X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=1a661be1e4bc9e4d9716c700180d61800e8860c0;hb=48b925b3dd950c86b1add0f2a90a2d0f8b6e316e;hp=c932962e14b849ce3e95074bcc8b60e3f8aa5762;hpb=f8534ee55f528a291d8802b1b4461296bf9ff460;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index c932962..1a661be 100755 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,20 +1,19 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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 . */ package jalview.appletgui; @@ -27,16 +26,23 @@ import jalview.datamodel.*; import jalview.schemes.*; import java.awt.Rectangle; -public class AnnotationColourChooser - extends Panel implements ActionListener, - AdjustmentListener, ItemListener, MouseListener +import javax.swing.BoxLayout; + +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) @@ -44,23 +50,22 @@ public class AnnotationColourChooser try { jbInit(); + } catch (Exception ex) + { } - catch (Exception ex) - {} oldcs = av.getGlobalColourScheme(); - if (av.alignment.getGroups() != null) + if (av.getAlignment().getGroups() != null) { oldgroupColours = new Hashtable(); - Vector allGroups = ap.av.alignment.getGroups(); - SequenceGroup sg; - for (int g = 0; g < allGroups.size(); g++) + for (SequenceGroup sg: ap.av.getAlignment().getGroups()) { - sg = (SequenceGroup) allGroups.elementAt(g); - if (sg.cs!=null) + if (sg.cs != null) + { + oldgroupColours.put(sg, sg.cs); + } + else { - oldgroupColours.put(sg, sg.cs); - } else { oldgroupColours.put(sg, "null"); } } @@ -71,69 +76,95 @@ public class AnnotationColourChooser slider.addAdjustmentListener(this); slider.addMouseListener(this); - if (av.alignment.getAlignmentAnnotation() == null) + if (av.getAlignment().getAlignmentAnnotation() == null) { return; } + setDefaultMinMax(); + 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); + currentColours.setState(acg.predefinedColours); + if (!acg.predefinedColours) { + minColour.setBackground(acg.getMinColour()); + maxColour.setBackground(acg.getMaxColour()); + } } adjusting = true; Vector list = new Vector(); int index = 1; - for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++) + for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) { - String label = av.alignment.getAlignmentAnnotation()[i].label; + String label = av.getAlignment().getAlignmentAnnotation()[i].label; if (!list.contains(label)) list.addElement(label); else - list.addElement(label+"_"+(index++)); + list.addElement(label + "_" + (index++)); } for (int i = 0; i < list.size(); i++) { - annotations.addItem(list.elementAt(i).toString()); + annotations.addItem(list.elementAt(i).toString()); } threshold.addItem("No Threshold"); threshold.addItem("Above Threshold"); threshold.addItem("Below Threshold"); + if (oldcs instanceof AnnotationColourGradient) + { + AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; + annotations.select(acg.getAnnotation()); + switch (acg.getAboveThreshold()) { + case AnnotationColourGradient.NO_THRESHOLD: + threshold.select("No Threshold"); + break; + case AnnotationColourGradient.ABOVE_THRESHOLD: + threshold.select("Above Threshold"); + break; + case AnnotationColourGradient.BELOW_THRESHOLD: + threshold.select("Below Threshold"); + break; + default: + throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient."); + } + thresholdIsMin.setState(acg.thresholdIsMinMax); + thresholdValue.setText(""+acg.getAnnotationThreshold()); + } + adjusting = false; changeColour(); frame = new Frame(); frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, 145); + jalview.bin.JalviewLite.addFrame(frame, "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) + } catch (Exception ex) { ex.printStackTrace(); } } - private void jbInit() - throws Exception + private void jbInit() throws Exception { minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11)); minColour.setLabel("Min Colour"); @@ -150,60 +181,96 @@ public class AnnotationColourChooser cancel.setLabel("Cancel"); cancel.addActionListener(this); - this.setLayout(borderLayout1); - jPanel2.setLayout(flowLayout1); + defColours.setLabel("Defaults"); + defColours.addActionListener(this); + 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.setPreferredSize(new Dimension(193,21)); slider.setEnabled(false); - slider.setBounds(new Rectangle(153, 3, 93, 21)); + thresholdValue.setPreferredSize(new Dimension(79,22)); thresholdValue.setEnabled(false); - thresholdValue.setBounds(new Rectangle(248, 2, 79, 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, 139, 22)); thresholdIsMin.setBackground(Color.white); thresholdIsMin.setLabel("Threshold is min/max"); - thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23)); + + 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); - 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); + + + 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) @@ -213,11 +280,11 @@ public class AnnotationColourChooser try { float f = new Float(thresholdValue.getText()).floatValue(); - slider.setValue( (int) (f * 1000)); + slider.setValue((int) (f * 1000)); adjustmentValueChanged(null); + } catch (NumberFormatException ex) + { } - catch (NumberFormatException ex) - {} } else if (evt.getSource() == minColour) { @@ -227,7 +294,10 @@ public class AnnotationColourChooser { maxColour_actionPerformed(null); } - + else if (evt.getSource() == defColours) + { + defColour_actionPerformed(); + } else if (evt.getSource() == ok) { changeColour(); @@ -267,9 +337,9 @@ public class AnnotationColourChooser { if (!adjusting) { - thresholdValue.setText( ( (float) slider.getValue() / 1000f) + ""); + thresholdValue.setText(((float) slider.getValue() / 1000f) + ""); if (currentColours.getState() - && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient)) + && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient)) { changeColour(); } @@ -289,8 +359,7 @@ public class AnnotationColourChooser } else { - new UserDefinedColours(this, "Min Colour", - minColour.getBackground()); + new UserDefinedColours(this, "Min Colour", minColour.getBackground()); } } @@ -305,11 +374,16 @@ public class AnnotationColourChooser } else { - new UserDefinedColours(this, "Max Colour", - maxColour.getBackground()); + 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 @@ -318,9 +392,8 @@ public class AnnotationColourChooser return; } - - currentAnnotation = av.alignment.getAlignmentAnnotation() - [annotations.getSelectedIndex()]; + currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations + .getSelectedIndex()]; int aboveThreshold = -1; if (threshold.getSelectedItem().equals("Above Threshold")) @@ -334,30 +407,31 @@ public class AnnotationColourChooser 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) + else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD + && currentAnnotation.threshold == null) { - currentAnnotation.setThreshold(new jalview.datamodel.GraphLine - ( (currentAnnotation.graphMax - - currentAnnotation.graphMin) / 2f, - "Threshold", - Color.black)); + 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)); + 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); @@ -367,21 +441,18 @@ public class AnnotationColourChooser AnnotationColourGradient acg = null; if (currentColours.getState()) { - acg = new AnnotationColourGradient( - currentAnnotation, - av.getGlobalColourScheme(), aboveThreshold); + acg = new AnnotationColourGradient(currentAnnotation, + av.getGlobalColourScheme(), aboveThreshold); } else { - acg = - new AnnotationColourGradient( - currentAnnotation, - minColour.getBackground(), - maxColour.getBackground(), + acg = new AnnotationColourGradient(currentAnnotation, + minColour.getBackground(), maxColour.getBackground(), aboveThreshold); } - if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f) + if (currentAnnotation.graphMin == 0f + && currentAnnotation.graphMax == 0f) { acg.predefinedColours = true; } @@ -390,14 +461,11 @@ public class AnnotationColourChooser av.setGlobalColourScheme(acg); - if (av.alignment.getGroups() != null) + if (av.getAlignment().getGroups() != null) { - Vector allGroups = ap.av.alignment.getGroups(); - SequenceGroup sg; - for (int g = 0; g < allGroups.size(); g++) + for (SequenceGroup sg:ap.av.getAlignment().getGroups()) { - sg = (SequenceGroup) allGroups.elementAt(g); - + if (sg.cs == null) { continue; @@ -405,40 +473,37 @@ public class AnnotationColourChooser if (currentColours.getState()) { - sg.cs = new AnnotationColourGradient( - currentAnnotation, - sg.cs, aboveThreshold); + sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs, + aboveThreshold); } else { - sg.cs = new AnnotationColourGradient( - currentAnnotation, - minColour.getBackground(), - maxColour.getBackground(), - aboveThreshold); + sg.cs = new AnnotationColourGradient(currentAnnotation, + minColour.getBackground(), maxColour.getBackground(), + aboveThreshold); } } } - ap.paintAlignment(false); + // update colours in linked windows + ap.paintAlignment(true); } void reset() { av.setGlobalColourScheme(oldcs); - if (av.alignment.getGroups() != null) + if (av.getAlignment().getGroups() != null) { - Vector allGroups = ap.av.alignment.getGroups(); - SequenceGroup sg; - for (int g = 0; g < allGroups.size(); g++) + for (SequenceGroup sg:ap.av.getAlignment().getGroups()) { - sg = (SequenceGroup) allGroups.elementAt(g); Object cs = oldgroupColours.get(sg); if (cs instanceof ColourSchemeI) { - sg.cs = (ColourSchemeI) cs; - } else { + sg.cs = (ColourSchemeI) cs; + } + else + { // probably the "null" string we set it to if it was null originally. sg.cs = null; } @@ -448,11 +513,25 @@ public class AnnotationColourChooser } - 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){} + 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) + { + } }