X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=5a942f1e752b8b835723bdfec10b5626e5a8437c;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=b0379aa2acfe085143d8efc2f4cd4f4d8b0060c4;hpb=7384a101e11711490956c31fcff4efb556d21c69;p=jalview.git diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java index b0379aa..5a942f1 100755 --- a/src/jalview/gui/AnnotationColourChooser.java +++ b/src/jalview/gui/AnnotationColourChooser.java @@ -1,6 +1,6 @@ /* - * 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 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -51,14 +51,11 @@ public class AnnotationColourChooser extends JPanel public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap) { 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.get(g); if (sg.cs != null) { oldgroupColours.put(sg, sg.cs); @@ -91,38 +88,28 @@ public class AnnotationColourChooser extends JPanel } }); - if (av.alignment.getAlignmentAnnotation() == null) + if (av.getAlignment().getAlignmentAnnotation() == null) { return; } // Always get default shading from preferences. setDefaultMinMax(); - + if (oldcs instanceof AnnotationColourGradient) { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; currentColours.setSelected(acg.predefinedColours); if (!acg.predefinedColours) { - minColour.setBackground(acg.getMinColour()); + minColour.setBackground(acg.getMinColour()); maxColour.setBackground(acg.getMaxColour()); } + seqAssociated.setSelected(acg.isSeqAssociated()); } - 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++)); - } - - annotations = new JComboBox(list); + annotations = new JComboBox( + getAnnotationItems(seqAssociated.isSelected())); threshold.addItem("No Threshold"); threshold.addItem("Above Threshold"); @@ -132,21 +119,23 @@ public class AnnotationColourChooser extends JPanel { AnnotationColourGradient acg = (AnnotationColourGradient) oldcs; annotations.setSelectedItem(acg.getAnnotation()); - switch (acg.getAboveThreshold()) { + switch (acg.getAboveThreshold()) + { case AnnotationColourGradient.NO_THRESHOLD: - threshold.setSelectedItem("No Threshold"); + threshold.setSelectedItem("No Threshold"); break; case AnnotationColourGradient.ABOVE_THRESHOLD: - threshold.setSelectedItem("Above Threshold"); + threshold.setSelectedItem("Above Threshold"); break; case AnnotationColourGradient.BELOW_THRESHOLD: threshold.setSelectedItem("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.setSelected(acg.thresholdIsMinMax); - thresholdValue.setText(""+acg.getAnnotationThreshold()); + thresholdValue.setText("" + acg.getAnnotationThreshold()); } try @@ -159,14 +148,58 @@ public class AnnotationColourChooser extends JPanel adjusting = false; changeColour(); - validate(); + frame.invalidate(); + frame.pack(); + + } + + private Vector getAnnotationItems(boolean isSeqAssociated) + { + Vector list = new Vector(); + int index = 1; + int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length]; + boolean enableSeqAss = false; + for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) + { + if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null) + { + if (isSeqAssociated) + { + continue; + } + } + else + { + enableSeqAss = true; + } + String label = av.getAlignment().getAlignmentAnnotation()[i].label; + if (!list.contains(label)) + { + anmap[list.size()] = i; + list.addElement(label); + } + else + { + if (!isSeqAssociated) + { + anmap[list.size()] = i; + list.addElement(label + "_" + (index++)); + } + } + } + seqAssociated.setEnabled(enableSeqAss); + annmap = new int[list.size()]; + System.arraycopy(anmap, 0, annmap, 0, annmap.length); + return list; } private void setDefaultMinMax() { - minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange)); - maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red)); + minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", + Color.orange)); + maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", + Color.red)); } public AnnotationColourChooser() @@ -230,17 +263,18 @@ public class AnnotationColourChooser extends JPanel }); defColours.setOpaque(false); defColours.setText("Defaults"); - defColours.setToolTipText("Reset min and max colours to defaults from user preferences."); + defColours + .setToolTipText("Reset min and max colours to defaults from user preferences."); defColours.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent arg0) { resetColours_actionPerformed(arg0); } }); - + annotations.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -290,28 +324,71 @@ public class AnnotationColourChooser extends JPanel thresholdIsMin_actionPerformed(actionEvent); } }); + seqAssociated.setBackground(Color.white); + seqAssociated.setFont(JvSwingUtils.getLabelFont()); + seqAssociated.setText("Per-sequence only"); + seqAssociated.