From f8534ee55f528a291d8802b1b4461296bf9ff460 Mon Sep 17 00:00:00 2001 From: jprocter Date: Fri, 2 May 2008 13:04:01 +0000 Subject: [PATCH] bugfix to avoid null pointer exceptions being raised for groups with no colourscheme set. --- src/jalview/appletgui/AnnotationColourChooser.java | 904 ++++++++++---------- 1 file changed, 458 insertions(+), 446 deletions(-) diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index 2db2bd0..c932962 100755 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,446 +1,458 @@ -/* - * 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(153, 3, 93, 21)); - 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)); - 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 + * 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); + 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.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(153, 3, 93, 21)); + 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)); + 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); + 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){} + + +} -- 1.7.10.2