X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAnnotationColourChooser.java;h=79d2f1f986468d365b34d5987abfc887139dbc32;hb=a6875ff6ca7894443c98b1d068f78ea25c5bfc87;hp=f85a07310d102f6c277a232a7efdf2e0e18c9e54;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationColourChooser.java b/src/jalview/appletgui/AnnotationColourChooser.java index f85a073..79d2f1f 100644 --- a/src/jalview/appletgui/AnnotationColourChooser.java +++ b/src/jalview/appletgui/AnnotationColourChooser.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,15 +20,35 @@ */ package jalview.appletgui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; -import jalview.schemes.*; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.SequenceGroup; +import jalview.schemes.AnnotationColourGradient; +import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; +import java.awt.BorderLayout; +import java.awt.Button; +import java.awt.Checkbox; +import java.awt.Choice; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.FlowLayout; +import java.awt.Font; +import java.awt.Frame; +import java.awt.Panel; +import java.awt.Scrollbar; +import java.awt.TextField; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.util.Hashtable; +import java.util.Vector; + public class AnnotationColourChooser extends Panel implements ActionListener, AdjustmentListener, ItemListener, MouseListener { @@ -77,7 +97,8 @@ public class AnnotationColourChooser extends Panel implements slider.addAdjustmentListener(this); slider.addMouseListener(this); - if (av.getAlignment().getAlignmentAnnotation() == null) + AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); + if (anns == null) { return; } @@ -98,15 +119,23 @@ public class AnnotationColourChooser extends Panel implements // seqAssociated.setState(acg.isSeqAssociated()); } - Vector list = new Vector(); + Vector list = new Vector(); int index = 1; - for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++) + for (int i = 0; i < anns.length; i++) { - String label = av.getAlignment().getAlignmentAnnotation()[i].label; + String label = anns[i].label; + if (anns[i].sequenceRef != null) + { + label = label + "_" + anns[i].sequenceRef.getName(); + } if (!list.contains(label)) + { list.addElement(label); + } else + { list.addElement(label + "_" + (index++)); + } } for (int i = 0; i < list.size(); i++) @@ -115,11 +144,11 @@ public class AnnotationColourChooser extends Panel implements } threshold.addItem(MessageManager - .getString("label.threshold_feature_no_thereshold")); + .getString("label.threshold_feature_no_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_above_thereshold")); + .getString("label.threshold_feature_above_threshold")); threshold.addItem(MessageManager - .getString("label.threshold_feature_below_thereshold")); + .getString("label.threshold_feature_below_threshold")); if (oldcs instanceof AnnotationColourGradient) { @@ -138,7 +167,8 @@ public class AnnotationColourChooser extends Panel implements break; default: throw new Error( - "Implementation error: don't know about threshold setting for current AnnotationColourGradient."); + MessageManager + .getString("error.implementation_error_dont_know_threshold_annotationcolourgradient")); } thresholdIsMin.setState(acg.thresholdIsMinMax); thresholdValue.setText("" + acg.getAnnotationThreshold()); @@ -285,6 +315,7 @@ public class AnnotationColourChooser extends Panel implements Checkbox thresholdIsMin = new Checkbox(); + @Override public void actionPerformed(ActionEvent evt) { if (evt.getSource() == thresholdValue) @@ -312,7 +343,6 @@ public class AnnotationColourChooser extends Panel implements } else if (evt.getSource() == ok) { - changeColour(); frame.setVisible(false); } else if (evt.getSource() == cancel) @@ -328,6 +358,7 @@ public class AnnotationColourChooser extends Panel implements } } + @Override public void itemStateChanged(ItemEvent evt) { if (evt.getSource() == currentColours) @@ -345,18 +376,19 @@ public class AnnotationColourChooser extends Panel implements changeColour(); } + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { if (!adjusting) { - thresholdValue.setText(((float) slider.getValue() / 1000f) + ""); + thresholdValue.setText((slider.getValue() / 1000f) + ""); if (currentColours.getState() && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient)) { changeColour(); } - currentAnnotation.threshold.value = (float) slider.getValue() / 1000f; + currentAnnotation.threshold.value = slider.getValue() / 1000f; ap.paintAlignment(false); } } @@ -529,23 +561,28 @@ public class AnnotationColourChooser extends Panel implements } + @Override public void mouseClicked(MouseEvent evt) { } + @Override public void mousePressed(MouseEvent evt) { } + @Override public void mouseReleased(MouseEvent evt) { ap.paintAlignment(true); } + @Override public void mouseEntered(MouseEvent evt) { } + @Override public void mouseExited(MouseEvent evt) { }