maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); + maxColour.setLabel(MessageManager.getString("label.max_colour")); + maxColour.addActionListener(this); + + thresholdIsMin.addItemListener(this); + ok.setLabel(MessageManager.getString("action.ok")); + ok.addActionListener(this); + + cancel.setLabel(MessageManager.getString("action.cancel")); + cancel.addActionListener(this); + + defColours.setLabel(MessageManager.getString("action.set_defaults")); + defColours.addActionListener(this); + + annotations.addItemListener(this); + + thresholdValue.addActionListener(this); + slider.setBackground(Color.white); + slider.setPreferredSize(new Dimension(193, 21)); + slider.setEnabled(false); + thresholdValue.setPreferredSize(new Dimension(79, 22)); + 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.addItemListener(this); + + thresholdIsMin.setBackground(Color.white); + thresholdIsMin.setLabel(MessageManager + .getString("label.threshold_minmax")); + + this.setLayout(borderLayout1); + + jPanel1.setBackground(Color.white); + + jPanel2.setLayout(new FlowLayout()); + jPanel2.setBackground(Color.white); + threshold.addItemListener(this); + jPanel3.setLayout(new FlowLayout()); + jPanel3.setBackground(Color.white); + Panel jPanel4 = new Panel(); + jPanel4.setLayout(new BorderLayout()); + jPanel4.setBackground(Color.white); + + jPanel1.add(ok); + jPanel1.add(cancel); + + jPanel2.add(annotations); + jPanel2.add(currentColours); + jPanel2.add(minColour); + jPanel2.add(maxColour); + + jPanel4.add(thresholdIsMin, BorderLayout.WEST); + jPanel4.add(slider, BorderLayout.CENTER); + jPanel4.add(thresholdValue, BorderLayout.EAST); + + Panel jPanel34 = new Panel(); + jPanel34.setLayout(new BorderLayout()); + jPanel34.setBackground(Color.white); + jPanel34.add(jPanel2, BorderLayout.NORTH); + jPanel34.add(threshold, BorderLayout.WEST); + jPanel3.add(defColours); + jPanel34.add(jPanel3, BorderLayout.EAST); + jPanel34.add(jPanel4, BorderLayout.SOUTH); + + this.add(jPanel34, java.awt.BorderLayout.CENTER); + this.add(jPanel1, java.awt.BorderLayout.SOUTH); + + } + + Choice annotations = new Choice(); + + Button minColour = new Button(); + + Button maxColour = new Button(); + + Button ok = new Button(); + + Button cancel = new Button(); + + Button defColours = new Button(); + + Panel jPanel1 = new Panel(); + + Panel jPanel2 = new Panel(); + + Choice threshold = new Choice(); + + FlowLayout flowLayout1 = new FlowLayout(); + + Panel jPanel3 = new Panel(); + + Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL); + + TextField thresholdValue = new TextField(20); + + Checkbox currentColours = new Checkbox(); + + BorderLayout borderLayout1 = new BorderLayout(); + + Checkbox thresholdIsMin = new Checkbox(); + + public void actionPerformed(ActionEvent evt) + { + if (evt.getSource() == thresholdValue) + { + try + { + float f = new Float(thresholdValue.getText()).floatValue(); + slider.setValue((int) (f * 1000)); + adjustmentValueChanged(null); + } catch (NumberFormatException ex) + { + } + } + else if (evt.getSource() == minColour) + { + minColour_actionPerformed(null); + } + else if (evt.getSource() == maxColour) + { + maxColour_actionPerformed(null); + } + else if (evt.getSource() == defColours) + { + defColour_actionPerformed(); + } + else if (evt.getSource() == ok) + { + frame.setVisible(false); + } + else if (evt.getSource() == cancel) + { + reset(); + ap.paintAlignment(true); + frame.setVisible(false); + } + + else + { + changeColour(); + } + } + + public void itemStateChanged(ItemEvent evt) + { + if (evt.getSource() == currentColours) + { + if (currentColours.getState()) + { + reset(); + } + + maxColour.setEnabled(!currentColours.getState()); + minColour.setEnabled(!currentColours.getState()); + + } + + changeColour(); + } + + public void adjustmentValueChanged(AdjustmentEvent evt) + { + if (!adjusting) + { + thresholdValue.setText((slider.getValue() / 1000f) + ""); + if (currentColours.getState() + && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient)) + { + changeColour(); + } + + currentAnnotation.threshold.value = slider.getValue() / 1000f; + ap.paintAlignment(false); + } + } + + public void minColour_actionPerformed(Color newCol) + { + if (newCol != null) + { + minColour.setBackground(newCol); + minColour.repaint(); + changeColour(); + } + else + { + new UserDefinedColours(this, "Min Colour", minColour.getBackground()); + } + + } + + public void maxColour_actionPerformed(Color newCol) + { + if (newCol != null) + { + maxColour.setBackground(newCol); + maxColour.repaint(); + changeColour(); + } + else + { + new UserDefinedColours(this, "Max Colour", maxColour.getBackground()); + } + } + + public void defColour_actionPerformed() + { + setDefaultMinMax(); + minColour.repaint(); + maxColour.repaint(); + changeColour(); + } + + void changeColour() + { + // Check if combobox is still adjusting + if (adjusting) + { + return; + } + + currentAnnotation = av.getAlignment().getAlignmentAnnotation()[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); + thresholdIsMin.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; + + 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.setEnabled(true); + thresholdValue.setEnabled(true); + adjusting = false; + } + + AnnotationColourGradient acg = null; + if (currentColours.getState()) + { + 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.setPredefinedColours(true); + } + + acg.thresholdIsMinMax = thresholdIsMin.getState(); + + av.setGlobalColourScheme(acg); + + // TODO: per group colour propagation not always desired + if (av.getAlignment().getGroups() != null) + { + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) + { + + if (sg.cs == null) + { + continue; + } + + if (currentColours.getState()) + { + sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs, + aboveThreshold); + } + else + { + sg.cs = new AnnotationColourGradient(currentAnnotation, + minColour.getBackground(), maxColour.getBackground(), + aboveThreshold); + } + + } + } + + // update colours in linked windows + ap.alignmentChanged(); + ap.paintAlignment(true); + } + + void reset() + { + av.setGlobalColourScheme(oldcs); + if (av.getAlignment().getGroups() != null) + { + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) + { + Object cs = oldgroupColours.get(sg); + if (cs instanceof ColourSchemeI) + { + sg.cs = (ColourSchemeI) cs; + } + else + { + // probably the "null" string we set it to if it was null originally. + sg.cs = null; + } + } + } + ap.paintAlignment(true); + + } + + public void mouseClicked(MouseEvent evt) + { + } + + public void mousePressed(MouseEvent evt) + { + } + + public void mouseReleased(MouseEvent evt) + { + ap.paintAlignment(true); + } + + public void mouseEntered(MouseEvent evt) + { + } + + public void mouseExited(MouseEvent evt) + { + } + +}