X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=4416ec34525ad64c4795f37f5e9a5609b6d22a7d;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=c932962e14b849ce3e95074bcc8b60e3f8aa5762;hpb=f8534ee55f528a291d8802b1b4461296bf9ff460;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index c932962..4416ec3 100755 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,17 +1,17 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * + * 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 @@ -27,16 +27,21 @@ import jalview.datamodel.*; import jalview.schemes.*; import java.awt.Rectangle; -public class AnnotationColourChooser - extends Panel implements ActionListener, - AdjustmentListener, ItemListener, MouseListener +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) @@ -44,9 +49,9 @@ public class AnnotationColourChooser try { jbInit(); + } catch (Exception ex) + { } - catch (Exception ex) - {} oldcs = av.getGlobalColourScheme(); if (av.alignment.getGroups() != null) @@ -57,10 +62,12 @@ public class AnnotationColourChooser for (int g = 0; g < allGroups.size(); g++) { 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"); } } @@ -98,12 +105,12 @@ public class AnnotationColourChooser 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"); @@ -116,7 +123,8 @@ public class AnnotationColourChooser frame = new Frame(); frame.add(this); - jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, 145); + jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, + 145); validate(); } @@ -125,15 +133,13 @@ public class 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"); @@ -191,19 +197,33 @@ public class AnnotationColourChooser } 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) @@ -213,11 +233,11 @@ 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) { @@ -267,9 +287,9 @@ 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 +309,7 @@ public class AnnotationColourChooser } else { - new UserDefinedColours(this, "Min Colour", - minColour.getBackground()); + new UserDefinedColours(this, "Min Colour", minColour.getBackground()); } } @@ -305,8 +324,7 @@ public class AnnotationColourChooser } else { - new UserDefinedColours(this, "Max Colour", - maxColour.getBackground()); + new UserDefinedColours(this, "Max Colour", maxColour.getBackground()); } } @@ -318,9 +336,8 @@ public class AnnotationColourChooser return; } - - currentAnnotation = av.alignment.getAlignmentAnnotation() - [annotations.getSelectedIndex()]; + currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations + .getSelectedIndex()]; int aboveThreshold = -1; if (threshold.getSelectedItem().equals("Above Threshold")) @@ -341,23 +358,22 @@ public class AnnotationColourChooser 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)); + 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)); + 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 +383,17 @@ 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(), - aboveThreshold); + 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; } @@ -405,17 +417,14 @@ 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); } } @@ -437,8 +446,10 @@ public class AnnotationColourChooser 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 +459,25 @@ 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) + { + } }