From dd40a60ce9bc04b00ae69523ccf8385640a82938 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Fri, 24 Mar 2006 15:25:59 +0000 Subject: [PATCH] Annotation colours added to applet --- src/jalview/appletgui/AnnotationColourChooser.java | 403 ++++++++++++++++++++ 1 file changed, 403 insertions(+) create mode 100755 src/jalview/appletgui/AnnotationColourChooser.java diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java new file mode 100755 index 0000000..1c73f7b --- /dev/null +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -0,0 +1,403 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2005 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.awt.event.*; +import java.awt.*; + +import jalview.schemes.*; +import java.util.*; +import jalview.datamodel.SequenceGroup; + +public class AnnotationColourChooser extends Panel implements ActionListener, + AdjustmentListener, ItemListener +{ + 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); + + 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; + for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++) + { + if (av.alignment.getAlignmentAnnotation()[i].graph > 0) + annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label); + } + + 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); + + 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(172, 7, 120, 16)); + thresholdValue.setEnabled(false); + thresholdValue.setBounds(new Rectangle(295, 4, 83, 22)); + thresholdValue.setColumns(10); + 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(19, 4, 141, 22)); + 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); + 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(); + + + 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.repaint(); + 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.repaint(); + } + } + + 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; + + // We removed the non-graph annotations when filling the combobox + // so allow for them again here + int nograph = 0, graph = -1; + for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++) + { + if (av.alignment.getAlignmentAnnotation()[i].graph == 0) + nograph++; + else + graph++; + + if (graph == annotations.getSelectedIndex()) + break; + } + + currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph]; + + 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); + + 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.repaint(); + } + + + 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.repaint(); + + } + + + +} -- 1.7.10.2