X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=d26680d0e4c5daf43c84f2c3b65e12ff18216361;hb=4ea6a00274e0a209a7dbec074f04a21ec1a80b28;hp=25e08b046099ee9e09236a0163a9b08f398e9f35;hpb=aaf78c2f304b237a9c800137126967ace9437c99;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index 25e08b0..d26680d 100755 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,13 +1,13 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 @@ -24,7 +24,6 @@ import java.awt.event.*; import jalview.datamodel.*; import jalview.schemes.*; -import java.awt.Rectangle; public class AnnotationColourChooser extends Panel implements ActionListener, AdjustmentListener, ItemListener, MouseListener @@ -53,14 +52,11 @@ public class AnnotationColourChooser extends Panel implements } 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) { oldgroupColours.put(sg, sg.cs); @@ -77,19 +73,19 @@ public class AnnotationColourChooser extends Panel implements slider.addAdjustmentListener(this); slider.addMouseListener(this); - if (av.alignment.getAlignmentAnnotation() == null) + if (av.getAlignment().getAlignmentAnnotation() == null) { return; } - minColour.setBackground(av.applet.getDefaultColourParameter("ANNOTATIONCOLOUR_MIN",Color.orange)); - maxColour.setBackground(av.applet.getDefaultColourParameter("ANNOTATIONCOLOUR_MAX",Color.red)); + setDefaultMinMax(); if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; currentColours.setState(acg.predefinedColours); - if (!acg.predefinedColours) { + if (!acg.predefinedColours) + { minColour.setBackground(acg.getMinColour()); maxColour.setBackground(acg.getMaxColour()); } @@ -99,9 +95,9 @@ public class AnnotationColourChooser extends Panel implements 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 @@ -121,21 +117,23 @@ public class AnnotationColourChooser extends Panel implements { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; annotations.select(acg.getAnnotation()); - switch (acg.getAboveThreshold()) { + switch (acg.getAboveThreshold()) + { case AnnotationColourGradient.NO_THRESHOLD: - threshold.select("No Threshold"); + threshold.select("No Threshold"); break; case AnnotationColourGradient.ABOVE_THRESHOLD: - threshold.select("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."); + default: + throw new Error( + "Implementation error: don't know about threshold setting for current AnnotationColourGradient."); } thresholdIsMin.setState(acg.thresholdIsMinMax); - thresholdValue.setText(""+acg.getAnnotationThreshold()); + thresholdValue.setText("" + acg.getAnnotationThreshold()); } adjusting = false; @@ -144,11 +142,20 @@ public class AnnotationColourChooser extends Panel implements 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 @@ -177,44 +184,62 @@ public class AnnotationColourChooser extends Panel implements 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(); @@ -227,6 +252,8 @@ public class AnnotationColourChooser extends Panel implements Button cancel = new Button(); + Button defColours = new Button(); + Panel jPanel1 = new Panel(); Panel jPanel2 = new Panel(); @@ -268,7 +295,10 @@ public class AnnotationColourChooser extends Panel implements { maxColour_actionPerformed(null); } - + else if (evt.getSource() == defColours) + { + defColour_actionPerformed(); + } else if (evt.getSource() == ok) { changeColour(); @@ -349,6 +379,14 @@ public class AnnotationColourChooser extends Panel implements } } + public void defColour_actionPerformed() + { + setDefaultMinMax(); + minColour.repaint(); + maxColour.repaint(); + changeColour(); + } + void changeColour() { // Check if combobox is still adjusting @@ -357,7 +395,7 @@ public class AnnotationColourChooser extends Panel implements return; } - currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations + currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annotations .getSelectedIndex()]; int aboveThreshold = -1; @@ -372,11 +410,13 @@ public class AnnotationColourChooser extends Panel implements 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 @@ -424,13 +464,10 @@ public class AnnotationColourChooser extends Panel implements 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) { @@ -459,13 +496,10 @@ public class AnnotationColourChooser extends Panel implements 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) {