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent arg0) + { + seqAssociated_actionPerformed(arg0); + } + }); + this.setLayout(borderLayout1); - jPanel2.setLayout(new MigLayout("","[left][center][right]","[][][]")); + jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]")); jPanel1.setBackground(Color.white); jPanel2.setBackground(Color.white); jPanel1.add(ok); jPanel1.add(cancel); - jPanel2.add(annotations); + jPanel2.add(annotations, "grow, wrap"); + jPanel2.add(seqAssociated); jPanel2.add(currentColours); JPanel colpanel = new JPanel(new FlowLayout()); colpanel.setBackground(Color.white); colpanel.add(minColour); colpanel.add(maxColour); jPanel2.add(colpanel, "wrap"); - jPanel2.add(threshold); - jPanel2.add(defColours,"skip 1, wrap"); + jPanel2.add(defColours, "skip 1, wrap"); jPanel2.add(thresholdIsMin); jPanel2.add(slider, "grow"); jPanel2.add(thresholdValue, "grow"); this.add(jPanel1, java.awt.BorderLayout.SOUTH); this.add(jPanel2, java.awt.BorderLayout.CENTER); + this.validate(); + } + + protected void seqAssociated_actionPerformed(ActionEvent arg0) + { + adjusting = true; + String cursel = (String) annotations.getSelectedItem(); + boolean isvalid = false, isseqs = seqAssociated.isSelected(); + this.annotations.removeAllItems(); + for (String anitem : getAnnotationItems(seqAssociated.isSelected())) + { + if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem))) + { + isvalid = true; + cursel = anitem; + } + this.annotations.addItem(anitem); + } + adjusting = false; + if (isvalid) + { + this.annotations.setSelectedItem(cursel); + } + else + { + if (annotations.getItemCount() > 0) + { + annotations.setSelectedIndex(0); + } + } } protected void resetColours_actionPerformed(ActionEvent arg0) @@ -322,22 +399,26 @@ public class AnnotationColourChooser extends JPanel JComboBox annotations; + int[] annmap; + JPanel minColour = new JPanel(); JPanel maxColour = new JPanel(); + JButton defColours = new JButton(); + JButton ok = new JButton(); JButton cancel = new JButton(); JPanel jPanel1 = new JPanel(); + JPanel jPanel2 = new JPanel(); - + BorderLayout borderLayout1 = new BorderLayout(); JComboBox threshold = new JComboBox(); - JSlider slider = new JSlider(); JTextField thresholdValue = new JTextField(20); @@ -346,6 +427,8 @@ public class AnnotationColourChooser extends JPanel JCheckBox thresholdIsMin = new JCheckBox(); + JCheckBox seqAssociated = new JCheckBox(); + public void minColour_actionPerformed() { Color col = JColorChooser.showDialog(this, @@ -378,8 +461,8 @@ public class AnnotationColourChooser extends JPanel return; } - currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations - .getSelectedIndex()]; + currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations + .getSelectedIndex()]]; int aboveThreshold = -1; if (threshold.getSelectedItem().equals("Above Threshold")) @@ -439,6 +522,7 @@ public class AnnotationColourChooser extends JPanel minColour.getBackground(), maxColour.getBackground(), aboveThreshold); } + acg.setSeqAssociated(seqAssociated.isSelected()); if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f) @@ -450,14 +534,11 @@ public class AnnotationColourChooser extends JPanel 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++) - { - sg = (SequenceGroup) allGroups.get(g); + for (SequenceGroup sg : ap.av.getAlignment().getGroups()) + { if (sg.cs == null) { continue; @@ -467,17 +548,24 @@ public class AnnotationColourChooser extends JPanel { sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs, aboveThreshold); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); + } else { sg.cs = new AnnotationColourGradient(currentAnnotation, minColour.getBackground(), maxColour.getBackground(), aboveThreshold); + ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated + .isSelected()); } } } - // ensure all associated views (overviews, structures, etc) are notified of updated colours. + ap.alignmentChanged(); + // ensure all associated views (overviews, structures, etc) are notified of + // updated colours. ap.paintAlignment(true); } @@ -495,7 +583,7 @@ public class AnnotationColourChooser extends JPanel public void cancel_actionPerformed(ActionEvent e) { reset(); - // ensure all original colouring is propagated to listeners. + // ensure all original colouring is propagated to listeners. ap.paintAlignment(true); try { @@ -508,13 +596,11 @@ public class AnnotationColourChooser extends JPanel 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.get(g); sg.cs = (ColourSchemeI) oldgroupColours.get(sg); } }